WorldWideScience

Sample records for deciphering rice phenotypic

  1. Gene expression profiles deciphering rice phenotypic variation between Nipponbare (Japonica and 93-11 (Indica during oxidative stress.

    Directory of Open Access Journals (Sweden)

    Fengxia Liu

    Full Text Available Rice is a very important food staple that feeds more than half the world's population. Two major Asian cultivated rice (Oryza sativa L. subspecies, japonica and indica, show significant phenotypic variation in their stress responses. However, the molecular mechanisms underlying this phenotypic variation are still largely unknown. A common link among different stresses is that they produce an oxidative burst and result in an increase of reactive oxygen species (ROS. In this study, methyl viologen (MV as a ROS agent was applied to investigate the rice oxidative stress response. We observed that 93-11 (indica seedlings exhibited leaf senescence with severe lesions under MV treatment compared to Nipponbare (japonica. Whole-genome microarray experiments were conducted, and 1,062 probe sets were identified with gene expression level polymorphisms between the two rice cultivars in addition to differential expression under MV treatment, which were assigned as Core Intersectional Probesets (CIPs. These CIPs were analyzed by gene ontology (GO and highlighted with enrichment GO terms related to toxin and oxidative stress responses as well as other responses. These GO term-enriched genes of the CIPs include glutathine S-transferases (GSTs, P450, plant defense genes, and secondary metabolism related genes such as chalcone synthase (CHS. Further insertion/deletion (InDel and regulatory element analyses for these identified CIPs suggested that there may be some eQTL hotspots related to oxidative stress in the rice genome, such as GST genes encoded on chromosome 10. In addition, we identified a group of marker genes individuating the japonica and indica subspecies. In summary, we developed a new strategy combining biological experiments and data mining to study the possible molecular mechanism of phenotypic variation during oxidative stress between Nipponbare and 93-11. This study will aid in the analysis of the molecular basis of quantitative traits.

  2. Phylogenetic and CRISPR/Cas9 Studies in Deciphering the Evolutionary Trajectory and Phenotypic Impacts of Rice ERECTA Genes

    Directory of Open Access Journals (Sweden)

    Yanchun Zhang

    2018-04-01

    Full Text Available The ERECTA family genes (ERfs have been found to play diverse functions in Arabidopsis, including controlling cell proliferation and cell growth, regulating stomata patterning, and responding to various stresses. This wide range of functions has rendered them as a potential candidate for crop improvement. However, information on their functional roles, particularly their morphological impact, in crop genomes, such as rice, is limited. Here, through evolutionary prediction, we first depict the evolutionary trajectory of the ER family, and show that the ER family is actually highly conserved across different species, suggesting that most of their functions may also be observed in other plant species. We then take advantage of the CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats–associated nuclease 9 system to assess their morphological impact on one of the most important crops, rice. Loss-of-function mutants of OsER1 and OsER2 display shortened plant stature and reduced panicle size, suggesting they possibly also functioned in regulating cell proliferation and cell growth in rice. In addition to functions similar to that in Arabidopsis, we also find clues that rice ERfs may play unique functional roles. The OsER2 displayed more severe phenotypic changes than OsER1, indicating putative differentiation in their functions. The OsERL might be of essential in its function, and the proper function of all three rice ER genes might be dependent of their genetic background. Future investigations relating to these functions are key to exploiting ERfs in crop development.

  3. Deciphering the Environmental Impacts on Rice Quality for Different Rice Cultivated Areas.

    Science.gov (United States)

    Li, Xiukun; Wu, Lian; Geng, Xin; Xia, Xiuhong; Wang, Xuhong; Xu, Zhengjin; Xu, Quan

    2018-01-19

    Rice (Oryza sativa L.) is cultivated in a wide range of climatic conditions, and is one of mankind's major staple foods. The interaction of environmental factors with genotype effects major agronomic traits such as yield, quality, and resistance in rice. However, studies on the environmental factors affecting agronomic traits are often difficult to conduct because most environmental factors are dynamic and constantly changing. A series of recombinant inbred lines (RILs) derived from an indica/japonica cross were planted into four typical rice cultivated areas arranging from latitude N22° to N42°. The environmental data from the heading to mature (45 days) stages were recorded for each RIL in the four areas. We determined that light, temperature, and humidity significantly affected the milling quality and cooking quality overall the four areas. Within each area, these environmental factors mainly affected the head rice ratio, grain length, alkali consumption, and amylose and protein content. Moreover, the effect of these environmental factors dynamically changed from heading to mature stage. Compared to light and humidity, temperature was more stable and predictable, and night temperature showed a stronger correlation efficiency to cooking quality than day temperature, and the daily temperature range had contrary effects compared to day and night temperature on grain quality. The present study evaluated the critical phase during the grain filling stage by calculating the dynamic changes of correlation efficiency between the quality traits and climate parameters. Our findings suggest that the sowing date could be adjusted to improve rice quality so as to adjust for environmental changes.

  4. Deciphering the Mechanisms of Developmental Disorders (DMDD: a new programme for phenotyping embryonic lethal mice

    Directory of Open Access Journals (Sweden)

    Timothy Mohun

    2013-05-01

    International efforts to test gene function in the mouse by the systematic knockout of each gene are creating many lines in which embryonic development is compromised. These homozygous lethal mutants represent a potential treasure trove for the biomedical community. Developmental biologists could exploit them in their studies of tissue differentiation and organogenesis; for clinical researchers they offer a powerful resource for investigating the origins of developmental diseases that affect newborns. Here, we outline a new programme of research in the UK aiming to kick-start research with embryonic lethal mouse lines. The ‘Deciphering the Mechanisms of Developmental Disorders’ (DMDD programme has the ambitious goal of identifying all embryonic lethal knockout lines made in the UK over the next 5 years, and will use a combination of comprehensive imaging and transcriptomics to identify abnormalities in embryo structure and development. All data will be made freely available, enabling individual researchers to identify lines relevant to their research. The DMDD programme will coordinate its work with similar international efforts through the umbrella of the International Mouse Phenotyping Consortium [see accompanying Special Article (Adams et al., 2013] and, together, these programmes will provide a novel database for embryonic development, linking gene identity with molecular profiles and morphology phenotypes.

  5. Deciphering the role of a miRNA in rice domestication

    Directory of Open Access Journals (Sweden)

    Swetha Chenna

    2017-10-01

    Full Text Available MicroRNAs (miRNAs are a class of 21 nt non-coding small RNAs (sRNAs produced from endogenously expressed MIR genes. miRNAs are mostly involved in development and disease resistance. We are interested in identifying key miRNAs that are differentially expressed among wild and cultivated rice species. Analysis of sRNA datasets from two wild species (O. nivara and O. rufipogon and one cultivated species of rice (O. sativa var. indica Pusa Basmati-1, revealed a surprisingly higher abundance of small RNAs originating from Chromosome 2 in wild rice species. This locus codes for a novel 22 nt miRNA. This novel miRNA was found to be highly abundant in flag leaf of wild species, a tissue that usually provides 70% of energy required for grain filling. This miRNA targets a group of proteins (Os03g0273200, Os01g0827300, Os01g0850700, Os11g0708100 and Os01g0842500 which are involved in secondary metabolite production, although a functional significance of this interaction has not been understood. The expression of these targets also differs across the species. Typical of 22 nt miRNAs, the identified miRNA also triggers a secondary cascade silencing by producing small interfering RNAs (siRNAs from target mRNAs in O. nivara. These secondary siRNAs are observed only among wild rice species but not in cultivated rice. Currently we are using a range of genetic, biochemical and molecular techniques to understand role of this novel miRNA in domestication of rice.

  6. Deciphering the factors associated with the colonization of rice plants by cyanobacteria.

    Science.gov (United States)

    Bidyarani, Ngangom; Prasanna, Radha; Chawla, Gautam; Babu, Santosh; Singh, Rajendra

    2015-04-01

    Cyanobacteria-rice plant interactions were analyzed using a hydroponics experiment. The activity of plant defense and pathogenesis-related enzymes, scanning electron microscopy, growth, nitrogen fixation (measured as ARA), and DNA fingerprinting assays proved useful in illustrating the nature of associations of cyanobacteria with rice plants. Microscopic analyses revealed the presence of short filaments and coiled masses of filaments of cyanobacteria near the epidermis and cortex of roots and shoot tissues. Among the six cyanobacterial strains employed, Calothrix sp. (RPC1), Anabaena laxa (RPAN8), and Anabaena azollae (C16) were the best performing strains, in terms of colonization in roots and stem. These strains also enhanced nitrogen fixation and stimulated the activity of plant defense/cell wall-degrading enzymes. A significantly high correlation was also recorded between the elicited plant enzymes, growth, and ARA. DNA fingerprinting using highly iterated palindromic sequences (HIP-TG) further helped in proving the establishment of inoculated organisms in the roots/shoots of rice plants. This study illustrated that the colonization of cyanobacteria in the plant tissues is facilitated by increased elicitation of plant enzymes, leading to improved plant growth, nutrient mobilization, and enhanced plant fitness. Such strains can be promising candidates for developing "cyanobacteria colonized-nitrogen-fixing rice plants" in the future. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  7. Deciphering Cis-Regulatory Element Mediated Combinatorial Regulation in Rice under Blast Infected Condition.

    Directory of Open Access Journals (Sweden)

    Arindam Deb

    Full Text Available Combinations of cis-regulatory elements (CREs present at the promoters facilitate the binding of several transcription factors (TFs, thereby altering the consequent gene expressions. Due to the eminent complexity of the regulatory mechanism, the combinatorics of CRE-mediated transcriptional regulation has been elusive. In this work, we have developed a new methodology that quantifies the co-occurrence tendencies of CREs present in a set of promoter sequences; these co-occurrence scores are filtered in three consecutive steps to test their statistical significance; and the significantly co-occurring CRE pairs are presented as networks. These networks of co-occurring CREs are further transformed to derive higher order of regulatory combinatorics. We have further applied this methodology on the differentially up-regulated gene-sets of rice tissues under fungal (Magnaporthe infected conditions to demonstrate how it helps to understand the CRE-mediated combinatorial gene regulation. Our analysis includes a wide spectrum of biologically important results. The CRE pairs having a strong tendency to co-occur often exhibit very similar joint distribution patterns at the promoters of rice. We couple the network approach with experimental results of plant gene regulation and defense mechanisms and find evidences of auto and cross regulation among TF families, cross-talk among multiple hormone signaling pathways, similarities and dissimilarities in regulatory combinatorics between different tissues, etc. Our analyses have pointed a highly distributed nature of the combinatorial gene regulation facilitating an efficient alteration in response to fungal attack. All together, our proposed methodology could be an important approach in understanding the combinatorial gene regulation. It can be further applied to unravel the tissue and/or condition specific combinatorial gene regulation in other eukaryotic systems with the availability of annotated genomic

  8. The rice growth image files - The Rice Growth Monitoring for The Phenotypic Functional Analysis | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us The Rice Growth Monitoring for The Phenotypic Functional Analysis The rice growth image file...s Data detail Data name The rice growth image files DOI 10.18908/lsdba.nbdc00945-004 Description of data contents The rice growth ima...ge files categorized based on file size. Data file File name: image files (director...y) File URL: ftp://ftp.biosciencedbc.jp/archive/agritogo-rice-phenome/LATEST/image...ite Policy | Contact Us The rice growth image files - The Rice Growth Monitoring for The Phenotypic Functional Analysis | LSDB Archive ...

  9. Machine learning approaches to decipher hormone and HER2 receptor status phenotypes in breast cancer.

    Science.gov (United States)

    Adabor, Emmanuel S; Acquaah-Mensah, George K

    2017-10-16

    Breast cancer prognosis and administration of therapies are aided by knowledge of hormonal and HER2 receptor status. Breast cancer lacking estrogen receptors, progesterone receptors and HER2 receptors are difficult to treat. Regarding large data repositories such as The Cancer Genome Atlas, available wet-lab methods for establishing the presence of these receptors do not always conclusively cover all available samples. To this end, we introduce median-supplement methods to identify hormonal and HER2 receptor status phenotypes of breast cancer patients using gene expression profiles. In these approaches, supplementary instances based on median patient gene expression are introduced to balance a training set from which we build simple models to identify the receptor expression status of patients. In addition, for the purpose of benchmarking, we examine major machine learning approaches that are also applicable to the problem of finding receptor status in breast cancer. We show that our methods are robust and have high sensitivity with extremely low false-positive rates compared with the well-established methods. A successful application of these methods will permit the simultaneous study of large collections of samples of breast cancer patients as well as save time and cost while standardizing interpretation of outcomes of such studies. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  10. Improving the phenotypic expression of rice genotypes: Rethinking “intensification” for production systems and selection practices for rice breeding

    Directory of Open Access Journals (Sweden)

    Norman Uphoff

    2015-06-01

    Full Text Available Intensification in rice crop production is generally understood as requiring increased use of material inputs: water, inorganic fertilizers, and agrochemicals. However, this is not the only kind of intensification available. More productive crop phenotypes, with traits such as more resistance to biotic and abiotic stresses and shorter crop cycles, are possible through modifications in the management of rice plants, soil, water, and nutrients, reducing rather than increasing material inputs. Greater factor productivity can be achieved through the application of new knowledge and more skill, and (initially more labor, as seen from the System of Rice Intensification (SRI, whose practices are used in various combinations by as many as 10 million farmers on about 4 million hectares in over 50 countries. The highest yields achieved with these management methods have come from hybrids and improved rice varieties, confirming the importance of making genetic improvements. However, unimproved varieties are also responsive to these changes, which induce better growth and functioning of rice root systems and more abundance, diversity, and activity of beneficial soil organisms. Some of these organisms as symbiotic endophytes can affect and enhance the expression of rice plants' genetic potential as well as their phenotypic resilience to multiple stresses, including those of climate change. SRI experience and data suggest that decades of plant breeding have been selecting for the best crop genetic endowments under suboptimal growing conditions, with crowding of plants that impedes their photosynthesis and growth, flooding of rice paddies that causes roots to degenerate and forgoes benefits derived from aerobic soil organisms, and overuse of agrochemicals that adversely affect these organisms as well as soil and human health. This review paper reports evidence from research in India and Indonesia that changes in crop and water management can improve the

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

    KAUST Repository

    Pires, Inês S.

    2015-07-22

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

  12. Salinity tolerance loci revealed in rice using high-throughput non-invasive phenotyping

    KAUST Repository

    Al-Tamimi, Nadia Ali; Brien, Chris; Oakey, Helena; Berger, Bettina; Saade, Stephanie; Ho, Yung Shwen; Schmö ckel, Sandra M.; Tester, Mark A.; Negrã o, Só nia

    2016-01-01

    High-throughput phenotyping produces multiple measurements over time, which require new methods of analyses that are flexible in their quantification of plant growth and transpiration, yet are computationally economic. Here we develop such analyses and apply this to a rice population genotyped with a 700k SNP high-density array. Two rice diversity panels, indica and aus, containing a total of 553 genotypes, are phenotyped in waterlogged conditions. Using cubic smoothing splines to estimate plant growth and transpiration, we identify four time intervals that characterize the early responses of rice to salinity. Relative growth rate, transpiration rate and transpiration use efficiency (TUE) are analysed using a new association model that takes into account the interaction between treatment (control and salt) and genetic marker. This model allows the identification of previously undetected loci affecting TUE on chromosome 11, providing insights into the early responses of rice to salinity, in particular into the effects of salinity on plant growth and transpiration.

  13. Salinity tolerance loci revealed in rice using high-throughput non-invasive phenotyping

    KAUST Repository

    Al-Tamimi, Nadia Ali

    2016-11-17

    High-throughput phenotyping produces multiple measurements over time, which require new methods of analyses that are flexible in their quantification of plant growth and transpiration, yet are computationally economic. Here we develop such analyses and apply this to a rice population genotyped with a 700k SNP high-density array. Two rice diversity panels, indica and aus, containing a total of 553 genotypes, are phenotyped in waterlogged conditions. Using cubic smoothing splines to estimate plant growth and transpiration, we identify four time intervals that characterize the early responses of rice to salinity. Relative growth rate, transpiration rate and transpiration use efficiency (TUE) are analysed using a new association model that takes into account the interaction between treatment (control and salt) and genetic marker. This model allows the identification of previously undetected loci affecting TUE on chromosome 11, providing insights into the early responses of rice to salinity, in particular into the effects of salinity on plant growth and transpiration.

  14. Comparison of phenotyping methods for resistance to stem rot and aggregated sheath spot in rice

    Science.gov (United States)

    Stem and sheath diseases caused by Sclerotium oryzae Cattaneo (SCL) and Rhizoctonia oryzae-sativae Sawada Mordue (ROS) can severely reduce rice (Oryza sativa L.) yield and grain quality. Genetic resistance is the best strategy to control them. Phenotypic selection for resistance is hampered due to a...

  15. Image-based phenotyping for non-destructive screening of different salinity tolerance traits in rice

    KAUST Repository

    Hairmansis, Aris

    2014-08-14

    Background Soil salinity is an abiotic stress wide spread in rice producing areas, limiting both plant growth and yield. The development of salt-tolerant rice requires efficient and high-throughput screening techniques to identify promising lines for salt affected areas. Advances made in image-based phenotyping techniques provide an opportunity to use non-destructive imaging to screen for salinity tolerance traits in a wide range of germplasm in a reliable, quantitative and efficient way. However, the application of image-based phenotyping in the development of salt-tolerant rice remains limited. Results A non-destructive image-based phenotyping protocol to assess salinity tolerance traits of two rice cultivars (IR64 and Fatmawati) has been established in this study. The response of rice to different levels of salt stress was quantified over time based on total shoot area and senescent shoot area, calculated from visible red-green-blue (RGB) and fluorescence images. The response of rice to salt stress (50, 75 and 100 mM NaCl) could be clearly distinguished from the control as indicated by the reduced increase of shoot area. The salt concentrations used had only a small effect on the growth of rice during the initial phase of stress, the shoot Na+ accumulation independent phase termed the ‘osmotic stress’ phase. However, after 20 d of treatment, the shoot area of salt stressed plants was reduced compared with non-stressed plants. This was accompanied by a significant increase in the concentration of Na+ in the shoot. Variation in the senescent area of the cultivars IR64 and Fatmawati in response to a high concentration of Na+ in the shoot indicates variation in tissue tolerance mechanisms between the cultivars. Conclusions Image analysis has the potential to be used for high-throughput screening procedures in the development of salt-tolerant rice. The ability of image analysis to discriminate between the different aspects of salt stress (shoot ion

  16. Deciphering Phosphate Deficiency-Mediated Temporal Effects on Different Root Traits in Rice Grown in a Modified Hydroponic System

    Science.gov (United States)

    Negi, Manisha; Sanagala, Raghavendrarao; Rai, Vandna; Jain, Ajay

    2016-01-01

    Phosphate (Pi), an essential macronutrient for growth and development of plant, is often limiting in soils. Plants have evolved an array of adaptive strategies including modulation of root system architecture (RSA) for optimal acquisition of Pi. In rice, a major staple food, RSA is complex and comprises embryonically developed primary and seminal roots and post-embryonically developed adventitious and lateral roots. Earlier studies have used variant hydroponic systems for documenting the effects of Pi deficiency largely on primary root growth. Here, we report the temporal effects of Pi deficiency in rice genotype MI48 on 15 ontogenetically distinct root traits by using easy-to-assemble and economically viable modified hydroponic system. Effects of Pi deprivation became evident after 4 days- and 7 days-treatments on two and eight different root traits, respectively. The effects of Pi deprivation for 7 days were also evident on different root traits of rice genotype Nagina 22 (N22). There were genotypic differences in the responses of primary root growth along with lateral roots on it and the number and length of seminal and adventitious roots. Notably though, there were attenuating effects of Pi deficiency on the lateral roots on seminal and adventitious roots and total root length in both these genotypes. The study thus revealed both differential and comparable effects of Pi deficiency on different root traits in these genotypes. Pi deficiency also triggered reduction in Pi content and induction of several Pi starvation-responsive (PSR) genes in roots of MI48. Together, the analyses validated the fidelity of this modified hydroponic system for documenting Pi deficiency-mediated effects not only on different traits of RSA but also on physiological and molecular responses. PMID:27200025

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

    OpenAIRE

    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 gen...

  18. Phenotype diversity analysis of red-grained rice landraces from Yuanyang Hani's terraced fields, China

    Science.gov (United States)

    Li, Lianjie; Cheng, Long

    2017-10-01

    There are many areas in the world have terraced fields, Yuanyang Rani's terraced fields are examples in the world, and their unique ecological diversity is beyond other terraced fields, rice landraces are very rich. In order to provide useful information for protection and utilization of red-grained rice landraces from Rani's terraced fields, 61 red-grained rice landraces were assessed based 20 quantitative traits. Principal component analysis (PCA) suggested that 20 quantitative characters could be simplified to seven principal components, and their accumulative contribution ration amounted to 78.699%. The first principal component (PC1) explained 18.375% of the total variance, which was contributed by filled grain number, 1000-grain weight, spikelets per panicle, secondary branch number, grain length, and grain thickness. PC2 accounted for 16.548% of the variance and featured flag leaf width, flag leaf area, panicle neck length and primary branch number. These traits were the most effective parameters to discriminate individuals. At the request of the proceedings editor and with the approval of all authors, article 040111 titled, "Phenotype diversity analysis of red-grained rice landraces from Yuanyang Hani's terraced fields, China," is being retracted from the public record due to the fact that it is a duplication of article 040110 published in the same volume.

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

    Science.gov (United States)

    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

  20. SLIFER Decipher

    International Nuclear Information System (INIS)

    Breding, D.R.; Worthen, G.S.; Loukota, J.J.; Fogel, D.; Watterberg, J.P.

    1977-10-01

    The SLIFER Decipher (SD) is a digital instrument that records a time-varying frequency signal in the range from 700 kHz to 1500 kHz with an amplitude greater than 200 mV. This signal is referenced to an input fiducial marker. The primary purpose of this instrument is to reduce data recorded on magnetic tape from the SLIFER system used in underground nuclear tests. The SD records 512 samples after the fiducial signal, with a sample interval of 50 μs (for a total recording time of 25.55 ms). The measurement essentially uses a 20-cycle period-averaging counter technique

  1. The impact of herbicide-resistant rice technology on phenotypic diversity and population structure of United States weedy rice.

    Science.gov (United States)

    Burgos, Nilda Roma; Singh, Vijay; Tseng, Te Ming; Black, Howard; Young, Nelson D; Huang, Zhongyun; Hyma, Katie E; Gealy, David R; Caicedo, Ana L

    2014-11-01

    The use of herbicide-resistant (HR) Clearfield rice (Oryza sativa) to control weedy rice has increased in the past 12 years to constitute about 60% of rice acreage in Arkansas, where most U.S. rice is grown. To assess the impact of HR cultivated rice on the herbicide resistance and population structure of weedy rice, weedy samples were collected from commercial fields with a history of Clearfield rice. Panicles from each weedy type were harvested and tested for resistance to imazethapyr. The majority of plants sampled had at least 20% resistant offspring. These resistant weeds were 97 to 199 cm tall and initiated flowering from 78 to 128 d, generally later than recorded for accessions collected prior to the widespread use of Clearfield rice (i.e. historical accessions). Whereas the majority (70%) of historical accessions had straw-colored hulls, only 30% of contemporary HR weedy rice had straw-colored hulls. Analysis of genotyping-by-sequencing data showed that HR weeds were not genetically structured according to hull color, whereas historical weedy rice was separated into straw-hull and black-hull populations. A significant portion of the local rice crop genome was introgressed into HR weedy rice, which was rare in historical weedy accessions. Admixture analyses showed that HR weeds tend to possess crop haplotypes in the portion of chromosome 2 containing the ACETOLACTATE SYNTHASE gene, which confers herbicide resistance to Clearfield rice. Thus, U.S. HR weedy rice is a distinct population relative to historical weedy rice and shows modifications in morphology and phenology that are relevant to weed management. © 2014 American Society of Plant Biologists. All Rights Reserved.

  2. Mutation Breeding and Selection for Phenotypic Mutants in Standard Rice Varieties by Ion Beam

    International Nuclear Information System (INIS)

    Puddhanon, Prawit; Pintanon, Prateep; Chaithep, Waree; Songjuntuke, Ksan

    2009-07-01

    Full text: Effects of 80 keV ion beam (10 16 ion/cm 2 on mutations of RD6 and Sanpatong 1 rice varieties were studied in 2006. In order to obtain the phenotypic mutants, each variety was sown in the laboratory and under field conditions at Maejo University in 2007 dry season. Seed germination noticeably declined. For RD6, only 45.1% germinated in the laboratory, and 18.1% were established under the field condition. Similarly, 62.3% of Sanpatong 1 germinated in the laboratory and 31.4% established in the field. No phenotypic mutants were observed in the first generation (M 1 ). The M2 seeds were harvested separately from 3 panicles of each M plant in RD6 and Sanpatong1, totaling 810 and 1,878 lines, respectively. In 2007 rainy season, they were planted on a panicle to row basis. It was found that more phenotypic mutants were observed in the M 2 for Sanpatong 1 than for RD6. The mutant characters included dwarf plants, early maturity, male sterility and larger panicle sizes. As a result, about 420 within line selections were collected and the M 3 seeds were harvested for further field condition and gene markers evaluations

  3. Phenotyping of VIGS-mediated gene silencing in rice using a vector derived from a DNA virus.

    Science.gov (United States)

    Kant, Ravi; Dasgupta, Indranil

    2017-07-01

    Target genes in rice can be optimally silenced if inserted in antisense or hairpin orientation in the RTBV-derived VIGS vector and plants grown at 28 °C and 80% humidity after inoculation. Virus induced gene silencing (VIGS) is a method used to transiently silence genes in dicot as well as monocot plants. For the important monocot species rice, the Rice tungro bacilliform virus (RTBV)-derived VIGS system (RTBV-VIGS), which uses agroinoculation to initiate silencing, has not been standardized for optimal use. Here, using RTBV-VIGS, three sets of conditions were tested to achieve optimal silencing of the rice marker gene phytoene desaturase (pds). The effect of orientation of the insert in the RTBV-VIGS plasmid (sense, antisense and hairpin) on the silencing of the target gene was then evaluated using rice magnesium chelatase subunit H (chlH). Finally, the rice Xa21 gene, conferring resistance against bacterial leaf blight disease (BLB) was silenced using RTBV-VIGS system. In each case, real-time PCR-based assessment indicated approximately 40-80% fall in the accumulation levels of the transcripts of pds, chlH and Xa21. In the case of pds, the appearance of white streaks in the emerging leaves, and for chlH, chlorophyll levels and F v /F m ratio were assessed as phenotypes for silencing. For Xa21, the resistance levels to BLB were assessed by measuring the lesion length and the percent diseased areas of leaves, following challenge inoculation with Xanthomonas oryzae. In each case, the RTBV-MVIGS system gave rise to a discernible phenotype indicating the silencing of the respective target gene using condition III (temperature 28 °C, humidity 80% and 1 mM MES and 20 µM acetosyringone in secondary agrobacterium culture), which revealed the robustness of this gene silencing system for rice.

  4. Graph of growth data - The Rice Growth Monitoring for The Phenotypic Functional Analysis | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us The Rice Growth Monitoring for The Phenotypic Functional Analysis Graph of growth data Data ...detail Data name Graph of growth data DOI 10.18908/lsdba.nbdc00945-003 Description of data contents The grap...h of chronological changes in root, coleoptile, the first leaf, and the second leaf. Data file File name: growth..._data_graph.zip File URL: ftp://ftp.biosciencedbc.jp/archive/agritogo-rice-phenome/LATEST/data/growth...e Update History of This Database Site Policy | Contact Us Graph of growth data -

  5. Image-based phenotyping for non-destructive screening of different salinity tolerance traits in rice

    KAUST Repository

    Hairmansis, Aris; Berger, Bettina; Tester, Mark A.; Roy, Stuart

    2014-01-01

    Soil salinity is an abiotic stress wide spread in rice producing areas, limiting both plant growth and yield. The development of salt-tolerant rice requires efficient and high-throughput screening techniques to identify promising lines

  6. Evaluation of rice genotypes under salt stress at the seedling and reproductive stages using phenotypic and molecular markers

    International Nuclear Information System (INIS)

    Rubel, M.H.; Hassan, L.

    2014-01-01

    Salinity screening for 27 rice genotypes was performed at the seedling and reproductive stages respectively, in the hydroponic system and in sustained water bath. Three selected SSR markers were used to determine salinity tolerance in rice genotypes. Phenotyping of the germplasm was done at EC 12dS/m and 6dS/m at seedling and reproductive stages, respectively. Based on modified standard evaluation score for visual salt injury at seedling stage, eight genotypes were salt tolerant, four were moderately tolerant and the rest fifteen were susceptible. At the reproductive stage, six genotypes were tolerant to EC 6dS/m whereas eleven of them were susceptible. SSR based marker identified seven genotypes as tolerant but ten of them were susceptible for all three markers compared to two checks. Six genotypes were tolerant in both phenotypic and SSR screening. The indentified salt tolerant genotypes can be potential germplasm sources for future breeding program. (author)

  7. Deciphering the Cryptic Genome: Genome-wide Analyses of the Rice Pathogen Fusarium fujikuroi Reveal Complex Regulation of Secondary Metabolism and Novel Metabolites

    Science.gov (United States)

    Studt, Lena; Niehaus, Eva-Maria; Espino, Jose J.; Huß, Kathleen; Michielse, Caroline B.; Albermann, Sabine; Wagner, Dominik; Bergner, Sonja V.; Connolly, Lanelle R.; Fischer, Andreas; Reuter, Gunter; Kleigrewe, Karin; Bald, Till; Wingfield, Brenda D.; Ophir, Ron; Freeman, Stanley; Hippler, Michael; Smith, Kristina M.; Brown, Daren W.; Proctor, Robert H.; Münsterkötter, Martin; Freitag, Michael; Humpf, Hans-Ulrich; Güldener, Ulrich; Tudzynski, Bettina

    2013-01-01

    The fungus Fusarium fujikuroi causes “bakanae” disease of rice due to its ability to produce gibberellins (GAs), but it is also known for producing harmful mycotoxins. However, the genetic capacity for the whole arsenal of natural compounds and their role in the fungus' interaction with rice remained unknown. Here, we present a high-quality genome sequence of F. fujikuroi that was assembled into 12 scaffolds corresponding to the 12 chromosomes described for the fungus. We used the genome sequence along with ChIP-seq, transcriptome, proteome, and HPLC-FTMS-based metabolome analyses to identify the potential secondary metabolite biosynthetic gene clusters and to examine their regulation in response to nitrogen availability and plant signals. The results indicate that expression of most but not all gene clusters correlate with proteome and ChIP-seq data. Comparison of the F. fujikuroi genome to those of six other fusaria revealed that only a small number of gene clusters are conserved among these species, thus providing new insights into the divergence of secondary metabolism in the genus Fusarium. Noteworthy, GA biosynthetic genes are present in some related species, but GA biosynthesis is limited to F. fujikuroi, suggesting that this provides a selective advantage during infection of the preferred host plant rice. Among the genome sequences analyzed, one cluster that includes a polyketide synthase gene (PKS19) and another that includes a non-ribosomal peptide synthetase gene (NRPS31) are unique to F. fujikuroi. The metabolites derived from these clusters were identified by HPLC-FTMS-based analyses of engineered F. fujikuroi strains overexpressing cluster genes. In planta expression studies suggest a specific role for the PKS19-derived product during rice infection. Thus, our results indicate that combined comparative genomics and genome-wide experimental analyses identified novel genes and secondary metabolites that contribute to the evolutionary success of F

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

    OpenAIRE

    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...

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

    KAUST Repository

    Pires, Inê s S.; Negrã o, Só nia; Oliveira, M. Margarida; Purugganan, Michael D.

    2015-01-01

    affected by salt stress in rice, which puts in question the importance of K+/Na+ when analyzing rice salt stress response. Not only do our results contribute to improve our global understanding of salt stress response in an important crop, but we also use

  10. License - The Rice Growth Monitoring for The Phenotypic Functional Analysis | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available s Database Last updated : 2011/11/08 You may use this database in compliance with the terms and conditions o...f the license described below. The license specifies the license terms regarding the use of this database an...d the requirements you must follow in using this database. The license for this database... is specified in the Creative Commons Attribution-Share Alike 2.1 Japan . If you use data from this database..., please be sure attribute this database as follows: The Rice Growth Monitoring for the Phenotypic Fu

  11. A Point Mutation in an F-Box Domain-Containing Protein Is Responsible for Brown Hull Phenotype in Rice

    Directory of Open Access Journals (Sweden)

    Xu Xia

    2016-01-01

    Full Text Available The accumulation of pigments affects the color of rice hulls while only limited information is known about its underlying mechanisms. In the present study, a rice brown hull 6 (bh6 mutant was isolated from an ethane methyl sulfonate (EMS-induced IR64 mutant bank. Brown pigments started to accumulate in bh6 rice hulls after heading and reached a higher level in mature seeds. Some major agronomic traits including panicle length and 1000-grain weight in bh6 were significantly lower than those in its corresponding wild type IR64, while other agronomic traits such as plant height, growth duration and seed-setting rate were largely similar between the two genotypes. The analysis of pigment content showed that the contents of total flavonoids and anthocyanin in bh6 hulls were significantly higher than those in IR64 hulls. Our results showed that the brown hull phenotype in bh6 was controlled by a single recessive gene which locates on the long arm of chromosome 9. Sequencing analysis detected a single base substitution (G/A at position 1013 of the candidate gene (LOC_Os09g12150 encoding an F-box domain-containing protein (FBX310. Functional complementation experiment using the wild type allele can rescue the phenotype in bh6. Thus, we named this mutated gene as OsFBX310bh6, an allele of OsFBX310 functioning as an inhibitor of brown hull. The isolation of OsFBX310bh6 and its wild type allele can provide useful experimental materials and will facilitate the studies on revealing the mechanisms of flavonoid metabolism in monocot plants.

  12. The list of strains and growth conditions - The Rice Growth Monitoring for The Phenotypic Functional Analysis | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us The Rice Growth Monitoring for The Phenotypic Functional Analysis The list of strains and growth... conditions Data detail Data name The list of strains and growth conditions DOI 10.18908/lsdba.nbdc00945...-001 Description of data contents The list of strains and growth conditions for respective samples. Data fil...servation Intervals of imaging Intervals of imaging Growth data Graph of chronological changes in growth Ima...History of This Database Site Policy | Contact Us The list of strains and growth conditions - The Rice Growth Monitoring for The Phenotypic Functional Analysis | LSDB Archive ...

  13. A Multidisciplinary Phenotyping and Genotyping Analysis of a Mapping Population Enables Quality to Be Combined with Yield in Rice

    Directory of Open Access Journals (Sweden)

    Mariafe Calingacion

    2017-05-01

    Full Text Available In this study a mapping population (F8 of ca 200 progeny from a cross between the commercial rice varieties Apo and IR64 has been both genotyped and phenotyped. A genotyping-by-sequencing approach was first used to identify 2,681 polymorphic SNP markers which gave dense coverage of the genome with a good distribution across all 12 chromosomes. The coefficient of parentage was also low, at 0.13, confirming that the parents are genetically distant from each other. The progeny, together with both parents, were grown under irrigated and water restricted conditions in a randomised block design. All grain was harvested to determine variation in yield across the population. The grains were then polished following standard procedures prior to performing the phenotyping analyses. A Gas Chromatography—Mass Spectrometry approach was used to determine the volatile biochemical profiles of each line and after data curation and processing, discriminatory metabolites were putatively identified based on in-house and commercial spectral libraries. These data were used to predict the potential role of these metabolites in determining differences in aroma between genotypes. A number of QTLs for yield and for individual metabolites have been identified. Following these combined multi-disciplinary analyses, it proved possible to identify a number of lines which appeared to combine the favourable aroma attributes of IR64 with the favourable (higher yield potential of Apo. As such, these lines are excellent candidates to assess further as potential genotypes to work up into a new variety of rice which has both good yield and good quality, thus meeting the needs of both farmer and consumer alike.

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

    Directory of Open Access Journals (Sweden)

    Hiroaki eSamejima

    2016-05-01

    Full Text Available 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 (DW in Umgar and NERICA5. Germination-inducing activity of root exudates, at 14 days after sowing onwards, 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

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

    Science.gov (United States)

    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 (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

  16. The Impact of Herbicide-Resistant Rice Technology on Phenotypic Diversity and Population Structure of United States Weedy Rice1[W][OPEN

    Science.gov (United States)

    Burgos, Nilda Roma; Singh, Vijay; Tseng, Te Ming; Black, Howard; Young, Nelson D.; Huang, Zhongyun; Hyma, Katie E.; Gealy, David R.; Caicedo, Ana L.

    2014-01-01

    The use of herbicide-resistant (HR) Clearfield rice (Oryza sativa) to control weedy rice has increased in the past 12 years to constitute about 60% of rice acreage in Arkansas, where most U.S. rice is grown. To assess the impact of HR cultivated rice on the herbicide resistance and population structure of weedy rice, weedy samples were collected from commercial fields with a history of Clearfield rice. Panicles from each weedy type were harvested and tested for resistance to imazethapyr. The majority of plants sampled had at least 20% resistant offspring. These resistant weeds were 97 to 199 cm tall and initiated flowering from 78 to 128 d, generally later than recorded for accessions collected prior to the widespread use of Clearfield rice (i.e. historical accessions). Whereas the majority (70%) of historical accessions had straw-colored hulls, only 30% of contemporary HR weedy rice had straw-colored hulls. Analysis of genotyping-by-sequencing data showed that HR weeds were not genetically structured according to hull color, whereas historical weedy rice was separated into straw-hull and black-hull populations. A significant portion of the local rice crop genome was introgressed into HR weedy rice, which was rare in historical weedy accessions. Admixture analyses showed that HR weeds tend to possess crop haplotypes in the portion of chromosome 2 containing the ACETOLACTATE SYNTHASE gene, which confers herbicide resistance to Clearfield rice. Thus, U.S. HR weedy rice is a distinct population relative to historical weedy rice and shows modifications in morphology and phenology that are relevant to weed management. PMID:25122473

  17. Comparing simple root phenotyping methods on a core set of rice genotypes.

    Science.gov (United States)

    Shrestha, R; Al-Shugeairy, Z; Al-Ogaidi, F; Munasinghe, M; Radermacher, M; Vandenhirtz, J; Price, A H

    2014-05-01

    Interest in belowground plant growth is increasing, especially in relation to arguments that shallow-rooted cultivars are efficient at exploiting soil phosphorus while deep-rooted ones will access water at depth. However, methods for assessing roots in large numbers of plants are diverse and direct comparisons of methods are rare. Three methods for measuring root growth traits were evaluated for utility in discriminating rice cultivars: soil-filled rhizotrons, hydroponics and soil-filled pots whose bottom was sealed with a non-woven fabric (a potential method for assessing root penetration ability). A set of 38 rice genotypes including the OryzaSNP set of 20 cultivars, additional parents of mapping populations and products of marker-assisted selection for root QTLs were assessed. A novel method of image analysis for assessing rooting angles from rhizotron photographs was employed. The non-woven fabric was the easiest yet least discriminatory method, while the rhizotron was highly discriminatory and allowed the most traits to be measured but required more than three times the labour of the other methods. The hydroponics was both easy and discriminatory, allowed temporal measurements, but is most likely to suffer from artefacts. Image analysis of rhizotrons compared favourably to manual methods for discriminating between cultivars. Previous observations that cultivars from the indica subpopulation have shallower rooting angles than aus or japonica cultivars were confirmed in the rhizotrons, and indica and temperate japonicas had lower maximum root lengths in rhizotrons and hydroponics. It is concluded that rhizotrons are the preferred method for root screening, particularly since root angles can be assessed. © 2013 German Botanical Society and The Royal Botanical Society of the Netherlands.

  18. Molecular characterization of a rice mutator-phenotype derived from an incompatible cross-pollination reveals transgenerational mobilization of multiple transposable elements and extensive epigenetic instability

    Directory of Open Access Journals (Sweden)

    Xu Chunming

    2009-05-01

    Full Text Available Abstract Background Inter-specific hybridization occurs frequently in plants, which may induce genetic and epigenetic instabilities in the resultant hybrids, allopolyploids and introgressants. It remains unclear however whether pollination by alien pollens of an incompatible species may impose a "biological stress" even in the absence of genome-merger or genetic introgression, whereby genetic and/or epigenetic instability of the maternal recipient genome might be provoked. Results We report here the identification of a rice mutator-phenotype from a set of rice plants derived from a crossing experiment involving two remote and apparently incompatible species, Oryza sativa L. and Oenothera biennis L. The mutator-phenotype (named Tong211-LP showed distinct alteration in several traits, with the most striking being substantially enlarged panicles. Expectably, gel-blotting by total genomic DNA of the pollen-donor showed no evidence for introgression. Characterization of Tong211-LP (S0 and its selfed progenies (S1 ruled out contamination (via seed or pollen or polyploidy as a cause for its dramatic phenotypic changes, but revealed transgenerational mobilization of several previously characterized transposable elements (TEs, including a MITE (mPing, and three LTR retrotransposons (Osr7, Osr23 and Tos17. AFLP and MSAP fingerprinting revealed extensive, transgenerational alterations in cytosine methylation and to a less extent also genetic variation in Tong211-LP and its immediate progenies. mPing mobility was found to correlate with cytosine methylation alteration detected by MSAP but not with genetic variation detected by AFLP. Assay by q-RT-PCR of the steady-state transcript abundance of a set of genes encoding for the various putative DNA methyltransferases, 5-methylcytosine DNA glycosylases, and small interference RNA (siRNA pathway-related proteins showed that, relative to the rice parental line, heritable perturbation in expression of 12 out of

  19. Nuclear and chloroplast diversity and phenotypic distribution of rice (Oryza sativa L.) germplasm from the democratic people’s republic of Korea (DPRK; North Korea)

    Science.gov (United States)

    2014-01-01

    Background Rice accounts for 43% of staple food production in the Democratic People’s Republic of Korea (DPRK). The most widely planted rice varieties were developed from a limited number of ancestral lines that were repeatedly used as parents in breeding programs. However, detailed pedigrees are not publicly available and little is known about the genetic, phenotypic, and geographical variation of DPRK varieties. Results We evaluated 80 O. sativa accessions from the DPRK, consisting of 67 improved varieties and 13 landraces. Based on nuclear SSR analysis, we divide the varieties into two genetic groups: Group 1 corresponds to the temperate japonica subpopulation and represents 78.75% of the accessions, while Group 2 shares recent ancestry with indica varieties. Interestingly, members of Group 1 are less diverse than Group 2 at the nuclear level, but are more diverse at the chloroplast level. All Group 2 varieties share a single Japonica maternal-haplotype, while Group 1 varieties trace maternal ancestry to both Japonica and Indica. Phenotypically, members of Group 1 have shorter grains than Group 2, and varieties from breeding programs have thicker and wider grains than landraces. Improved varieties in Group 1 also show similar and/or better levels of cold tolerance for most traits, except for spikelet number per panicle. Finally, geographic analysis demonstrates that the majority of genetic variation is located within regions that have the most intensive rice cultivation, including the Western territories near the capital city Pyungyang. This is consistent with the conscious and highly centralized role of human selection in determining local dispersion patterns of rice in the DPRK. Conclusions Diversity studies of DPRK rice germplasm revealed two genetic groups. The most widely planted group has a narrow genetic base and would benefit from the introduction of new genetic variation from cold tolerant landraces, wild accessions, and/or cultivated gene pools to

  20. [Index screening and comprehensive evaluation of phenotypic traits of low nitrogen tolerance using BILs population derived from Dongxiang wild rice (Oryza rufipogon Griff)].

    Science.gov (United States)

    Hu, Biao-lin; Li, Xia; Wan, Yong; Qiu, Zai-hui; Nie, Yuan-yuan; Xie, Jian-kun

    2015-08-01

    To identify the low nitrogen tolerance of Dongxiang wild rice (DXWR) and its progenies, ten phenotypic traits including plant height (PH), heading day (HD), panicle length (PL), number of effective tillers per plant (NETP), number of filled grains per panicle (NFGP), number of grains per panicle (NGP), grain density (GD), spikelet fertility (SF), 1000-grain mass (TGM) and grain yield per plant (GYP) were studied under normal and low nitrogen treatments, using backcross inbred lines (BILs) of Xieqingzao B//DXWR/Xieqingzao B in BC1 F12. Comprehensive evaluation on the low nitrogen tolerance of the BILs population was conducted using principal component analysis and the subordinate function. The evaluation results indicated that the low nitrogen tolerance of the line 116, 143 and 157 was the strongest, which could be served as the intermediate materials for genetic studies on the low nitrogen tolerance of DXWR and breeding for the low nitrogen tolerance in rice. The optimal regression equation of the low nitrogen tolerance in rice was established using stepwise regression analysis. The relative values of five traits including PH, NGP, SF, TGM and GYP were screened out and could be used as comprehensive evaluation indices for the low nitrogen tolerance in the whole growth stage. Therefore, more attention should be paid to the relative values of these five traits, especially for NGP and GYP, in the genetic improvement of the low nitrogen tolerance in rice.

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

    Science.gov (United States)

    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.

  2. Domesticated, Genetically Engineered, and Wild Plant Relatives Exhibit Unintended Phenotypic Differences: A Comparative Meta-Analysis Profiling Rice, Canola, Maize, Sunflower, and Pumpkin

    Directory of Open Access Journals (Sweden)

    Alejandra Hernández-Terán

    2017-12-01

    Full Text Available Agronomic management of plants is a powerful evolutionary force acting on their populations. The management of cultivated plants is carried out by the traditional process of human selection or plant breeding and, more recently, by the technologies used in genetic engineering (GE. Even though crop modification through GE is aimed at specific traits, it is possible that other non-target traits can be affected by genetic modification due to the complex regulatory processes of plant metabolism and development. In this study, we conducted a meta-analysis profiling the phenotypic consequences of plant breeding and GE, and compared modified cultivars with wild relatives in five crops of global economic and cultural importance: rice, maize, canola, sunflower, and pumpkin. For these five species, we analyzed the literature with documentation of phenotypic traits that are potentially related to fitness for the same species in comparable conditions. The information was analyzed to evaluate whether the different processes of modification had influenced the phenotype in such a way as to cause statistical differences in the state of specific phenotypic traits or grouping of the organisms depending on their genetic origin [wild, domesticated with genetic engineering (domGE, and domesticated without genetic engineering (domNGE]. In addition, we tested the hypothesis that, given that transgenic plants are a construct designed to impact, in many cases, a single trait of the plant (e.g., lepidopteran resistance, the phenotypic differences between domGE and domNGE would be either less (or inexistent than between the wild and domesticated relatives (either domGE or domNGE. We conclude that (1 genetic modification (either by selective breeding or GE can be traced phenotypically when comparing wild relatives with their domesticated relatives (domGE and domNGE and (2 the existence and the magnitude of the phenotypic differences between domGE and domNGE of the same crop

  3. Patterns of nucleotide diversity and phenotypes of two domestication related genes (OsC1 and Wx) in indigenous rice varieties in Northeast India.

    Science.gov (United States)

    Choudhury, Baharul Islam; Khan, Mohammed Latif; Dayanandan, Selvadurai

    2014-06-16

    During the domestication of crops, individual plants with traits desirable for human needs have been selected from their wild progenitors. Consequently, genetic and nucleotide diversity of genes associated with these selected traits in crop plants are expected to be lower than their wild progenitors. In the present study, we surveyed the pattern of nucleotide diversity of two selected trait specific genes, Wx and OsC1, which regulate amylose content and apiculus coloration respectively in cultivated rice varieties. The analyzed samples were collected from a wide geographic area in Northeast (NE) India, and included contrasting phenotypes considered to be associated with selected genes, namely glutinous and nonglutinous grains and colored and colorless apiculus. No statistically significant selection signatures were detected in both Wx and OsC1gene sequences. However, low level of selection that varied across the length of each gene was evident. The glutinous type varieties showed higher levels of nucleotide diversity at the Wx locus (πtot = 0.0053) than nonglutinous type varieties (πtot = 0.0043). The OsC1 gene revealed low levels of selection among the colorless apiculus varieties with lower nucleotide diversity (πtot = 0.0010) than in the colored apiculus varieties (πtot = 0.0023). The results revealed that functional mutations at Wx and OsC1genes considered to be associated with specific phenotypes do not necessarily correspond to the phenotypes in indigenous rice varieties in NE India. This suggests that other than previously reported genomic regions may also be involved in determination of these phenotypes.

  4. Deciphering Periodic Methanol Masers

    Science.gov (United States)

    Stecklum, Bringfried; Caratti o Garatti, Alessio; Henning, Thomas; Hodapp, Klaus; Hopp, Ulrich; Kraus, Alex; Linz, Hendrik; Sanna, Alberto; Sobolev, Andrej; Wolf, Verena

    2018-05-01

    Impressive progress has been made in recent years on massive star formation, yet the involved high optical depths even at submm/mm wavelengths make it difficult to reveal its details. Recently, accretion bursts of massive YSOs have been identified to cause flares of Class II methanol masers (methanol masers for short) due to enhanced mid-IR pumping. This opens a new window to protostellar accretion variability, and implies that periodic methanol masers hint at cyclic accretion. Pinning down the cause of the periodicity requires joint IR and radio monitoring. We derived the first IR light curve of a periodic maser host from NEOWISE data. The source, G107.298+5.639, is an intermediate-mass YSO hosting methanol and water masers which flare every 34.5 days. Our recent joint K-band and radio observations yielded first but marginal evidence for a phase lag between the rise of IR and maser emission, respectively, and revealed that both NEOWISE and K-band light curves are strongly affected by the light echo from the ambient dust. Both the superior resolution of IRAC over NEOWISE and the longer wavelengths compared to our ground-based imaging are required to inhibit the distractive contamination by the light echo. Thus, we ask for IRAC monitoring of G107 to cover one flare cycle, in tandem with 100-m Effelsberg and 2-m Wendelstein radio and NIR observations to obtain the first high-quality synoptic measurements of this kind of sources. The IR-maser phase lag, the intrinsic shape of the IR light curves and their possible color variation during the cycle allow us to constrain models for the periodic maser excitation. Since methanol masers are signposts of intermediate-mass and massive YSOs, deciphering their variability offers a clue to the dynamics of the accretion-mediated growth of massive stars and their feedback onto the immediate natal environment. The Spitzer light curve of such a maser-hosting YSO would be a legacy science product of the mission.

  5. Eficiência produtiva de cultivares de arroz com divergência fenotípica Production efficiency of rice cultivars with phenotypic diversity

    Directory of Open Access Journals (Sweden)

    Cleber M. Guimarães

    2008-10-01

    Full Text Available O objetivo do trabalho foi avaliar, fenotipicamente, as cultivares de arroz tradicionais Guarani e Caiapó, e as modernas, CIRAD L(-141, Maravilha, BR IRGA 409 e Metica 1, por meio da associação entre os vários componentes da produtividade de grãos, para prover base de seleção genética em populações de plantas. O estudo foi conduzido na estação chuvosa do ano agrícola de 2003-2004, na área experimental da Embrapa Arroz e Feijão, em Santo Antônio de Goiás, GO. Em condições de sequeiro, com suplementação hídrica, as cultivares de arroz de terras altas CIRAD L(-141, Guarani, Caiapó e Maravilha, apresentaram maiores índices de colheita e menores percentagens de esterilidade de espiguetas que as de arroz irrigado BR IRGA 409 e Metica 1. Concluiu-se que a maior produção de biomassa pelas cultivares de arroz irrigado não se refletiu na produtividade de grãos. A CIRAD L(-141 por apresentar alta área foliar, panículas densas com alto número de grãos e um comportamento intermediário em todos os componentes avaliados, como índice de colheita, massa dos grãos, fertilidade de perfilhos, perfilhamento, esterilidade de espiguetas e taxa de crescimento, produziu 12,5% a mais que a segunda mais produtiva. O aumento do índice de colheita e da massa dos grãos e a redução da esterilidade das espiguetas devido às suas altas correlações com a produtividade, são considerados prioritários em programas de melhoramento de arroz que visem obter cultivares mais produtivas.The objective of this study was to phenotypically evaluate the traditional rice cultivars Guarani and Caiapó, and the modern rice cultivars CIRAD L(-141, Maravilha, BR IRGA 409, and Metica 1 through association among various yield components to establish a genetic selection base in plant population. The study was conducted during the rainy season of 2003-2004, at the Embrapa Rice & Beans experimental station, in Santo Antônio de Goiás, Goiás, Brazil. With

  6. Envirotyping for deciphering environmental impacts on crop plants.

    Science.gov (United States)

    Xu, Yunbi

    2016-04-01

    Global climate change imposes increasing impacts on our environments and crop production. To decipher environmental impacts on crop plants, the concept "envirotyping" is proposed, as a third "typing" technology, complementing with genotyping and phenotyping. Environmental factors can be collected through multiple environmental trials, geographic and soil information systems, measurement of soil and canopy properties, and evaluation of companion organisms. Envirotyping contributes to crop modeling and phenotype prediction through its functional components, including genotype-by-environment interaction (GEI), genes responsive to environmental signals, biotic and abiotic stresses, and integrative phenotyping. Envirotyping, driven by information and support systems, has a wide range of applications, including environmental characterization, GEI analysis, phenotype prediction, near-iso-environment construction, agronomic genomics, precision agriculture and breeding, and development of a four-dimensional profile of crop science involving genotype (G), phenotype (P), envirotype (E) and time (T) (developmental stage). In the future, envirotyping needs to zoom into specific experimental plots and individual plants, along with the development of high-throughput and precision envirotyping platforms, to integrate genotypic, phenotypic and envirotypic information for establishing a high-efficient precision breeding and sustainable crop production system based on deciphered environmental impacts.

  7. Phenotypic performance of transgenic potato (Solanum tuberosum L.) plants with pyramided rice cystatin genes (OCI and OCII)

    Science.gov (United States)

    The evaluation of transgenic plants commonly carried out under controlled conditions in culture rooms and greenhouses can give valuable information about the influence of introduced genes on transgenic plant phenotype. However, an overall assessment of plant performance can only be made by testing t...

  8. Estimating rice yield related traits and quantitative trait loci analysis under different nitrogen treatments using a simple tower-based field phenotyping system with modified single-lens reflex cameras

    Science.gov (United States)

    Naito, Hiroki; Ogawa, Satoshi; Valencia, Milton Orlando; Mohri, Hiroki; Urano, Yutaka; Hosoi, Fumiki; Shimizu, Yo; Chavez, Alba Lucia; Ishitani, Manabu; Selvaraj, Michael Gomez; Omasa, Kenji

    2017-03-01

    Application of field based high-throughput phenotyping (FB-HTP) methods for monitoring plant performance in real field conditions has a high potential to accelerate the breeding process. In this paper, we discuss the use of a simple tower based remote sensing platform using modified single-lens reflex cameras for phenotyping yield traits in rice under different nitrogen (N) treatments over three years. This tower based phenotyping platform has the advantages of simplicity, ease and stability in terms of introduction, maintenance and continual operation under field conditions. Out of six phenological stages of rice analyzed, the flowering stage was the most useful in the estimation of yield performance under field conditions. We found a high correlation between several vegetation indices (simple ratio (SR), normalized difference vegetation index (NDVI), transformed vegetation index (TVI), corrected transformed vegetation index (CTVI), soil-adjusted vegetation index (SAVI) and modified soil-adjusted vegetation index (MSAVI)) and multiple yield traits (panicle number, grain weight and shoot biomass) across a three trials. Among all of the indices studied, SR exhibited the best performance in regards to the estimation of grain weight (R2 = 0.80). Under our tower-based field phenotyping system (TBFPS), we identified quantitative trait loci (QTL) for yield related traits using a mapping population of chromosome segment substitution lines (CSSLs) and a single nucleotide polymorphism data set. Our findings suggest the TBFPS can be useful for the estimation of yield performance during early crop development. This can be a major opportunity for rice breeders whom desire high throughput phenotypic selection for yield performance traits.

  9. Activation of gibberellin 2-oxidase 6 decreases active gibberellin levels and creates a dominant semi-dwarf phenotype in rice (Oryza sativa L.).

    Science.gov (United States)

    Huang, Jian; Tang, Ding; Shen, Yi; Qin, Baoxiang; Hong, Lilan; You, Aiqing; Li, Ming; Wang, Xin; Yu, Hengxiu; Gu, Minghong; Cheng, Zhukuan

    2010-01-01

    Gibberellin (GA) 2-oxidase plays a key role in the GA catabolic pathway through 2beta-hydroxylation. In the present study, we isolated a CaMV 35S-enhancer activation tagged mutant, H032. This mutant exhibited a dominant dwarf and GA-deficient phenotype, with a final stature that was less than half of its wild-type counterpart. The endogenous bioactive GAs are markedly decreased in the H032 mutant, and application of bioactive GAs (GA(3) or GA(4)) can reverse the dwarf phenotype. The integrated T-DNA was detected 12.8 kb upstream of the OsGA2ox6 in the H032 genome by TAIL-PCR. An increased level of OsGA2ox6 mRNA was detected at a high level in the H032 mutant, which might be due to the enhancer role of the CaMV 35S promoter. RNAi and ectopic expression analysis of OsGA2ox6 indicated that the dwarf trait and the decreased levels of bioactive GAs in the H032 mutant were a result of the up-regulation of the OsGA2ox6 gene. BLASTP analysis revealed that OsGA2ox6 belongs to the class III of GA 2-oxidases, which is a novel type of GA2ox that uses C20-GAs (GA(12) and/or GA(53)) as the substrates. Interestingly, we found that a GA biosynthesis inhibitor, paclobutrazol, positively regulated the OsGA2ox6 gene. Unlike the over-expression of OsGA2ox1, which led to a high rate of seed abortion, the H032 mutant retained normal flowering and seed production. These results indicate that OsGA2ox6 mainly affects plant stature, and the dominant dwarf trait of the H032 mutant can be used as an efficient dwarf resource in rice breeding. Copyright 2010 Institute of Genetics and Developmental Biology and the Genetics Society of China. Published by Elsevier Ltd. All rights reserved.

  10. Decipher

    CERN Multimedia

    2002-01-01

    Review of a new fiction work by Stel Pavlou whose starting point is the lifecycle of the sun and the implications for human civilization. The story invokes the use of the CERN accelerator to analyze a special type of crystal found in Antartica which may hold the key to the legend of the city of Atlantis (1/2 page).

  11. Bacillomycin L and surfactin contribute synergistically to the phenotypic features of Bacillus subtilis 916 and the biocontrol of rice sheath blight induced by Rhizoctonia solani.

    Science.gov (United States)

    Luo, Chuping; Zhou, Huafei; Zou, Jincheng; Wang, Xiaoyu; Zhang, Rongsheng; Xiang, Yaping; Chen, Zhiyi

    2015-02-01

    The antagonistic activity of lipopeptides in Bacillus subtilis 916 has been well documented, yet relatively little is known about their mechanism in biofilm formation and environmental colonization. This study sought to examine the interaction of B. subtilis 916 on Rhizoctonia solani-infected rice sheath to elucidate the mechanism of colonization on plant leaves. Results showed that the mutants Δbac, Δsrf, and Δsrf + bac of B. subtilis 916, deficient in bacillomycin L and surfactin production, respectively, not only altered colony morphology but also changed swarming motility, reduced antagonistic activity, and decreased biofilm formation. In particular, biofilm formation in mutant Δbac, not Δsrf or Δsrf + bac, were restored with addition of surfactin and bacillomycin L at 10 and 50 μg/mL, respectively. Moreover, surfactin and bacillomycin L were able to restore or enhance swarming motility in the corresponding mutants at 10 μg/mL, respectively. With the aid of green fluorescent protein tagging, it was demonstrated that B. subtilis 916 formed a robust biofilm on the rice sheath blight lesion and colonized well on R. solani-infected rice sheath, while its corresponding mutants performed poorly. These observations also correlated with the rice cultivar pot experiments, in which B. subtilis 916 exhibited greater biocontrol than its mutants. Our results suggest that surfactin and bacillomycin L contribute differently but synergistically to the biocontrol of rice sheath blight in B. subtilis 916 through its antifungal activity, biofilm formation, and colonization.

  12. Deciphering the Cognitive and Neural Mechanisms Underlying ...

    International Development Research Centre (IDRC) Digital Library (Canada)

    Deciphering the Cognitive and Neural Mechanisms Underlying Auditory Learning. This project seeks to understand the brain mechanisms necessary for people to learn to perceive sounds. Neural circuits and learning. The research team will test people with and without musical training to evaluate their capacity to learn ...

  13. Quantitative monitoring of sucrose, reducing sugar and total sugar dynamics for phenotyping of water-deficit stress tolerance in rice through spectroscopy and chemometrics

    Science.gov (United States)

    Das, Bappa; Sahoo, Rabi N.; Pargal, Sourabh; Krishna, Gopal; Verma, Rakesh; Chinnusamy, Viswanathan; Sehgal, Vinay K.; Gupta, Vinod K.; Dash, Sushanta K.; Swain, Padmini

    2018-03-01

    In the present investigation, the changes in sucrose, reducing and total sugar content due to water-deficit stress in rice leaves were modeled using visible, near infrared (VNIR) and shortwave infrared (SWIR) spectroscopy. The objectives of the study were to identify the best vegetation indices and suitable multivariate technique based on precise analysis of hyperspectral data (350 to 2500 nm) and sucrose, reducing sugar and total sugar content measured at different stress levels from 16 different rice genotypes. Spectral data analysis was done to identify suitable spectral indices and models for sucrose estimation. Novel spectral indices in near infrared (NIR) range viz. ratio spectral index (RSI) and normalised difference spectral indices (NDSI) sensitive to sucrose, reducing sugar and total sugar content were identified which were subsequently calibrated and validated. The RSI and NDSI models had R2 values of 0.65, 0.71 and 0.67; RPD values of 1.68, 1.95 and 1.66 for sucrose, reducing sugar and total sugar, respectively for validation dataset. Different multivariate spectral models such as artificial neural network (ANN), multivariate adaptive regression splines (MARS), multiple linear regression (MLR), partial least square regression (PLSR), random forest regression (RFR) and support vector machine regression (SVMR) were also evaluated. The best performing multivariate models for sucrose, reducing sugars and total sugars were found to be, MARS, ANN and MARS, respectively with respect to RPD values of 2.08, 2.44, and 1.93. Results indicated that VNIR and SWIR spectroscopy combined with multivariate calibration can be used as a reliable alternative to conventional methods for measurement of sucrose, reducing sugars and total sugars of rice under water-deficit stress as this technique is fast, economic, and noninvasive.

  14. The APETALA-2-like transcription factor OsAP2-39 controls key interactions between abscisic acid and gibberellin in rice.

    Science.gov (United States)

    Yaish, Mahmoud W; El-Kereamy, Ashraf; Zhu, Tong; Beatty, Perrin H; Good, Allen G; Bi, Yong-Mei; Rothstein, Steven J

    2010-09-09

    The interaction between phytohormones is an important mechanism which controls growth and developmental processes in plants. Deciphering these interactions is a crucial step in helping to develop crops with enhanced yield and resistance to environmental stresses. Controlling the expression level of OsAP2-39 which includes an APETALA 2 (AP2) domain leads to phenotypic changes in rice. Overexpression of OsAP2-39 leads to a reduction in yield by decreasing the biomass and the number of seeds in the transgenic rice lines. Global transcriptome analysis of the OsAP2-39 overexpression transgenic rice revealed the upregulation of a key abscisic acid (ABA) biosynthetic gene OsNCED-I which codes for 9-cis-epoxycarotenoid dioxygenase and leads to an increase in the endogenous ABA level. In addition to OsNCED-1, the gene expression analysis revealed the upregulation of a gene that codes for the Elongation of Upper most Internode (EUI) protein, an enzyme that catalyzes 16α, 17-epoxidation of non-13-hydroxylated GAs, which has been shown to deactivate gibberellins (GAs) in rice. The exogenous application of GA restores the wild-type phenotype in the transgenic line and ABA application induces the expression of EUI and suppresses the expression of OsAP2-39 in the wild-type line. These observations clarify the antagonistic relationship between ABA and GA and illustrate a mechanism that leads to homeostasis of these hormones. In vivo and in vitro analysis showed that the expression of both OsNCED-1 and EUI are directly controlled by OsAP2-39. Together, these results reveal a novel mechanism for the control of the ABA/GA balance in rice which is regulated by OsAP2-39 that in turn regulates plant growth and seed production.

  15. The APETALA-2-like transcription factor OsAP2-39 controls key interactions between abscisic acid and gibberellin in rice.

    Directory of Open Access Journals (Sweden)

    Mahmoud W Yaish

    2010-09-01

    Full Text Available The interaction between phytohormones is an important mechanism which controls growth and developmental processes in plants. Deciphering these interactions is a crucial step in helping to develop crops with enhanced yield and resistance to environmental stresses. Controlling the expression level of OsAP2-39 which includes an APETALA 2 (AP2 domain leads to phenotypic changes in rice. Overexpression of OsAP2-39 leads to a reduction in yield by decreasing the biomass and the number of seeds in the transgenic rice lines. Global transcriptome analysis of the OsAP2-39 overexpression transgenic rice revealed the upregulation of a key abscisic acid (ABA biosynthetic gene OsNCED-I which codes for 9-cis-epoxycarotenoid dioxygenase and leads to an increase in the endogenous ABA level. In addition to OsNCED-1, the gene expression analysis revealed the upregulation of a gene that codes for the Elongation of Upper most Internode (EUI protein, an enzyme that catalyzes 16α, 17-epoxidation of non-13-hydroxylated GAs, which has been shown to deactivate gibberellins (GAs in rice. The exogenous application of GA restores the wild-type phenotype in the transgenic line and ABA application induces the expression of EUI and suppresses the expression of OsAP2-39 in the wild-type line. These observations clarify the antagonistic relationship between ABA and GA and illustrate a mechanism that leads to homeostasis of these hormones. In vivo and in vitro analysis showed that the expression of both OsNCED-1 and EUI are directly controlled by OsAP2-39. Together, these results reveal a novel mechanism for the control of the ABA/GA balance in rice which is regulated by OsAP2-39 that in turn regulates plant growth and seed production.

  16. Deciphering psoriasis. A bioinformatic approach.

    Science.gov (United States)

    Melero, Juan L; Andrades, Sergi; Arola, Lluís; Romeu, Antoni

    2018-02-01

    Psoriasis is an immune-mediated, inflammatory and hyperproliferative disease of the skin and joints. The cause of psoriasis is still unknown. The fundamental feature of the disease is the hyperproliferation of keratinocytes and the recruitment of cells from the immune system in the region of the affected skin, which leads to deregulation of many well-known gene expressions. Based on data mining and bioinformatic scripting, here we show a new dimension of the effect of psoriasis at the genomic level. Using our own pipeline of scripts in Perl and MySql and based on the freely available NCBI Gene Expression Omnibus (GEO) database: DataSet Record GDS4602 (Series GSE13355), we explore the extent of the effect of psoriasis on gene expression in the affected tissue. We give greater insight into the effects of psoriasis on the up-regulation of some genes in the cell cycle (CCNB1, CCNA2, CCNE2, CDK1) or the dynamin system (GBPs, MXs, MFN1), as well as the down-regulation of typical antioxidant genes (catalase, CAT; superoxide dismutases, SOD1-3; and glutathione reductase, GSR). We also provide a complete list of the human genes and how they respond in a state of psoriasis. Our results show that psoriasis affects all chromosomes and many biological functions. If we further consider the stable and mitotically inheritable character of the psoriasis phenotype, and the influence of environmental factors, then it seems that psoriasis has an epigenetic origin. This fit well with the strong hereditary character of the disease as well as its complex genetic background. Copyright © 2017 Japanese Society for Investigative Dermatology. Published by Elsevier B.V. All rights reserved.

  17. Rice microstructure

    Science.gov (United States)

    An understanding of plant structure is desirable to obtain a clear idea of the overall impact of a crop. A mature rice plant consists of leafy components (left in the field post-harvest) and paddy rice (collected). The rice plant is supported by a hollow stem (culm) with leaf sheaths attached to nod...

  18. Rice epigenomics and epigenetics: challenges and opportunities.

    Science.gov (United States)

    Chen, Xiangsong; Zhou, Dao-Xiu

    2013-05-01

    During recent years rice genome-wide epigenomic information such as DNA methylation and histone modifications, which are important for genome activity has been accumulated. The function of a number of rice epigenetic regulators has been studied, many of which are found to be involved in a diverse range of developmental and stress-responsive pathways. Analysis of epigenetic variations among different rice varieties indicates that epigenetic modification may lead to inheritable phenotypic variation. Characterizing phenotypic consequences of rice epigenomic variations and the underlining chromatin mechanism and identifying epialleles related to important agronomic traits may provide novel strategies to enhance agronomically favorable traits and grain productivity in rice. Copyright © 2013 Elsevier Ltd. All rights reserved.

  19. Population Structure, Diversity and Trait Association Analysis in Rice (Oryza sativa L. Germplasm for Early Seedling Vigor (ESV Using Trait Linked SSR Markers.

    Directory of Open Access Journals (Sweden)

    Annamalai Anandan

    Full Text Available Early seedling vigor (ESV is the essential trait for direct seeded rice to dominate and smother the weed growth. In this regard, 629 rice genotypes were studied for their morphological and physiological responses in the field under direct seeded aerobic situation on 14th, 28th and 56th days after sowing (DAS. It was determined that the early observations taken on 14th and 28th DAS were reliable estimators to study ESV as compared to 56th DAS. Further, 96 were selected from 629 genotypes by principal component (PCA and discriminate function analyses. The selected genotypes were subjected to decipher the pattern of genetic diversity in terms of both phenotypic and genotypic by using ESV QTL linked simple sequence repeat (SSR markers. To assess the genetic structure, model and distance based approaches were used. Genotyping of 96 rice lines using 39 polymorphic SSRs produced a total of 128 alleles with the phenotypic information content (PIC value of 0.24. The model based population structure approach grouped the accession into two distinct populations, whereas unrooted tree grouped the genotypes into three clusters. Both model based and structure based approach had clearly distinguished the early vigor genotypes from non-early vigor genotypes. Association analysis revealed that 16 and 10 SSRs showed significant association with ESV traits by general linear model (GLM and mixed linear model (MLM approaches respectively. Marker alleles on chromosome 2 were associated with shoot dry weight on 28 DAS, vigor index on 14 and 28 DAS. Improvement in the rate of seedling growth will be useful for identifying rice genotypes acquiescent to direct seeded conditions through marker-assisted selection.

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

    Science.gov (United States)

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

    2016-04-26

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

  1. Deciphering interactions in moving animal groups.

    Directory of Open Access Journals (Sweden)

    Jacques Gautrais

    Full Text Available Collective motion phenomena in large groups of social organisms have long fascinated the observer, especially in cases, such as bird flocks or fish schools, where large-scale highly coordinated actions emerge in the absence of obvious leaders. However, the mechanisms involved in this self-organized behavior are still poorly understood, because the individual-level interactions underlying them remain elusive. Here, we demonstrate the power of a bottom-up methodology to build models for animal group motion from data gathered at the individual scale. Using video tracks of fish shoal in a tank, we show how a careful, incremental analysis at the local scale allows for the determination of the stimulus/response function governing an individual's moving decisions. We find in particular that both positional and orientational effects are present, act upon the fish turning speed, and depend on the swimming speed, yielding a novel schooling model whose parameters are all estimated from data. Our approach also leads to identify a density-dependent effect that results in a behavioral change for the largest groups considered. This suggests that, in confined environment, the behavioral state of fish and their reaction patterns change with group size. We debate the applicability, beyond the particular case studied here, of this novel framework for deciphering interactions in moving animal groups.

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

    Science.gov (United States)

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

  3. Engineered Dwarf Male-Sterile Rice: A Promising Genetic Tool for Facilitating Recurrent Selection in Rice.

    Science.gov (United States)

    Ansari, Afsana; Wang, Chunlian; Wang, Jian; Wang, Fujun; Liu, Piqing; Gao, Ying; Tang, Yongchao; Zhao, Kaijun

    2017-01-01

    Rice is a crop feeding half of the world's population. With the continuous raise of yield potential via genetic improvement, rice breeding has entered an era where multiple genes conferring complex traits must be efficiently manipulated to increase rice yield further. Recurrent selection is a sound strategy for manipulating multiple genes and it has been successfully performed in allogamous crops. However, the difficulties in emasculation and hand pollination had obstructed efficient use of recurrent selection in autogamous rice. Here, we report development of the dwarf male-sterile rice that can facilitate recurrent selection in rice breeding. We adopted RNAi technology to synergistically regulate rice plant height and male fertility to create the dwarf male-sterile rice. The RNAi construct pTCK-EGGE, targeting the OsGA20ox2 and OsEAT1 genes, was constructed and used to transform rice via Agrobacterium -mediated transformation. The transgenic T0 plants showing largely reduced plant height and complete male-sterile phenotypes were designated as the dwarf male-sterile plants. Progenies of the dwarf male-sterile plants were obtained by pollinating them with pollens from the wild-type. In the T1 and T2 populations, half of the plants were still dwarf male-sterile; the other half displayed normal plant height and male fertility which were designated as tall and male-fertile plants. The tall and male-fertile plants are transgene-free and can be self-pollinated to generate new varieties. Since emasculation and hand pollination for dwarf male-sterile rice plants is no longer needed, the dwarf male-sterile rice can be used to perform recurrent selection in rice. A dwarf male-sterile rice-based recurrent selection model has been proposed.

  4. (PGMS) rice

    African Journals Online (AJOL)

    user

    2011-04-18

    Apr 18, 2011 ... tics, led us to predict that pollen cell abortion in this type of rice when ... averages of natural day-light-lengths and temperatures were used. A natural long ... blocks were allowed to grow under natural growth conditions (which.

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

    Science.gov (United States)

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

  6. Termometria infravermelha na fenotipagem para resistência à seca de linhagens inter e intraespecíficas de arroz Infrared thermometry for drought phenotyping of inter and intra specific upland rice lines

    Directory of Open Access Journals (Sweden)

    Cleber M. Guimarães

    2010-02-01

    Full Text Available Propôs-se avaliar, no presente estudo, a técnica da termometria ao infravermelho na caracterização de linhagens interespecíficas (Oryza glaberrima x Oryza sativa cv Caiapó e intraespecíficas de arroz para tolerância a seca. O experimento, conduzido em Porangatu, GO, foi submetido a condições adequadas de umidade no solo até 30 dias após a emergência, quando então foi implantado um tratamento com deficiência hídrica moderada (aproximadamente 50% da irrigação aplicada em uma parcela testemunha, com condições adequadas de umidade no solo. Verificou-se que as linhagens mais produtivas em condições de deficiência hídrica apresentaram plantas mais altas, com panículas mais densas e com grãos mais bem formados, com menor esterilidade de espiguetas. Observou-se, também, que a temperatura das folhas se correlacionou positivamente com a esterilidade de espiguetas e negativamente com a massa de 100 grãos, altura das plantas, fertilidade de perfilhos e produtividade. Exceto a fertilidade de perfilhos, os demais componentes se correlacionaram com a produtividade de grãos, sendo que com a esterilidade de espiguetas a correlação foi negativa. Concluiu-se que a O. glaberrima confere, às suas progênies, maior rusticidade à deficiência hídrica e que a termometria ao infravermelho é uma técnica auxiliar importante na fenotipagem para tolerância a seca.The purpose of the present study was to evaluate the use of infrared thermometry in the characterization of inter specific (Oryza glaberrima x Oryza sativa cv Caiapó and intra specific upland rice lines for drought tolerance. The experiment, carried out at Porangatu in the State of Goiás, was submitted to adequate soil moisture for up to 30 days following emergence when a moderate water stress treatment was imposed (about 50% of the applied irrigation in a control plot in which adequate conditions of soil moisture were maintained. It has been observed that lines with higher

  7. Malaysian weedy rice shows its true stripes: wild Oryza and elite rice cultivars shape agricultural weed evolution in Southeast Asia.

    Science.gov (United States)

    Song, Beng-Kah; Chuah, Tse-Seng; Tam, Sheh May; Olsen, Kenneth M

    2014-10-01

    Weedy rice is a close relative of domesticated rice (Oryza sativa) that competes aggressively with the crop and limits rice productivity worldwide. Most genetic studies of weedy rice have focused on populations in regions where no reproductively compatible wild Oryza species occur (North America, Europe and northern Asia). Here, we examined the population genetics of weedy rice in Malaysia, where wild rice (O. rufipogon) can be found growing in close proximity to cultivated and weedy rice. Using 375 accessions and a combined analysis of 24 neutral SSR loci and two rice domestication genes (sh4, controlling seed shattering, and Bh4, controlling hull colour), we addressed the following questions: (i) What is the relationship of Malaysian weedy rice to domesticated and wild rice, and to weedy rice strains in the USA? (ii) To what extent does the presence of O. rufipogon influence the genetic and phenotypic diversity of Malaysian weeds? (iii) What do the distributions of sh4 and Bh4 alleles and associated phenotypes reveal about the origin and contemporary evolution of Malaysian weedy rice? Our results reveal the following: independent evolutionary origins for Malaysian weeds and US strains, despite their very close phenotypic resemblance; wild-to-weed gene flow in Malaysian weed populations, including apparent adaptive introgression of seed-shattering alleles; and a prominent role for modern Malaysian cultivars in the origin and recent proliferation of Malaysian weeds. These findings suggest that the genetic complexity and adaptability of weedy crop relatives can be profoundly influenced by proximity to reproductively compatible wild and domesticated populations. © 2014 John Wiley & Sons Ltd.

  8. Mutant heterosis in rice

    International Nuclear Information System (INIS)

    1987-01-01

    In the variety TKM6 a high yielding semidwarf mutant has been induced. This TKM6 mutant was used in test crosses with a number of other varieties and mutants to examine the extent of heterosis of dwarfs in rice and to select superior crosses. An excerpt of the published data is given. It appears from the backcross of the mutant with its original variety, that an increase in number of productive tillers occurs in the hybrid, leading to a striking grain yield increase, while the semi-dwarf culm length (the main mutant character) reverts to the normal phenotype. In the cross with IR8 on the other hand, there is only a minimal increase in tiller number but a substantial increase in TGW leading to more than 30% yield increase over the better parent

  9. Genetic analyses for deciphering the status and role of ...

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Genetics; Volume 96; Issue 1. Genetic analyses for deciphering the status and role of photoperiodic and maturity genes in major Indian soybean cultivars. SANJAY GUPTA VIRENDER SINGH BHATIA GIRIRAJ KUMAWAT DEVSHREE THAKUR GOURAV SINGH RACHANA TRIPATHI GYANESH ...

  10. Deciphering dendritic cell heterogenity in immunity

    Directory of Open Access Journals (Sweden)

    Michaël eChopin

    2012-02-01

    Full Text Available Dendritic cells (DCs are specialized antigen presenting cells that are exquisitely adapted to sense pathogens and induce the development of adaptive immune responses. They form a complex network of phenotypically and functionally distinct subsets. Within this network, individual DC subsets display highly specific roles in local immunosurveillance, migration and antigen presentation. This division of labor amongst DCs offers great potential to tune the immune response by harnessing subset-specific attributes of DCs in the clinical setting. Until recently, our understanding of DC subsets has been limited and paralleled by poor clinical translation and efficacy. We have now begun to unravel how different DC subsets develop within a complex multilayered system. These finding open up exciting possibilities for targeted manipulation of DC subsets. Furthermore, ground-breaking developments overcoming a major translational obstacle – identification of similar DC populations in mouse and man – now set the stage for significant advances in the field. Here we explore the determinants that underpin cellular and transcriptional heterogeneity within the DC network, how these influence DC distribution and localization at steady-state, and the capacity of DCs to present antigens via direct or cross-presentation during pathogen infection.

  11. Review of functional markers for improving cooking, eating, and the nutritional qualities of rice

    Science.gov (United States)

    Lau, Wendy C. P.; Rafii, Mohd Y.; Ismail, Mohd R.; Puteh, Adam; Latif, Mohammad A.; Ramli, Asfaliza

    2015-01-01

    After yield, quality is one of the most important aspects of rice breeding. Preference for rice quality varies among cultures and regions; therefore, rice breeders have to tailor the quality according to the preferences of local consumers. Rice quality assessment requires routine chemical analysis procedures. The advancement of molecular marker technology has revolutionized the strategy in breeding programs. The availability of rice genome sequences and the use of forward and reverse genetics approaches facilitate gene discovery and the deciphering of gene functions. A well-characterized gene is the basis for the development of functional markers, which play an important role in plant genotyping and, in particular, marker-assisted breeding. In addition, functional markers offer advantages that counteract the limitations of random DNA markers. Some functional markers have been applied in marker-assisted breeding programs and have successfully improved rice quality to meet local consumers’ preferences. Although functional markers offer a plethora of advantages over random genetic markers, the development and application of functional markers should be conducted with care. The decreasing cost of sequencing will enable more functional markers for rice quality improvement to be developed, and application of these markers in rice quality breeding programs is highly anticipated. PMID:26528304

  12. Preprocessing Algorithm for Deciphering Historical Inscriptions Using String Metric

    Directory of Open Access Journals (Sweden)

    Lorand Lehel Toth

    2016-07-01

    Full Text Available The article presents the improvements in the preprocessing part of the deciphering method (shortly preprocessing algorithm for historical inscriptions of unknown origin. Glyphs used in historical inscriptions changed through time; therefore, various versions of the same script may contain different glyphs for each grapheme. The purpose of the preprocessing algorithm is reducing the running time of the deciphering process by filtering out the less probable interpretations of the examined inscription. However, the first version of the preprocessing algorithm leads incorrect outcome or no result in the output in certain cases. Therefore, its improved version was developed to find the most similar words in the dictionary by relaying the search conditions more accurately, but still computationally effectively. Moreover, a sophisticated similarity metric used to determine the possible meaning of the unknown inscription is introduced. The results of the evaluations are also detailed.

  13. Delineating the psychiatric and behavioral phenotype of recurrent 2q13 deletions and duplications

    DEFF Research Database (Denmark)

    Wolfe, Kate; McQuillin, Andrew; Alesi, Viola

    2018-01-01

    . Participants were recruited via the Unique chromosomal disorder support group, U.K. National Health Service Regional Genetics Centres, and the DatabasE of genomiC varIation and Phenotype in Humans using Ensembl Resources (DECIPHER) database. A review of published 2q13 patient case reports was undertaken...

  14. Quantitative Trait Loci Analysis of Allelopathy in Rice

    DEFF Research Database (Denmark)

    Jensen, L B; Courtois, B; Olofsdotter, M

    2008-01-01

    The allelopathic potential of rice (Oryza sativa L.) against Echinochloa crus-galli (L.) Beauv. was investigated under both laboratory and greenhouse conditions. A population of 150 recombinant inbred lines (RILs) was derived through single-seed descent from a cross between the indica cultivar AC...... the population phenotype was normally distributed. Two quantitative trait loci (QTLs) were located on chromosomes 4 and 7, explaining 20% of the phenotypic variation. A second relay seeding experiment was set up, this time including charcoal in the perlite. This screening showed that the allelopathic rice...... varieties did not have any effect on the weed species when grown with charcoal, the charcoal reversing the effect of any potential allelochemicals exuded from the rice roots. The second phenotypic experiment was conducted under greenhouse conditions in pots. Thirteen QTLs were detected for four different...

  15. Rice peasants and rice research in Colombia

    NARCIS (Netherlands)

    Spijkers, P.A.N.M.

    1983-01-01

    Rice has been grown as a food crop in Latin America from early colonial times. In Colombia rice became a prominent subsistence crop especially on the north coast where it has been grown since the 17th century, sometimes also as a commercial crop. During the last twenty years there has been a sharp

  16. Immunotoxicological Evaluation of Genetically Modified Rice Expressing Cry1Ab/Ac Protein (TT51-1) by a 6-Month Feeding Study on Cynomolgus Monkeys

    Science.gov (United States)

    Tan, Xiaoyan; Zhou, Xiaobing; Tang, Yao; Lv, Jianjun; Zhang, Lin; Sun, Li; Yang, Yanwei; Miao, Yufa; Jiang, Hua; Chen, Gaofeng; Huang, Zhiying; Wang, Xue

    2016-01-01

    The present study was performed to evaluate the food safety of TT51-1, a new type of genetically modified rice that expresses the Cry1Ab/Ac protein (Bt toxin) and is highly resistant to most lepidopteran pests. Sixteen male and 16 female cynomolgus monkeys were randomly divided into four groups: conventional rice (non-genetically modified rice, non-GM rice), positive control, 17.5% genetically modified rice (GM rice) and 70% GM rice. Monkeys in the non-GM rice, positive control, and GM rice groups were fed on diets containing 70% non-GM rice, 17.5% GM rice or 70% GM rice, respectively, for 182 days, whereas animals in the positive group were intravenously injected with cyclophosphamide every other day for a total of four injections before the last treatment. Six months of treatment did not yield abnormal observations. Specifically, the following parameters did not significantly differ between the non-GM rice group and GM rice groups: body weight, food consumption, electrocardiogram, hematology, immuno-phenotyping of lymphocytes in the peripheral blood, mitogen-induced peripheral blood lymphocyte proliferation, splenocyte proliferation, KLH-T cell-dependent antibody response, organ weights and ratios, and histological appearance (p>0.05). Animals from the GM rice group differed from animals in the non-GM rice group (pGM rice. In conclusion, a 6-month feeding study of TT51-1 did not show adverse immunotoxicological effects on cynomolgus monkeys. PMID:27684490

  17. Linkage Mapping of Stem Saccharification Digestibility in Rice.

    Directory of Open Access Journals (Sweden)

    Bohan Liu

    Full Text Available Rice is the staple food of almost half of the world population, and in excess 90% of it is grown and consumed in Asia, but the disposal of rice straw poses a problem for farmers, who often burn it in the fields, causing health and environmental problems. However, with increased focus on the development of sustainable biofuel production, rice straw has been recognized as a potential feedstock for non-food derived biofuel production. Currently, the commercial realization of rice as a biofuel feedstock is constrained by the high cost of industrial saccharification processes needed to release sugar for fermentation. This study is focused on the alteration of lignin content, and cell wall chemotypes and structures, and their effects on the saccharification potential of rice lignocellulosic biomass. A recombinant inbred lines (RILs population derived from a cross between the lowland rice variety IR1552 and the upland rice variety Azucena with 271 molecular markers for quantitative trait SNP (QTS analyses was used. After association analysis of 271 markers for saccharification potential, 1 locus and 4 pairs of epistatic loci were found to contribute to the enzymatic digestibility phenotype, and an inverse relationship between reducing sugar and lignin content in these recombinant inbred lines was identified. As a result of QTS analyses, several cell-wall associated candidate genes are proposed that may be useful for marker-assisted breeding and may aid breeders to produce potential high saccharification rice varieties.

  18. Reviews in modern astronomy, deciphering the universe through spectroscopy

    CERN Document Server

    von Berlepsch, Regina

    2011-01-01

    This 22nd volume in the series contains 15 invited reviews and highlight contributions from outstanding speakers presented during the 2009 annual meeting of the Astronomical Society on the subject of ""Deciphering the Universe through Spectroscopy"", held in Potsdam, Germany. Topics range from the measurements of magnetic fields on the surface of the sun via detailed measurements of abundances in stellar atmospheres to the kinematics of the universe at its largest scales. The result is a systematic overview of the latest astronomical and cosmological research.

  19. Molecular evolution of shattering loci in U.S. weedy rice.

    Science.gov (United States)

    Thurber, Carrie S; Reagon, Michael; Gross, Briana L; Olsen, Kenneth M; Jia, Yulin; Caicedo, Ana L

    2010-08-01

    Cultivated rice fields worldwide are plagued with weedy rice, a conspecific weed of cultivated rice (Oryza sativa L.). The persistence of weedy rice has been attributed, in part, to its ability to shatter (disperse) seed prior to crop harvesting. In the United States, separately evolved weedy rice groups have been shown to share genomic identity with exotic domesticated cultivars. Here, we investigate the shattering phenotype in a collection of U.S. weedy rice accessions, as well as wild and cultivated relatives. We find that all U.S. weedy rice groups shatter seeds easily, despite multiple origins, and in contrast to a decrease in shattering ability seen in cultivated groups. We assessed allelic identity and diversity at the major shattering locus, sh4, in weedy rice; we find that all cultivated and weedy rice, regardless of population, share similar haplotypes at sh4, and all contain a single derived mutation associated with decreased seed shattering. Our data constitute the strongest evidence to date of an evolution of weeds from domesticated backgrounds. The combination of a shared cultivar sh4 allele and a highly shattering phenotype, suggests that U.S. weedy rice have re-acquired the shattering trait after divergence from their progenitors through alternative genetic mechanisms.

  20. Deciphering the evolutionary history of open and closed mitosis.

    Science.gov (United States)

    Sazer, Shelley; Lynch, Michael; Needleman, Daniel

    2014-11-17

    The origin of the nucleus at the prokaryote-to-eukaryote transition represents one of the most important events in the evolution of cellular organization. The nuclear envelope encircles the chromosomes in interphase and is a selectively permeable barrier between the nucleoplasm and cytoplasm and an organizational scaffold for the nucleus. It remains intact in the 'closed' mitosis of some yeasts, but loses its integrity in the 'open' mitosis of mammals. Instances of both types of mitosis within two evolutionary clades indicate multiple evolutionary transitions between open and closed mitosis, although the underlying genetic changes that influenced these transitions remain unknown. A survey of the diversity of mitotic nuclei that fall between these extremes is the starting point from which to determine the physiologically relevant characteristics distinguishing open from closed mitosis and to understand how they evolved and why they are retained in present-day organisms. The field is now poised to begin addressing these issues by defining and documenting patterns of mitotic nuclear variation within and among species and mapping them onto a phylogenic tree. Deciphering the evolutionary history of open and closed mitosis will complement cell biological and genetic approaches aimed at deciphering the fundamental organizational principles of the nucleus. Copyright © 2014 Elsevier Ltd. All rights reserved.

  1. Endophytic Colonization and In Planta Nitrogen Fixation by a Herbaspirillum sp. Isolated from Wild Rice Species

    Science.gov (United States)

    Elbeltagy, Adel; Nishioka, Kiyo; Sato, Tadashi; Suzuki, Hisa; Ye, Bin; Hamada, Toru; Isawa, Tsuyoshi; Mitsui, Hisayuki; Minamisawa, Kiwamu

    2001-01-01

    Nitrogen-fixing bacteria were isolated from the stems of wild and cultivated rice on a modified Rennie medium. Based on 16S ribosomal DNA (rDNA) sequences, the diazotrophic isolates were phylogenetically close to four genera: Herbaspirillum, Ideonella, Enterobacter, and Azospirillum. Phenotypic properties and signature sequences of 16S rDNA indicated that three isolates (B65, B501, and B512) belong to the Herbaspirillum genus. To examine whether Herbaspirillum sp. strain B501 isolated from wild rice, Oryza officinalis, endophytically colonizes rice plants, the gfp gene encoding green fluorescent protein (GFP) was introduced into the bacteria. Observations by fluorescence stereomicroscopy showed that the GFP-tagged bacteria colonized shoots and seeds of aseptically grown seedlings of the original wild rice after inoculation of the seeds. Conversely, for cultivated rice Oryza sativa, no GFP fluorescence was observed for shoots and only weak signals were observed for seeds. Observations by fluorescence and electron microscopy revealed that Herbaspirillum sp. strain B501 colonized mainly intercellular spaces in the leaves of wild rice. Colony counts of surface-sterilized rice seedlings inoculated with the GFP-tagged bacteria indicated significantly more bacterial populations inside the original wild rice than in cultivated rice varieties. Moreover, after bacterial inoculation, in planta nitrogen fixation in young seedlings of wild rice, O. officinalis, was detected by the acetylene reduction and 15N2 gas incorporation assays. Therefore, we conclude that Herbaspirillum sp. strain B501 is a diazotrophic endophyte compatible with wild rice, particularly O. officinalis. PMID:11679357

  2. Variation in cooking and eating quality traits in Japanese rice germplasm accessions.

    Science.gov (United States)

    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.

  3. A rice kinase-protein interaction map.

    Science.gov (United States)

    Ding, Xiaodong; Richter, Todd; Chen, Mei; Fujii, Hiroaki; Seo, Young Su; Xie, Mingtang; Zheng, Xianwu; Kanrar, Siddhartha; Stevenson, Rebecca A; Dardick, Christopher; Li, Ying; Jiang, Hao; Zhang, Yan; Yu, Fahong; Bartley, Laura E; Chern, Mawsheng; Bart, Rebecca; Chen, Xiuhua; Zhu, Lihuang; Farmerie, William G; Gribskov, Michael; Zhu, Jian-Kang; Fromm, Michael E; Ronald, Pamela C; Song, Wen-Yuan

    2009-03-01

    Plants uniquely contain large numbers of protein kinases, and for the vast majority of the 1,429 kinases predicted in the rice (Oryza sativa) genome, little is known of their functions. Genetic approaches often fail to produce observable phenotypes; thus, new strategies are needed to delineate kinase function. We previously developed a cost-effective high-throughput yeast two-hybrid system. Using this system, we have generated a protein interaction map of 116 representative rice kinases and 254 of their interacting proteins. Overall, the resulting interaction map supports a large number of known or predicted kinase-protein interactions from both plants and animals and reveals many new functional insights. Notably, we found a potential widespread role for E3 ubiquitin ligases in pathogen defense signaling mediated by receptor-like kinases, particularly by the kinases that may have evolved from recently expanded kinase subfamilies in rice. We anticipate that the data provided here will serve as a foundation for targeted functional studies in rice and other plants. The application of yeast two-hybrid and TAPtag analyses for large-scale plant protein interaction studies is also discussed.

  4. Rice (Oryza) hemoglobins

    Science.gov (United States)

    Hemoglobins (Hbs) corresponding to non-symbiotic (nsHb) and truncated (tHb) Hbs have been identified in rice (Oryza). This review discusses the major findings from the current studies on rice Hbs. At the molecular level, a family of the nshb genes, consisting of hb1, hb2, hb3, hb4 and hb5, and a sin...

  5. The Use of Animal Models to Decipher Physiological and Neurobiological Alterations of Anorexia Nervosa Patients

    Science.gov (United States)

    Méquinion, Mathieu; Chauveau, Christophe; Viltart, Odile

    2015-01-01

    Extensive studies were performed to decipher the mechanisms regulating feeding due to the worldwide obesity pandemy and its complications. The data obtained might be adapted to another disorder related to alteration of food intake, the restrictive anorexia nervosa. This multifactorial disease with a complex and unknown etiology is considered as an awful eating disorder since the chronic refusal to eat leads to severe, and sometimes, irreversible complications for the whole organism, until death. There is an urgent need to better understand the different aspects of the disease to develop novel approaches complementary to the usual psychological therapies. For this purpose, the use of pertinent animal models becomes a necessity. We present here the various rodent models described in the literature that might be used to dissect central and peripheral mechanisms involved in the adaptation to deficient energy supplies and/or the maintenance of physiological alterations on the long term. Data obtained from the spontaneous or engineered genetic models permit to better apprehend the implication of one signaling system (hormone, neuropeptide, neurotransmitter) in the development of several symptoms observed in anorexia nervosa. As example, mutations in the ghrelin, serotonin, dopamine pathways lead to alterations that mimic the phenotype, but compensatory mechanisms often occur rendering necessary the use of more selective gene strategies. Until now, environmental animal models based on one or several inducing factors like diet restriction, stress, or physical activity mimicked more extensively central and peripheral alterations decribed in anorexia nervosa. They bring significant data on feeding behavior, energy expenditure, and central circuit alterations. Animal models are described and criticized on the basis of the criteria of validity for anorexia nervosa. PMID:26042085

  6. Archaeological sites along the Gujarat coast: Proxies to decipher the past shoreline

    Digital Repository Service at National Institute of Oceanography (India)

    Vora, K.H.; Gaur, A; Sundaresh

    on northwestern Saurashtra coast presents a classical case of shoreline shift in recent past. The paper discusses the archaeological evidences to decipher the past shoreline of the Saurashtra region...

  7. Studies on combining ability and heritability of milling and physical properties in indica hybrid rice

    International Nuclear Information System (INIS)

    Zhang Lihua; Wang Linyou; Wang Jianjun

    2003-01-01

    14 different qualities parents of indica hybrid rice, including 7 CMS lines and 7 restorers, were chosen to analyze the combining ability of milling property and physical property by way of p x q incomplete diallel cross (NC II) design. The results showed that: 1) Both general combining ability (gca) and specific combining ability (sca) were highly significant in all 12 characters; the genetic additive effects was principal in brown rice length (BRL), brown rice width (BRW), ratio of length to width of brown rice (RLWBR), milled rice length (MRL), milled rice width (MRW), ratio of length to width of milled rice (RLWMR) and chalkyness (CN); while the nonadditive effects were greater in brown rice rate (BRR), milled rice rate (MRR), head rice rate (HRR), chalky rice percentage (CRP) and area of chalky rice (ACR). 2) Through the analysis of the contribution ratio of the male, female and their interaction to the total variance of the quality characters in F 1 hybrids, the results showed that BRR, MRR, BRL, MRL and ACR were influenced more greatly by restorer line than by CMS line, but the others were influenced more greatly by CMS line than by restorer line. 3) The gca and sca effects were independent each other, which suggests that it is essential to make widely testcrosses in the selection of hybrid combinations. There existed a positive correlation between gca and phenotypic value of parents, which indicates that great attention must be paid to the improvement of parent own characters in hybrid rice breeding. 4) BRL, BRW, RLWBR, MRL, MRW and RLWMR had higher narrow heritabilities (h N 2 ), and these characters may be used as indirect traits in early breeding generation

  8. Study on increasing mutagenic efficiency of radiation breeding for rice

    International Nuclear Information System (INIS)

    Wan Xianguo; Pang Boliang; Zhu Xiaoqi

    1993-04-01

    Increasing mutagenic efficiency and improving selection method are of important topics for crop mutation breeding. Investigation on the radiation breeding for rice (Oryza Sativa L.) showed that the crossing in combination with gamma ray irradiation or laser irradiation and proper selection of dosage rate can increase mutagenic efficiency. According to the correlation of phenotype in M 1 generation and mutation frequency in M 2 for rice, the materials with certain characters were chose as seeds, thus the works of generation selections will be reduced

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

    Science.gov (United States)

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

    2011-11-01

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

  10. Genome-Wide Transcriptome Analysis of Cadmium Stress in Rice

    Directory of Open Access Journals (Sweden)

    Youko Oono

    2016-01-01

    Full Text Available Rice growth is severely affected by toxic concentrations of the nonessential heavy metal cadmium (Cd. To elucidate the molecular basis of the response to Cd stress, we performed mRNA sequencing of rice following our previous study on exposure to high concentrations of Cd (Oono et al., 2014. In this study, rice plants were hydroponically treated with low concentrations of Cd and approximately 211 million sequence reads were mapped onto the IRGSP-1.0 reference rice genome sequence. Many genes, including some identified under high Cd concentration exposure in our previous study, were found to be responsive to low Cd exposure, with an average of about 11,000 transcripts from each condition. However, genes expressed constitutively across the developmental course responded only slightly to low Cd concentrations, in contrast to their clear response to high Cd concentration, which causes fatal damage to rice seedlings according to phenotypic changes. The expression of metal ion transporter genes tended to correlate with Cd concentration, suggesting the potential of the RNA-Seq strategy to reveal novel Cd-responsive transporters by analyzing gene expression under different Cd concentrations. This study could help to develop novel strategies for improving tolerance to Cd exposure in rice and other cereal crops.

  11. Deciphering the Astrocyte Reaction in Alzheimer’s Disease

    Directory of Open Access Journals (Sweden)

    Beatriz G. Perez-Nievas

    2018-04-01

    Full Text Available Reactive astrocytes were identified as a component of senile amyloid plaques in the cortex of Alzheimer’s disease (AD patients several decades ago. However, their role in AD pathophysiology has remained elusive ever since, in part owing to the extrapolation of the literature from primary astrocyte cultures and acute brain injury models to a chronic neurodegenerative scenario. Recent accumulating evidence supports the idea that reactive astrocytes in AD acquire neurotoxic properties, likely due to both a gain of toxic function and a loss of their neurotrophic effects. However, the diversity and complexity of this glial cell is only beginning to be unveiled, anticipating that astrocyte reaction might be heterogeneous as well. Herein we review the evidence from mouse models of AD and human neuropathological studies and attempt to decipher the main conundrums that astrocytes pose to our understanding of AD development and progression. We discuss the morphological features that characterize astrocyte reaction in the AD brain, the consequences of astrocyte reaction for both astrocyte biology and AD pathological hallmarks, and the molecular pathways that have been implicated in this reaction.

  12. Deciphering fluid inclusions in high-grade rocks

    Directory of Open Access Journals (Sweden)

    Alfons van den Kerkhof

    2014-09-01

    Full Text Available The study of fluid inclusions in high-grade rocks is especially challenging as the host minerals have been normally subjected to deformation, recrystallization and fluid-rock interaction so that primary inclusions, formed at the peak of metamorphism are rare. The larger part of the fluid inclusions found in metamorphic minerals is typically modified during uplift. These late processes may strongly disguise the characteristics of the “original” peak metamorphic fluid. A detailed microstructural analysis of the host minerals, notably quartz, is therefore indispensable for a proper interpretation of fluid inclusions. Cathodoluminescence (CL techniques combined with trace element analysis of quartz (EPMA, LA-ICPMS have shown to be very helpful in deciphering the rock-fluid evolution. Whereas high-grade metamorphic quartz may have relatively high contents of trace elements like Ti and Al, low-temperature re-equilibrated quartz typically shows reduced trace element concentrations. The resulting microstructures in CL can be basically distinguished in diffusion patterns (along microfractures and grain boundaries, and secondary quartz formed by dissolution-reprecipitation. Most of these textures are formed during retrograde fluid-controlled processes between ca. 220 and 500 °C, i.e. the range of semi-brittle deformation (greenschist-facies and can be correlated with the fluid inclusions. In this way modified and re-trapped fluids can be identified, even when there are no optical features observed under the microscope.

  13. Deciphering the landscape of host barriers to Listeria monocytogenes infection.

    Science.gov (United States)

    Zhang, Ting; Abel, Sören; Abel Zur Wiesch, Pia; Sasabe, Jumpei; Davis, Brigid M; Higgins, Darren E; Waldor, Matthew K

    2017-06-13

    Listeria monocytogenes is a common food-borne pathogen that can disseminate from the intestine and infect multiple organs. Here, we used sequence tag-based analysis of microbial populations (STAMP) to investigate L monocytogenes population dynamics during infection. We created a genetically barcoded library of murinized L monocytogenes and then used deep sequencing to track the pathogen's dissemination routes and quantify its founding population ( N b ) sizes in different organs. We found that the pathogen disseminates from the gastrointestinal tract to distal sites through multiple independent routes and that N b sizes vary greatly among tissues, indicative of diverse host barriers to infection. Unexpectedly, comparative analyses of sequence tags revealed that fecally excreted organisms are largely derived from the very small number of L. monocytogenes cells that colonize the gallbladder. Immune depletion studies suggest that distinct innate immune cells restrict the pathogen's capacity to establish replicative niches in the spleen and liver. Finally, studies in germ-free mice suggest that the microbiota plays a critical role in the development of the splenic, but not the hepatic, barriers that prevent L. monocytogenes from seeding these organs. Collectively, these observations illustrate the potency of the STAMP approach to decipher the impact of host factors on population dynamics of pathogens during infection.

  14. Transfer of gaseous iodine from atmosphere to rough rice, brown rice and polished rice

    International Nuclear Information System (INIS)

    Sumiya, Misako; Uchida, Shigeo; Muramatsu, Yasuyuki; Ohmomo, Yoichiro; Yamaguchi, Shuho; Obata, Hitoshi.

    1987-01-01

    Experiments were carried out in order to obtain information required for establishing transfer coefficients of gaseous iodine (I 2 ) to rough rice, brown rice and polished rice. The gaseous iodine deposited on young rice plants before the heading period was scarcely found in the rough rice harvested at the full ripe stage. The biological half life of iodine in hull, however, was much slower than that in leaves of 14 days. The translocation of iodine from leaves and stalks to rough rice was not clearly recognized. Therefore, it was deduced that iodine found in brown rice mainly should originate from that deposited on the hull. The distribution ratios of iodine between rough rice and brown rice, and between brown rice and polished rice were 100:4 and 100:30 on 100 grains basis, respectively. If average normalized deposition velocity (V d(m) ) or derived deposition velocity (V s ) are given, the transfer coefficients of gaseous iodine to rough rice (TF r ), brown rice (TF b ) and polished rice (TF p ) could be calculated. (author)

  15. Timing is everything: early degradation of abscission layer is associated with increased seed shattering in U.S. weedy rice

    Directory of Open Access Journals (Sweden)

    Hepler Peter K

    2011-01-01

    Full Text Available Abstract Background Seed shattering, or shedding, is an important fitness trait for wild and weedy grasses. U.S. weedy rice (Oryza sativa is a highly shattering weed, thought to have evolved from non-shattering cultivated ancestors. All U.S. weedy rice individuals examined to date contain a mutation in the sh4 locus associated with loss of shattering during rice domestication. Weedy individuals also share the shattering trait with wild rice, but not the ancestral shattering mutation at sh4; thus, how weedy rice reacquired the shattering phenotype is unknown. To establish the morphological basis of the parallel evolution of seed shattering in weedy rice and wild, we examined the abscission layer at the flower-pedicel junction in weedy individuals in comparison with wild and cultivated relatives. Results Consistent with previous work, shattering wild rice individuals possess clear, defined abscission layers at flowering, whereas non-shattering cultivated rice individuals do not. Shattering weedy rice from two separately evolved populations in the U.S. (SH and BHA show patterns of abscission layer formation and degradation distinct from wild rice. Prior to flowering, the abscission layer has formed in all weedy individuals and by flowering it is already degrading. In contrast, wild O. rufipogon abscission layers have been shown not to degrade until after flowering has occurred. Conclusions Seed shattering in weedy rice involves the formation and degradation of an abscission layer in the flower-pedicel junction, as in wild Oryza, but is a developmentally different process from shattering in wild rice. Weedy rice abscission layers appear to break down earlier than wild abscission layers. The timing of weedy abscission layer degradation suggests that unidentified regulatory genes may play a critical role in the reacquisition of shattering in weedy rice, and sheds light on the morphological basis of parallel evolution for shattering in weedy and wild

  16. Deciphering free-radical code of radiation effects

    International Nuclear Information System (INIS)

    Volovyk, S.; Bazyka, D.; Loganovsky, K.; Bebeshko, V.

    2007-01-01

    Complete text of publication follows. Objective: Ionizing radiation is fundamental environmental factor for life origin and evolution. Free radicals, primordial 'sea' for life conceiving and existence, induced by cosmic and terrestrial background radiation, are evolutionally archetypal, ubiquitous, and omnipotent in physiological- pathophysiological dichotomy. Classical free-radical paradigm in radiation biology and medicine, focused in essence on oxidative damage, needs new conceptualization and generalization. Methods: Suggested novel insights into free radicals dual immanent nature and functions in organism systems are based on original concepts of radicals dynamic charge transfer (CT) - redox ambivalence (interactional nucleo-, electro-, and ambiphilicity spectrum); pertinent chemical reactivity and selectivity delocalization model; physiological functional ambivalence and complementarity, and dynamic free-radical homeostasis. Results: Subtle perturbations in radicals CT spatiotemporal homeodynamics, in responsive signaling / controlling networks, concomitant alterations in genes expression, transcription, and apoptosis, redox control of mitochondrial ET chain, telomere/telomerase balance, DNA CT, circadian clock, hemispheric biochemical dominance/accentuation, including alteration of nitric oxide-superoxide complementarity, membranes permeability, neurotransmission pattern, synaptic circuitry, etc under radiation exposure have more fundamental impact on organism systems (especially CNS and CVS) deterioration than simple radicals inflicted oxidative (nitrosative) damage of cellular constituents. Conclusions: This novel conceptualization of free-radical paradigm constitutes new dimension in deciphering molecular mechanisms of radiation effects on subtle borderline norm-pathology and continuity-discontinuity dichotomy in organisms systems disorders - CT(redox)omics, which involves investigation of CT, redox, and spin states of free radicals, DNA bases

  17. Functional metagenomics to decipher food-microbe-host crosstalk.

    Science.gov (United States)

    Larraufie, Pierre; de Wouters, Tomas; Potocki-Veronese, Gabrielle; Blottière, Hervé M; Doré, Joël

    2015-02-01

    The recent developments of metagenomics permit an extremely high-resolution molecular scan of the intestinal microbiota giving new insights and opening perspectives for clinical applications. Beyond the unprecedented vision of the intestinal microbiota given by large-scale quantitative metagenomics studies, such as the EU MetaHIT project, functional metagenomics tools allow the exploration of fine interactions between food constituents, microbiota and host, leading to the identification of signals and intimate mechanisms of crosstalk, especially between bacteria and human cells. Cloning of large genome fragments, either from complex intestinal communities or from selected bacteria, allows the screening of these biological resources for bioactivity towards complex plant polymers or functional food such as prebiotics. This permitted identification of novel carbohydrate-active enzyme families involved in dietary fibre and host glycan breakdown, and highlighted unsuspected bacterial players at the top of the intestinal microbial food chain. Similarly, exposure of fractions from genomic and metagenomic clones onto human cells engineered with reporter systems to track modulation of immune response, cell proliferation or cell metabolism has allowed the identification of bioactive clones modulating key cell signalling pathways or the induction of specific genes. This opens the possibility to decipher mechanisms by which commensal bacteria or candidate probiotics can modulate the activity of cells in the intestinal epithelium or even in distal organs such as the liver, adipose tissue or the brain. Hence, in spite of our inability to culture many of the dominant microbes of the human intestine, functional metagenomics open a new window for the exploration of food-microbe-host crosstalk.

  18. Deciphering neuronal population codes for acute thermal pain

    Science.gov (United States)

    Chen, Zhe; Zhang, Qiaosheng; Phuong Sieu Tong, Ai; Manders, Toby R.; Wang, Jing

    2017-06-01

    Objective. Pain is defined as an unpleasant sensory and emotional experience associated with actual or potential tissue damage, or described in terms of such damage. Current pain research mostly focuses on molecular and synaptic changes at the spinal and peripheral levels. However, a complete understanding of pain mechanisms requires the physiological study of the neocortex. Our goal is to apply a neural decoding approach to read out the onset of acute thermal pain signals, which can be used for brain-machine interface. Approach. We used micro wire arrays to record ensemble neuronal activities from the primary somatosensory cortex (S1) and anterior cingulate cortex (ACC) in freely behaving rats. We further investigated neural codes for acute thermal pain at both single-cell and population levels. To detect the onset of acute thermal pain signals, we developed a novel latent state-space framework to decipher the sorted or unsorted S1 and ACC ensemble spike activities, which reveal information about the onset of pain signals. Main results. The state space analysis allows us to uncover a latent state process that drives the observed ensemble spike activity, and to further detect the ‘neuronal threshold’ for acute thermal pain on a single-trial basis. Our method achieved good detection performance in sensitivity and specificity. In addition, our results suggested that an optimal strategy for detecting the onset of acute thermal pain signals may be based on combined evidence from S1 and ACC population codes. Significance. Our study is the first to detect the onset of acute pain signals based on neuronal ensemble spike activity. It is important from a mechanistic viewpoint as it relates to the significance of S1 and ACC activities in the regulation of the acute pain onset.

  19. Deciphering the porcine intestinal microRNA transcriptome

    Directory of Open Access Journals (Sweden)

    Keller Andreas

    2010-04-01

    Full Text Available Abstract Background While more than 700 microRNAs (miRNAs are known in human, a comparably low number has been identified in swine. Because of the close phylogenetic distance to humans, pigs serve as a suitable model for studying e.g. intestinal development or disease. Recent studies indicate that miRNAs are key regulators of intestinal development and their aberrant expression leads to intestinal malignancy. Results Here, we present the identification of hundreds of apparently novel miRNAs in the porcine intestine. MiRNAs were first identified by means of deep sequencing followed by miRNA precursor prediction using the miRDeep algorithm as well as searching for conserved miRNAs. Second, the porcine miRNAome along the entire intestine (duodenum, proximal and distal jejunum, ileum, ascending and transverse colon was unraveled using customized miRNA microarrays based on the identified sequences as well as known porcine and human ones. In total, the expression of 332 intestinal miRNAs was discovered, of which 201 represented assumed novel porcine miRNAs. The identified hairpin forming precursors were in part organized in genomic clusters, and most of the precursors were located on chromosomes 3 and 1, respectively. Hierarchical clustering of the expression data revealed subsets of miRNAs that are specific to distinct parts of the intestine pointing to their impact on cellular signaling networks. Conclusions In this study, we have applied a straight forward approach to decipher the porcine intestinal miRNAome for the first time in mammals using a piglet model. The high number of identified novel miRNAs in the porcine intestine points out their crucial role in intestinal function as shown by pathway analysis. On the other hand, the reported miRNAs may share orthologs in other mammals such as human still to be discovered.

  20. Sequential Logic Model Deciphers Dynamic Transcriptional Control of Gene Expressions

    Science.gov (United States)

    Yeo, Zhen Xuan; Wong, Sum Thai; Arjunan, Satya Nanda Vel; Piras, Vincent; Tomita, Masaru; Selvarajoo, Kumar; Giuliani, Alessandro; Tsuchiya, Masa

    2007-01-01

    Background Cellular signaling involves a sequence of events from ligand binding to membrane receptors through transcription factors activation and the induction of mRNA expression. The transcriptional-regulatory system plays a pivotal role in the control of gene expression. A novel computational approach to the study of gene regulation circuits is presented here. Methodology Based on the concept of finite state machine, which provides a discrete view of gene regulation, a novel sequential logic model (SLM) is developed to decipher control mechanisms of dynamic transcriptional regulation of gene expressions. The SLM technique is also used to systematically analyze the dynamic function of transcriptional inputs, the dependency and cooperativity, such as synergy effect, among the binding sites with respect to when, how much and how fast the gene of interest is expressed. Principal Findings SLM is verified by a set of well studied expression data on endo16 of Strongylocentrotus purpuratus (sea urchin) during the embryonic midgut development. A dynamic regulatory mechanism for endo16 expression controlled by three binding sites, UI, R and Otx is identified and demonstrated to be consistent with experimental findings. Furthermore, we show that during transition from specification to differentiation in wild type endo16 expression profile, SLM reveals three binary activities are not sufficient to explain the transcriptional regulation of endo16 expression and additional activities of binding sites are required. Further analyses suggest detailed mechanism of R switch activity where indirect dependency occurs in between UI activity and R switch during specification to differentiation stage. Conclusions/Significance The sequential logic formalism allows for a simplification of regulation network dynamics going from a continuous to a discrete representation of gene activation in time. In effect our SLM is non-parametric and model-independent, yet providing rich biological

  1. Sequential logic model deciphers dynamic transcriptional control of gene expressions.

    Directory of Open Access Journals (Sweden)

    Zhen Xuan Yeo

    Full Text Available BACKGROUND: Cellular signaling involves a sequence of events from ligand binding to membrane receptors through transcription factors activation and the induction of mRNA expression. The transcriptional-regulatory system plays a pivotal role in the control of gene expression. A novel computational approach to the study of gene regulation circuits is presented here. METHODOLOGY: Based on the concept of finite state machine, which provides a discrete view of gene regulation, a novel sequential logic model (SLM is developed to decipher control mechanisms of dynamic transcriptional regulation of gene expressions. The SLM technique is also used to systematically analyze the dynamic function of transcriptional inputs, the dependency and cooperativity, such as synergy effect, among the binding sites with respect to when, how much and how fast the gene of interest is expressed. PRINCIPAL FINDINGS: SLM is verified by a set of well studied expression data on endo16 of Strongylocentrotus purpuratus (sea urchin during the embryonic midgut development. A dynamic regulatory mechanism for endo16 expression controlled by three binding sites, UI, R and Otx is identified and demonstrated to be consistent with experimental findings. Furthermore, we show that during transition from specification to differentiation in wild type endo16 expression profile, SLM reveals three binary activities are not sufficient to explain the transcriptional regulation of endo16 expression and additional activities of binding sites are required. Further analyses suggest detailed mechanism of R switch activity where indirect dependency occurs in between UI activity and R switch during specification to differentiation stage. CONCLUSIONS/SIGNIFICANCE: The sequential logic formalism allows for a simplification of regulation network dynamics going from a continuous to a discrete representation of gene activation in time. In effect our SLM is non-parametric and model-independent, yet

  2. Prevalence of Rice Yellow Mottle Virus (RYMV) on Rice Plants ...

    African Journals Online (AJOL)

    Abstract. Incidence of Rice yellow mottle virus (RYMV) on rice plants (ofada) grown in two local government areas (LGAs) of Ogun State had been evaluated during a two year field survey. Six month old rice plants were observed for symptom expression and leaf samples collected for serological indexing. Of the 60 leaf ...

  3. A major QTL controlling deep rooting on rice chromosome 4.

    Science.gov (United States)

    Uga, Yusaku; Yamamoto, Eiji; Kanno, Noriko; Kawai, Sawako; Mizubayashi, Tatsumi; Fukuoka, Shuichi

    2013-10-24

    Drought is the most serious abiotic stress that hinders rice production under rainfed conditions. Breeding for deep rooting is a promising strategy to improve the root system architecture in shallow-rooting rice cultivars to avoid drought stress. We analysed the quantitative trait loci (QTLs) for the ratio of deep rooting (RDR) in three F₂ mapping populations derived from crosses between each of three shallow-rooting varieties ('ARC5955', 'Pinulupot1', and 'Tupa729') and a deep-rooting variety, 'Kinandang Patong'. In total, we detected five RDR QTLs on chromosomes 2, 4, and 6. In all three populations, QTLs on chromosome 4 were found to be located at similar positions; they explained from 32.0% to 56.6% of the total RDR phenotypic variance. This suggests that one or more key genetic factors controlling the root growth angle in rice is located in this region of chromosome 4.

  4. Comparison study of genetic diversity between rice varieties from northeast China and Japan

    International Nuclear Information System (INIS)

    Li Hongyu; Wang Haize; Zhang Longhai; Liu Menghong; Xu Zhengjin; Zhao Minghui; Xu Hai; Wang Jiayu; Si Yang

    2011-01-01

    The genetic diversity of 18 rice varieties from northeast China and 13 rice varieties from Japan were investigated by 20 phenotypic traits and SSR assay with 40 pairs of primers. The results showed that 82 phenotypic variation and 108 alleles were detected. With an average of 2.54 alleles on every locus the phenotypic variation and alleles in northeast China were 72 and 103, respectively, and 63 and 94 were respectively with an average of 2.32 alleles on every locus in Japanese varieties. Genetic variation among different varieties varied greatly and among different groups varied slightly. Genetic diversity of varieties in northeast China was much higher than those in Japan, and 94.7% of the alleles from Japanese varieties were included in the varieties from northeast China. The available specific alleles were already very limited in the varieties from Japan and can not meet the rice breeding requirements for northeastern China. (authors)

  5. Genetic assessment of some phenotypic variants of rice (Oryza spp ...

    African Journals Online (AJOL)

    African Journal of Biotechnology ... replications at two different environments (1st at Regional Research Station, New Alluvial Zone (NAZ), ... High heritability coupled with moderate to high genetic advance as percent of mean for plant height, ...

  6. 7 CFR 868.310 - Grades and grade requirements for the classes Long Grain Milled Rice, Medium Grain Milled Rice...

    Science.gov (United States)

    2010-01-01

    ... Grain Milled Rice, Medium Grain Milled Rice, Short Grain Milled Rice, and Mixed Milled Rice. (See also Â... Milled Rice Principles Governing Application of Standards § 868.310 Grades and grade requirements for the classes Long Grain Milled Rice, Medium Grain Milled Rice, Short Grain Milled Rice, and Mixed Milled Rice...

  7. Determination of rice panicle numbers during heading by multi-angle imaging

    Directory of Open Access Journals (Sweden)

    Lingfeng Duan

    2015-06-01

    Full Text Available Plant phenomics has the potential to accelerate progress in understanding gene functions and environmental responses. Progress has been made in automating high-throughput plant phenotyping. However, few studies have investigated automated rice panicle counting. This paper describes a novel method for automatically and nonintrusively determining rice panicle numbers during the full heading stage by analyzing color images of rice plants taken from multiple angles. Pot-grown rice plants were transferred via an industrial conveyer to an imaging chamber. Color images from different angles were automatically acquired as a turntable rotated the plant. The images were then analyzed and the panicle number of each plant was determined. The image analysis pipeline consisted of extracting the i2 plane from the original color image, segmenting the image, discriminating the panicles from the rest of the plant using an artificial neural network, and calculating the panicle number in the current image. The panicle number of the plant was taken as the maximum of the panicle numbers extracted from all 12 multi-angle images. A total of 105 rice plants during the full heading stage were examined to test the performance of the method. The mean absolute error of the manual and automatic count was 0.5, with 95.3% of the plants yielding absolute errors within ± 1. The method will be useful for evaluating rice panicles and will serve as an important supplementary method for high-throughput rice phenotyping.

  8. Extraction of rice bran oil from local rice husk

    International Nuclear Information System (INIS)

    Anwar, J.; Zaman, W.; Salman, M.; Jabeen, N.

    2006-01-01

    Rice Bran Oil is widely used in pharmaceutical, food and chemical industries due to its unique properties and high medicinal value. In the present work, extraction of rice bran oil from different samples of rice husk collected from local rice shellers by solvent extraction method has been studied. Experiments were conducted using a soxhelt apparatus, to extract rice bran oil using hexane, petroleum ether, ethanol and methanol as the solvents and the yields obtained under different conditions were compared. Batch extraction tests showed that the rate of extraction decreases with time and the solution approaches saturation at an exponential rate. (author)

  9. Deciphering the role of RND efflux transporters in Burkholderia cenocepacia.

    Directory of Open Access Journals (Sweden)

    Silvia Bazzini

    Full Text Available Burkholderia cenocepacia J2315 is representative of a highly problematic group of cystic fibrosis (CF pathogens. Eradication of B. cenocepacia is very difficult with the antimicrobial therapy being ineffective due to its high resistance to clinically relevant antimicrobial agents and disinfectants. RND (Resistance-Nodulation-Cell Division efflux pumps are known to be among the mediators of multidrug resistance in gram-negative bacteria. Since the significance of the 16 RND efflux systems present in B. cenocepacia (named RND-1 to -16 has been only partially determined, the aim of this work was to analyze mutants of B. cenocepacia strain J2315 impaired in RND-4 and RND-9 efflux systems, and assess their role in the efflux of toxic compounds. The transcriptomes of mutants deleted individually in RND-4 and RND-9 (named D4 and D9, and a double-mutant in both efflux pumps (named D4-D9, were compared to that of the wild-type B. cenocepacia using microarray analysis. Microarray data were confirmed by qRT-PCR, phenotypic experiments, and by Phenotype MicroArray analysis. The data revealed that RND-4 made a significant contribution to the antibiotic resistance of B. cenocepacia, whereas RND-9 was only marginally involved in this process. Moreover, the double mutant D4-D9 showed a phenotype and an expression profile similar to D4. The microarray data showed that motility and chemotaxis-related genes appeared to be up-regulated in both D4 and D4-D9 strains. In contrast, these gene sets were down-regulated or expressed at levels similar to J2315 in the D9 mutant. Biofilm production was enhanced in all mutants. Overall, these results indicate that in B. cenocepacia RND pumps play a wider role than just in drug resistance, influencing additional phenotypic traits important for pathogenesis.

  10. Reading Hidden Messages Through Deciphered Manual Alphabets on Classic Artwork

    Science.gov (United States)

    Castronovo, Joseph Anthony, Jr.

    1998-10-01

    Decipherment is the tool used to uncover several types of hand signs that played vital roles in the creation of hidden messages in classic artwork. A 3,100 B.C. bas-relief of The 'Kaph' Telescope, formerly named The Narmer Palette, and Michaelangelo Buonarrotte's Battle of Cascina of 1506 were two key works of art that show certain similarities even though separated by 4,500 years. It is evident that Renaissance humanists provided artists with certain knowledge of the ancients. Results of incorporating a number of minor works of art showed that the competence of ancient Egyptians, Cretans and Australian Aboriginals, to name a few, as astronomers, was underestimated. Some deciphered Indus seals attested to a global understanding of the universe, with Gemini and the star of Thuban at the center of their attention. Certain forms of secrecy had to be undertaken for various reasons throughout the millennia. Three examples are: (1) In Italy, to keep controversial and truthful teachings discreet and hidden, artists embedded them in artwork long before the plight of Galileo Galilei and his discoveries. (2) Among Jewish Kabbalists, a well-known design was obscured in The Arnolfini Wedding painting for fear it would be lost due to persecution. (3) Michaelangelo Buonarrotte indicated several meanings through the hands of The Statue of Moses. They were overlooked by several societies, including the gesticulating culture of Italy, because they oppressed the value of signed languages. Spatial decipherment may testify to a need for the restoration of a spatial writing system for expanded linguistic accessibility. A 21st century model community for sign language residents and employees will benefit visual learners, particularly visual artists and non-phonetic decipherers, to better uncover, understand and perhaps use ancient hand forms to restore ancient knowledge. Moreover, the National Association of Teaching English (NATE) has recently endorsed the addition of two skills

  11. Gasification of rice husks

    Energy Technology Data Exchange (ETDEWEB)

    Marzetti, P. (ENEA, Rome (Italy). Dipt. Fonti Alternative e Risparmio Energetico)

    The paper outlines the thermochemical processes and equipment involved in the gasification of rice husks. An assessment is made of the feasibility (availability, technology requirements, economics of production and marketing) of this renewable energy source. Results, reported here in tabular form, of experimental trials at an Italian pilot plant (producing, with the use of 165 kg/h of rice husks, 350,000 kcal/h of gas with a conversion yield of 70%) indicated good feasibility. More research is required to improve the combustion qualities of the final product.

  12. Short communication. A spontaneous mutant of L-202 rice

    Energy Technology Data Exchange (ETDEWEB)

    Garcia-Yzaguire, A.; Padrones, T.

    2009-07-01

    A new spontaneous phenotype of the rice cultivar L-202 was found. Mendelian analysis indicates that it is a monogenic, recessive mutant. Its distinguishing features are: dark blue-green colour, short and narrow leaves, high tillering and relatively short height. The objectives of this study were: to characterize it, to determine if it is heritable and if so, its genetic basis. Its distinguishing features are: dark blue-green colour, short and narrow leaves, high tillering and relatively short height. Selfing the new phenotype resulted in a uniform progeny, with the traits of the parent plant (wild type). Crossing the new phenotype with the normal L-202 cultivar resulted in a uniform F1 hybrid generation, with the wild type. The F2 generation showed a mendelian segregation which did not depart significantly from three normal plants : one new phenotype. It is concluded that it is a monogenic, recessive mutant. (Author) 3 refs.

  13. Comparison of Effect of Brassinosteroid and Gibberellin Biosynthesis Inhibitors on Growth of Rice Seedlings

    Directory of Open Access Journals (Sweden)

    Tadashi Matusmoto

    2016-01-01

    Full Text Available Brassinosteroid (BR and gibberellin (GA are two predominant plant hormones that regulate plant cell elongation. Mutants disrupt the biosynthesis of these hormones and display different degrees of dwarf phenotypes in rice. Although the role of each plant hormone in promoting the longitudinal growth of plants has been extensively studied using genetic methods, their relationship is still poorly understood. In this study, we used two specific inhibitors targeting BR and GA biosynthesis to investigate the roles of BR and GA in growth of rice seedlings. Yucaizol, a specific inhibitor of BR biosynthesis, and Trinexapac-ethyl, a commercially available inhibitor of GA biosynthesis, were used. The effect of Yucaizol on rice seedlings indicated that Yucaizol significantly retarded stem elongation. The IC50 value was found to be approximately 0.8 μmol/L. Yucaizol also induced small leaf angle phenocopy in rice seedlings, similarly to BR-deficient rice, while Trinexapac-ethyl did not. When Yucaizol combined with Trinexapac-ethyl was applied to the rice plants, the mixture of these two inhibitors retarded stem elongation of rice at lower doses. Our results suggest that the use of a BR biosynthesis inhibitor combined with a GA biosynthesis inhibitor may be useful in the development of new technologies for controlling rice plant height.

  14. Genetic control of a transition from black to straw-white seed hull in rice domestication.

    Science.gov (United States)

    Zhu, Bo-Feng; Si, Lizhen; Wang, Zixuan; Zhou, Yan; Zhu, Jinjie; Shangguan, Yingying; Lu, Danfeng; Fan, Danlin; Li, Canyang; Lin, Hongxuan; Qian, Qian; Sang, Tao; Zhou, Bo; Minobe, Yuzo; Han, Bin

    2011-03-01

    The genetic mechanism involved in a transition from the black-colored seed hull of the ancestral wild rice (Oryza rufipogon and Oryza nivara) to the straw-white seed hull of cultivated rice (Oryza sativa) during grain ripening remains unknown. We report that the black hull of O. rufipogon was controlled by the Black hull4 (Bh4) gene, which was fine-mapped to an 8.8-kb region on rice chromosome 4 using a cross between O. rufipogon W1943 (black hull) and O. sativa indica cv Guangluai 4 (straw-white hull). Bh4 encodes an amino acid transporter. A 22-bp deletion within exon 3 of the bh4 variant disrupted the Bh4 function, leading to the straw-white hull in cultivated rice. Transgenic study indicated that Bh4 could restore the black pigment on hulls in cv Guangluai 4 and Kasalath. Bh4 sequence alignment of all taxa with the outgroup Oryza barthii showed that the wild rice maintained comparable levels of nucleotide diversity that were about 70 times higher than those in the cultivated rice. The results from the maximum likelihood Hudson-Kreitman-Aguade test suggested that the significant reduction in nucleotide diversity in rice cultivars could be caused by artificial selection. We propose that the straw-white hull was selected as an important visual phenotype of nonshattered grains during rice domestication.

  15. An Integrative Bioinformatics Framework for Genome-scale Multiple Level Network Reconstruction of Rice

    Directory of Open Access Journals (Sweden)

    Liu Lili

    2013-06-01

    Full Text Available Understanding how metabolic reactions translate the genome of an organism into its phenotype is a grand challenge in biology. Genome-wide association studies (GWAS statistically connect genotypes to phenotypes, without any recourse to known molecular interactions, whereas a molecular mechanistic description ties gene function to phenotype through gene regulatory networks (GRNs, protein-protein interactions (PPIs and molecular pathways. Integration of different regulatory information levels of an organism is expected to provide a good way for mapping genotypes to phenotypes. However, the lack of curated metabolic model of rice is blocking the exploration of genome-scale multi-level network reconstruction. Here, we have merged GRNs, PPIs and genome-scale metabolic networks (GSMNs approaches into a single framework for rice via omics’ regulatory information reconstruction and integration. Firstly, we reconstructed a genome-scale metabolic model, containing 4,462 function genes, 2,986 metabolites involved in 3,316 reactions, and compartmentalized into ten subcellular locations. Furthermore, 90,358 pairs of protein-protein interactions, 662,936 pairs of gene regulations and 1,763 microRNA-target interactions were integrated into the metabolic model. Eventually, a database was developped for systematically storing and retrieving the genome-scale multi-level network of rice. This provides a reference for understanding genotype-phenotype relationship of rice, and for analysis of its molecular regulatory network.

  16. Rice as commodity and anti-commodity

    NARCIS (Netherlands)

    Richards, P.

    2016-01-01

    On the Upper West Africa coast rice belongs to two species — African rice (Oryza glaberrima Steud.) and Asian rice (Oryza sativa L.). African rice was domesticated in the region, perhaps three millennia ago, from a presumed wild ancestor, O. barthii. Asian rice was introduced via trans-Saharan

  17. Diseases of wild rice

    Science.gov (United States)

    Diseases are much more pronounced in cultivated wild rice than in natural stands, most likely due to the narrower genetic base of the populations, plant stress due to high planting density and floodwater removal prior to harvest, and high relative humidity in the plant canopy. Yield losses occur as ...

  18. Promising rice mutants

    International Nuclear Information System (INIS)

    Hakim, L.; Azam, M.A.; Miah, A.J.; Mansur, M.A.; Akanda, H.R.

    1988-01-01

    Two induced mutants namely, Mut NS 1 (tall) and Mut NS 5 (semi-dwarf) derived from rice variety Nizersail were evaluated for various agronomic characters at four locations in Bangladesh. Both the mutants matured about three weeks earlier and yielded significantly higher than the parent variety Nizersail. (author). 3 tabs., 9 refs

  19. Investigating differences in light stable isotopes between Thai jasmine rice and Sungyod rice

    Science.gov (United States)

    Kukusamude, C.; Kongsri, S.

    2017-10-01

    We report the differences in light stable isotopes between two kinds of Thai rice (Thai jasmine and Sungyod rice). Thai jasmine rice and Sungyod rice were cultivated in the northeast and the south of Thailand. Light isotopes including 13C, 15N and 18O of Thai jasmine rice and Sungyod rice samples were carried out using isotope ratio mass spectrometry (IRMS). Thai jasmine rice (Khao Dawk Mali 105) was cultivated from Thung Kula Rong Hai area, whereas Sungyod rice was cultivated from Phathalung province. Hypothesis testing of difference of each isotope between Thai jasmine rice and Sungyod rice was also studied. The study was the feasibility test whether the light stable isotopes can be the variables to identify Thai jasmine rice and Sungyod rice. The result shows that there was difference in the isotope patterns of Thai jasmine rice and Sungyod rice. Our results may provide the useful information in term of stable isotope profiles of Thai rice.

  20. Radiation disinfestation of Basmati rice

    International Nuclear Information System (INIS)

    Rao, V.S.; Gholap, A.S.; Adhikari, H.R.; Nair, P.M.

    1994-01-01

    Effect of low dose γ-radiation on prepackaged Basmati rice was studied in order to achieve disinfestation of rice. Basmati rice procured from local market was repacked in 1 kg pouches made from high density polyethylene (HDP) and biaxially oriented polypropylene: low density polyethylene (BOPP/LDP) laminate and irradiated at doses from 0.25-1.0 kGy. Within one month of storage at room temperature, unirradiated (control) Basmati rice developed heavy infestation. No infestation was observed in any of the irradiated samples even at 0.25 kGy and the rice could be stored for 6 months in a clean state. Irradiation (at 0.25 kGy) did not alter the moisture content of the rice. Likewise, no significant change was noted due to irradiation in the functional properties of rice such as swelling index and water absorption and in total volatile components responsible for flavour of Basmati rice. In organoleptic evaluation, no significant difference was found between the acceptability of irradiated (0.25 kGy) and control rice. These results are significant in view of the high export potential of Basmati rice and the transit losses at present due to infestation. (author). 24 refs., 5 tabs., 1 fig

  1. Study of Rice Marketing System in Iran

    OpenAIRE

    Feizabadi, Yaser

    2011-01-01

    Rice comes second after wheat in Iran`s food consumption economy. Rising population and recent growth in GDP has made Iran one of the greatest rice importer countries all over the world. That is why rice marketing has always been a controversial issue in Iran`s agricultural economics. To study rice marketing system in Iran, this paper aims to calculate rice marketing margin, market efficiency and marketing cost coefficient in seaside Mazandaran province( where 70 percent of domestic rice prod...

  2. Transgenic expression of an unedited mitochondrial orfB gene product from wild abortive (WA) cytoplasm of rice (Oryza sativa L.) generates male sterility in fertile rice lines.

    Science.gov (United States)

    Chakraborty, Anirban; Mitra, Joy; Bhattacharyya, Jagannath; Pradhan, Subrata; Sikdar, Narattam; Das, Srirupa; Chakraborty, Saikat; Kumar, Sachin; Lakhanpaul, Suman; Sen, Soumitra K

    2015-06-01

    Over-expression of the unedited mitochondrial orfB gene product generates male sterility in fertile indica rice lines in a dose-dependent manner. Cytoplasmic male sterility (CMS) and nuclear-controlled fertility restoration are widespread developmental features in plant reproductive systems. In self-pollinated crop plants, these processes often provide useful tools to exploit hybrid vigour. The wild abortive CMS has been employed in the majority of the "three-line" hybrid rice production since 1970s. In the present study, we provide experimental evidence for a positive functional relationship between the 1.1-kb unedited orfB gene transcript, and its translated product in the mitochondria with male sterility. The generation of the 1.1-kb unedited orfB gene transcripts increased during flowering, resulting in low ATP synthase activity in sterile plants. Following insertion of the unedited orfB gene into the genome of male-fertile plants, the plants became male sterile in a dose-dependent manner with concomitant reduction of ATPase activity of F1F0-ATP synthase (complex V). Fertility of the transgenic lines and normal activity of ATP synthase were restored by down-regulation of the unedited orfB gene expression through RNAi-mediated silencing. The genetic elements deciphered in this study could further be tested for their use in hybrid rice development.

  3. Nicaragua - Rice and Banana Farmers

    Data.gov (United States)

    Millennium Challenge Corporation — This report is an impact evaluation of two components of the Rural Business Development Program (RBD) in Nicaragua, specifically the components benefitting rice and...

  4. Sorghum and rice: Mali

    International Nuclear Information System (INIS)

    2003-01-01

    Agriculture is the mainstay of the Malian economy and yet cereal imports absorb 6.5% of GDP. Food self-sufficiency is therefore a national priority. The Joint FAO/IAEA Division is supporting a programme to improve local varieties of sorghum and rice by using nuclear techniques to develop new cultivars that will produce higher yields under Mali's semi-arid climatic conditions. (IAEA)

  5. Diversity of some endophytic fungi associated with rice black bug Paraeucosmetus pallicornis on rice plant

    OpenAIRE

    Nur, Amin; La Daha; Nurariaty, Agus; Ade, Rosmana; Muh., Fadlan

    2015-01-01

    A new rice insect pest was sighted in some rice producing areas of South Sulawesi Province, Indonesia. This pest is rice black bugs Paraeucosmetus pallicornis. The research aimed to isolation of fungi associated with rice black bugs Paraeucosmetus pallicornis, so as to know the cause of a bitter taste to the rice. The isolation of the fungi consist of three kinds of treatment, namely rice black bugs without sterilization, with sterilization and rice black bugs cut and sterilized. The resul...

  6. Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes

    DEFF Research Database (Denmark)

    Xu, Xun; Liu, Xin; Ge, Song

    2012-01-01

    Rice is a staple crop that has undergone substantial phenotypic and physiological changes during domestication. Here we resequenced the genomes of 40 cultivated accessions selected from the major groups of rice and 10 accessions of their wild progenitors (Oryza rufipogon and Oryza nivara) to >15 x...... diversity in cultivated but not wild rice, which represent candidate regions selected during domestication. Some of these variants are associated with important biological features, whereas others have yet to be functionally characterized. The molecular markers we have identified should be valuable...... raw data coverage. We investigated genome-wide variation patterns in rice and obtained 6.5 million high-quality single nucleotide polymorphisms (SNPs) after excluding sites with missing data in any accession. Using these population SNP data, we identified thousands of genes with significantly lower...

  7. Genetic diversity of high performance cultivars of upland and irrigated Brazilian rice.

    Science.gov (United States)

    Coelho, G R C; Brondani, C; Hoffmann, L V; Valdisser, P A M R; Borba, T C O; Mendonça, J A; Rodrigues, L A; de Menezes, I P P

    2017-09-21

    The objective of this study was to analyze the diversity and discrimination of high-performance Brazilian rice cultivars using microsatellite markers. Twenty-nine rice cultivars belonging to EMBRAPA Arroz e Feijão germplasm bank in Brazil were genotyped by 24 SSR markers to establish their structure and genetic discrimination. It was demonstrated that the analyzed germplasm of rice presents an expressive and significant genetic diversity with low heterogeneity among the cultivars. All 29 cultivars were differentiated genetically, and were organized into two groups related to their upland and irrigated cultivation systems. These groups showed a high genetic differentiation, with greater diversity within the group that includes the cultivars for irrigated system. The genotyping data of these cultivars, with the morphological e phenotypical data, are valuable information to be used by rice breeding programs to develop new improved cultivars.

  8. Associating mapping of stigma characteristics using the USDA rice core collection

    Science.gov (United States)

    A mini-core from the USDA rice core collection was phenotyped for nine traits of stigma and spikelet and genotyped with 109 DNA markers. Marker-trait association mapping was used to identify the regions associated with the nine traits. Resulting associations were adjusted using false discovery rate ...

  9. Ecogeographic variation in the morphology of two Asian wild rice species Oryza nivara and O. ruftipogon.

    NARCIS (Netherlands)

    Banaticla, M.C.N.; Sosef, M.S.M.; McNally, K.L.; Sackville Hamilton, R.; Berg, van den R.G.

    2013-01-01

    To search for variation patterns and diagnostic features between Asian wild rice species, several numerical methods were applied to phenotypic data obtained from 116 accessions representing sympatric populations of Oryza nivara and Oryza rufipogon from tropical continental Asia and O. rufipogon

  10. Genetic control of plasticity in root morphology and anatomy of rice in response to water deficit

    NARCIS (Netherlands)

    Kadam, Niteen N.; Tamilselvan, Anandhan; Lawas, Lovely M.F.; Quinones, Cherryl; Bahuguna, Rajeev N.; Thomson, Michael J.; Dingkuhn, Michael; Muthurajan, Raveendran; Struik, Paul C.; Yin, Xinyou; Jagadish, Krishna S.V.

    2017-01-01

    Elucidating the genetic control of rooting behavior under water-deficit stress is essential to breed climate-robust rice (Oryza sativa) cultivars. Using a diverse panel of 274 indica genotypes grown under control and water-deficit conditions during vegetative growth, we phenotyped 35 traits, mostly

  11. Broken rice kernels and the kinetics of rice hydration and texture during cooking.

    Science.gov (United States)

    Saleh, Mohammed; Meullenet, Jean-Francois

    2013-05-01

    During rice milling and processing, broken kernels are inevitably present, although to date it has been unclear as to how the presence of broken kernels affects rice hydration and cooked rice texture. Therefore, this work intended to study the effect of broken kernels in a rice sample on rice hydration and texture during cooking. Two medium-grain and two long-grain rice cultivars were harvested, dried and milled, and the broken kernels were separated from unbroken kernels. Broken rice kernels were subsequently combined with unbroken rice kernels forming treatments of 0, 40, 150, 350 or 1000 g kg(-1) broken kernels ratio. Rice samples were then cooked and the moisture content of the cooked rice, the moisture uptake rate, and rice hardness and stickiness were measured. As the amount of broken rice kernels increased, rice sample texture became increasingly softer (P hardness was negatively correlated to the percentage of broken kernels in rice samples. Differences in the proportions of broken rice in a milled rice sample play a major role in determining the texture properties of cooked rice. Variations in the moisture migration kinetics between broken and unbroken kernels caused faster hydration of the cores of broken rice kernels, with greater starch leach-out during cooking affecting the texture of the cooked rice. The texture of cooked rice can be controlled, to some extent, by varying the proportion of broken kernels in milled rice. © 2012 Society of Chemical Industry.

  12. Molecular analysis of waxy mutants in rice

    International Nuclear Information System (INIS)

    Yatou, O.; Amano, E.

    1990-01-01

    Full text: The 'waxy' gene is a structural gene coding a glycosyl transferase which synthesises amylose in the endosperm tissue. 'Non-waxy' rice cultivars have an active gene and their amylose content is 18-25% depending upon gene performance and modifier genes. In 'waxy' rice, no amylose is found because the enzyme is absent. In mutants induced by gamma rays, neutrons, EI or EMS, amylose content ranged from 0 to 20%, i.e. there are intermediate phenotypes as well. Some of them had the same amount of the enzyme as a 'non-waxy' cultivar, even fully 'waxy' mutants showed a certain amount of the enzyme. This suggests that in mutants there may be no structural change in the enzyme gene but the enzyme produced might be less active. By molecular analysis of the mutants' genes it was found that only two mutants induced by thermal neutrons show structural alterations, the changes in other mutants are either too small to be detected by Southern analysis or are outside the structural gene in question. (author)

  13. "Tinni" Rice ( Oryza rufipogon Griff.) Production: An Integrated Sociocultural Agroecosystem in Eastern Uttar Pradesh of India

    Science.gov (United States)

    Singh, Ranjay K.; Turner, Nancy J.; Pandey, C. B.

    2012-01-01

    This study reports how Traditional Ecological Knowledge (TEK) and informal cultural institutions have conserved key varieties of the wildgrowing rice, ` tinni' (red rice, or brownbeard rice, Oriza rufipogon Griff.), within the Bhar community of eastern Uttar Pradesh, India. The study was conducted, using conventional and participatory methods, in 10 purposively selected Bhar villages. Two distinct varieties of tinni (` tinni patali' and ` tinni moti') with differing habitats and phenotypic characters were identified. Seven microecosystems (Kari, Badaila, Chammo, Karmol, Bhainsiki, Bhainsala and Khodailia) were found to support these varieties in differing proportions. Tinni rice can withstand more extreme weather conditions (the highest as well as lowest temperatures and rainfall regimes) than the `genetically improved' varieties of rice ( Oriza sativa L.) grown in the region. Both tinni varieties are important bioresources for the Bhar's subsistence livelihoods, and they use distinctive conservation approaches in their maintenance. Bhar women are the main custodians of tinni rice agrobiodiversity, conserving tinni through an institution called Sajha. Democratic decision-making at meetings organized by village elders determines the market price of the tinni varieties. Overall, the indigenous institutions and women's participation seem to have provided safeguards from excessive exploitation of tinni rice varieties. The maintenance of tinni through cultural knowledge and institutions serves as an example of the importance of locally maintained crop varieties in contributing to people's resilience and food security in times of rapid social and environmental change.

  14. Occurrence of Aspergillus section Flavi and aflatoxins in Brazilian rice: From field to market.

    Science.gov (United States)

    Katsurayama, Aline M; Martins, Ligia M; Iamanaka, Beatriz T; Fungaro, Maria Helena P; Silva, Josué J; Frisvad, Jens C; Pitt, John I; Taniwaki, Marta H

    2018-02-02

    The guarantee of the high quality of rice is of utmost importance because any toxic contaminant may affect consumer health, especially in countries such as Brazil where rice is part of the daily diet. A total of 187 rice samples, from field, processing and market from two different production systems, wetland from the state of Rio Grande do Sul, dryland, from the state of Maranhão and market samples from the state of São Paulo, were analyzed for fungi belonging to Aspergillus section Flavi and the presence of aflatoxins. Twenty-three soil samples from wetland and dryland were also analyzed. A total of 383 Aspergillus section Flavi strains were isolated from rice and soil samples. Using a polyphasic approach, with phenotypic (morphology and extrolite profiles) and molecular data (beta-tubulin gene sequences), five species were identified: A. flavus, A. caelatus, A. novoparasiticus, A. arachidicola and A. pseudocaelatus. This is the first report of these last three species from rice and rice plantation soil. Only seven (17%) of the A. flavus isolates produced type B aflatoxins, but 95% produced kojic acid and 69% cyclopiazonic acid. Less than 14% of the rice samples were contaminated with aflatoxins, but two of the market samples were well above the maximum tolerable limit (5μg/kg), established by the Brazilian National Health Surveillance Agency. Copyright © 2017 Elsevier B.V. All rights reserved.

  15. The Haitian Rice Tariff

    Directory of Open Access Journals (Sweden)

    Mats Lundahl

    2016-04-01

    Full Text Available Se ha argumentado que los problemas agríco-las de Haití derivan de la tarifa del arroz de a mediados de los años noventa. Antes, supues-tamente, Haití fue autosuficiente, abastecida por su producción doméstica. Después de la reducción, el mercado haitiano se inundó en importaciones de arroz barato de los EEUU, lo cual despojó a los campesinos de sus fincas, convirtiendolos en migrantes internos, hacia los empleos de bajo pago de las ciudades. El artículo rechaza ese argumento y demuestra que es falso. La malnutrición fue un fenómeno extendido en Haití mucho antes de la reducción de la tarifa del arroz, la cual tampoco tuvo un gran impacto en la importación y la producción doméstica del arroz. Lo que sí impulsó el aumento de las importaciones fue el crecimiento de la población. También el artículo argumenta que un aumento de la tarifa del arroz no solucionará el problema de la alimentación que sufre Haití. English: It has been argued that Haiti’s agricultural problems derive from the reduction of the rice tariff in the mid-1990s. Before that Haiti was allegedly able to meet its food needs by domestic production. After the reduction the Haitian market was swamped by imports of cheap American rice which drove the farmers off their lands and forced them to migrate to low-wage industrial jobs in the cities. The article demonstrates that the argument is false. Malnutrition was widespread in Haiti long before the rice tariff reduction, and the latter did not have much of an impact on rice imports and domestic production. Instead, the main driving force behind imports appears to be population growth. It is also shown that an increase of the rice tariff will not solve Haiti’s food problem.

  16. Asthma phenotypes in childhood.

    Science.gov (United States)

    Reddy, Monica B; Covar, Ronina A

    2016-04-01

    This review describes the literature over the past 18 months that evaluated childhood asthma phenotypes, highlighting the key aspects of these studies, and comparing these studies to previous ones in this area. Recent studies on asthma phenotypes have identified new phenotypes on the basis of statistical analyses (using cluster analysis and latent class analysis methodology) and have evaluated the outcomes and associated risk factors of previously established early childhood asthma phenotypes that are based on asthma onset and patterns of wheezing illness. There have also been investigations focusing on immunologic, physiologic, and genetic correlates of various phenotypes, as well as identification of subphenotypes of severe childhood asthma. Childhood asthma remains a heterogeneous condition, and investigations into these various presentations, risk factors, and outcomes are important since they can offer therapeutic and prognostic relevance. Further investigation into the immunopathology and genetic basis underlying childhood phenotypes is important so therapy can be tailored accordingly.

  17. Nutritional test of rice in rats

    International Nuclear Information System (INIS)

    Horii, Masaji; Yoshikawa, Seiji

    1980-01-01

    Behaviors on N derived from rice were followed up by means of 15 N-labeled rice. In the first test, the single unpolished rice diet and the diet of rice and bean lecithin (4.5%) produced urinary excretion of 10 - 12% of 15 N, and that of rice and mannan from devil's tongue (3%), 16 - 20%. The single unpolished rice diet showed slightly more urinary excretion of 15 N, and the other 2 diets showed a similar proportion of 15 N in 3 days. The results indicated that the diet containing mannan from devil's tongue resulted in a poor N absorption by rice, a large quantity of N being excreted over a long period of time. This suggested differences and time lags in the excretion of rice N into the stool and urine depending on the diet constitution. With the unpolished rice diet, a small quantity of rice protein was not absorbed, but was excreted. In the 2nd test with 15 N-polished rice, the urinary excretion rate was 11.44% for a single rice diet, 11.16% for a mixed diet of rice and bean (1:1 in protein), 10.99% for rice and egg yolk, 9.66% for rice, bean and egg yolk and 8.10% for rice and bean lecithin. This decrease in urinary excretion indicated a corresponding increase in absorption of rice protein. (Chiba, N.)

  18. Genetic diversity of Iranian rice germplasm based on morphological traits

    Directory of Open Access Journals (Sweden)

    nade ali bagheri

    2009-06-01

    Full Text Available Study of genetic diversity of rice is very important for rice breeders. In this study 64 genotypes for 14 agronomic traits were evaluated. Phenotypic variation coefficients of some of traits were high which showed essential variation in this traits. Principal component analysis detected 6 components which explained 74.66 percent of the total variations. The first component was related to generative traits such as number of spiklet per panicle, number of full grain per panicle, date of 50% flowering and length of panicle. In the third component, the date of complete maturity with -0.730 has negative effects on yield. Correlation analysis of morphological traits indicated a negative and significant relationship between early maturity and plant height, which showed early maturity cultivars had higher plant type. Results of stepwise regression analysis for early maturity, indicated that three traits such as date of 50% flowering, number of full grain per panicle and plant height showed higher variation and explained 54.3 percent of total early maturity variations. All traits were classified into 2 groups, by cluster analysis and traits belonged to early maturity classified as a sub-group. Genotypes were classified into 4 groups by using method of Ward,s minimum variance and squared Euclidean distance. Native cultivars from the view point of early maturity and yield components had useful information for rice breeding. Key words: Genetic diversity, rice, morphological traits.

  19. Deciphering hepatocellular responses to metabolic and oncogenic stress

    Directory of Open Access Journals (Sweden)

    Kathrina L. Marcelo

    2015-08-01

    Full Text Available Each cell type responds uniquely to stress and fractionally contributes to global and tissue-specific stress responses. Hepatocytes, liver macrophages (MΦ, and sinusoidal endothelial cells (SEC play functionally important and interdependent roles in adaptive processes such as obesity and tumor growth. Although these cell types demonstrate significant phenotypic and functional heterogeneity, their distinctions enabling disease-specific responses remain understudied. We developed a strategy for the simultaneous isolation and quantification of these liver cell types based on antigenic cell surface marker expression. To demonstrate the utility and applicability of this technique, we quantified liver cell-specific responses to high-fat diet (HFD or diethylnitrosamine (DEN, a liver-specific carcinogen, and found that while there was only a marginal increase in hepatocyte number, MΦ and SEC populations were quantitatively increased. Global gene expression profiling of hepatocytes, MΦ and SEC identified characteristic gene signatures that define each cell type in their distinct physiological or pathological states. Integration of hepatic gene signatures with available human obesity and liver cancer microarray data provides further insight into the cell-specific responses to metabolic or oncogenic stress. Our data reveal unique gene expression patterns that serve as molecular “fingerprints” for the cell-centric responses to pathologic stimuli in the distinct microenvironment of the liver. The technical advance highlighted in this study provides an essential resource for assessing hepatic cell-specific contributions to metabolic and oncogenic stress, information that could unveil previously unappreciated molecular mechanisms for the cellular crosstalk that underlies the continuum from metabolic disruption to obesity and ultimately hepatic cancer.

  20. Deciphering defective amelogenesis using in vitro culture systems.

    Science.gov (United States)

    Arinawati, Dian Yosi; Miyoshi, Keiko; Tanimura, Ayako; Horiguchi, Taigo; Hagita, Hiroko; Noma, Takafumi

    2018-04-01

    The conventional two-dimensional (2D) in vitro culture system is frequently used to analyze the gene expression with or without extracellular signals. However, the cells derived from primary culture and cell lines frequently deviate the gene expression profile compared to the corresponding in vivo samples, which sometimes misleads the actual gene regulation in vivo. To overcome this gap, we developed the comparative 2D and 3D in vitro culture systems and applied them to the genetic study of amelogenesis imperfecta (AI) as a model. Recently, we found specificity protein 6 (Sp6) mutation in an autosomal-recessive AI rat that was previously named AMI. We constructed 3D structure of ARE-B30 cells (AMI-derived rat dental epithelial cells) or G5 (control wild type cells) combined with RPC-C2A cells (rat pulp cell line) separated by the collagen membrane, while in 2D structure, ARE-B30 or G5 was cultured with or without the collagen membrane. Comparative analysis of amelogenesis-related gene expression in ARE-B30 and G5 using our 2D and 3D in vitro systems revealed distinct expression profiles, showing the causative outcomes. Bone morphogenetic protein 2 and follistatin were reciprocally expressed in G5, but not in ARE-B30 cells. All-or-none expression of amelotin, kallikrein-related peptidase 4, and nerve growth factor receptor was observed in both cell types. In conclusion, our in vitro culture systems detected the phenotypical differences in the expression of the stage-specific amelogenesis-related genes. Parallel analysis with 2D and 3D culture systems may provide a platform to understand the molecular basis for defective amelogenesis caused by Sp6 mutation. Copyright © 2017 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

  1. Geochemical patterns and microbial contribution to iron plaque formation in the rice plant rhizosphere

    Science.gov (United States)

    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

  2. Geographic and Research Center Origins of Rice Resistance to Asian Planthoppers and Leafhoppers: Implications for Rice Breeding and Gene Deployment

    Directory of Open Access Journals (Sweden)

    Finbarr G. Horgan

    2017-09-01

    Full Text Available This study examines aspects of virulence to resistant rice varieties among planthoppers and leafhoppers. Using a series of resistant varieties, brown planthopper, Nilaparvata lugens, virulence was assessed in seedlings and early-tillering plants at seven research centers in South and East Asia. Virulence of the whitebacked planthopper, Sogatella furcifera, in Taiwan and the Philippines was also assessed. Phylogenetic analysis of the varieties using single-nucleotide polymorphisms (SNPs indicated a clade of highly resistant varieties from South Asia with two further South Asian clades of moderate resistance. Greenhouse bioassays indicated that planthoppers can develop virulence against multiple resistance genes including genes introgressed from wild rice species. Nilaparvata lugens populations from Punjab (India and the Mekong Delta (Vietnam were highly virulent to a range of key resistance donors irrespective of variety origin. Sogatella furcifera populations were less virulent to donors than N. lugens; however, several genes for resistance to S. furcifera are now ineffective in East Asia. A clade of International Rice Research Institute (IRRI-bred varieties and breeding lines, without identified leafhopper-resistance genes, were highly resistant to the green leafhopper, Nephotettix virescens. Routine phenotyping during breeding programs likely maintains high levels of quantitative resistance to leafhoppers. We discuss these results in the light of breeding and deploying resistant rice in Asia.

  3. 21 CFR 137.350 - Enriched rice.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 2 2010-04-01 2010-04-01 false Enriched rice. 137.350 Section 137.350 Food and... Related Products § 137.350 Enriched rice. (a) The foods for which definitions and standards of identity are prescribed by this section are forms of milled rice (except rice coated with talc and glucose and...

  4. Genetically engineered Rice with transcription factor DREB genes for abiotic stress tolerance(abstract)

    International Nuclear Information System (INIS)

    Datta, S.K.; Datta, K.

    2005-01-01

    Water stress (drought and Salinity) is the most severe limitation to rice productivity. Several breeding approaches (MAS, QTL) applied to suitable genotypes are in place at IRRI and elsewhere. Phenotyping of water stress tolerance is in progress with potential predictability. Dr. Shinozaki's group has cloned a number of transcription factor genes, which have been shown to work in Arabidopsis to achieve drought, cold, and salinity tolerant plants. None of these genes have as yet displayed their potential functioning in rice. Genetic engineering aims at cross talk between different stress signaling pathways leading to stress tolerance. Osmotic Adjustment (OA) is an effective component of abiotic stress (drought and salinity) tolerance in many plants including rice. When plant experiences water stress, OA contributes to turgor maintenance of both shoots and roots. Conventional breeding could not achieve the OA in rice excepting a few rice cultivars, which are partially adapted to water-stress conditions. Several stress-related genes have now been cloned and transferred in to enhance the osmolytes and some transgenic lines showed increased tolerance to osmotic stress. A few strategies could be effectively deployed for a better understanding of water-stress tolerance in rice and to develop transgenic rice, which can survive for a critical period of water-stress conditions: 1) Switching on of transcription factor regulating the expression of several genes related to abiotic stress, 2) Use of a suitable stress inducible promoter driving the target gene for an efficient and directed expression in plants, 3) Understanding of phenotyping and GxE in a given environment, 4) Selection of a few adaptive rice cultivars suitable in drought/salinity prone areas, 5) Microarray, proteomics, QTL and MAS may expedite the cloning and characterizing the stress induced genes, and 6) Finally, the efficient transformation system for generating a large number of transgenic rice of different

  5. Brassinosteroids Antagonize Gibberellin- and Salicylate-Mediated Root Immunity in Rice1[C][W][OA

    Science.gov (United States)

    De Vleesschauwer, David; Van Buyten, Evelien; Satoh, Kouji; Balidion, Johny; Mauleon, Ramil; Choi, Il-Ryong; Vera-Cruz, Casiana; Kikuchi, Shoshi; Höfte, Monica

    2012-01-01

    Brassinosteroids (BRs) are a unique class of plant steroid hormones that orchestrate myriad growth and developmental processes. Although BRs have long been known to protect plants from a suite of biotic and abiotic stresses, our understanding of the underlying molecular mechanisms is still rudimentary. Aiming to further decipher the molecular logic of BR-modulated immunity, we have examined the dynamics and impact of BRs during infection of rice (Oryza sativa) with the root oomycete Pythium graminicola. Challenging the prevailing view that BRs positively regulate plant innate immunity, we show that P. graminicola exploits BRs as virulence factors and hijacks the rice BR machinery to inflict disease. Moreover, we demonstrate that this immune-suppressive effect of BRs is due, at least in part, to negative cross talk with salicylic acid (SA) and gibberellic acid (GA) pathways. BR-mediated suppression of SA defenses occurred downstream of SA biosynthesis, but upstream of the master defense regulators NONEXPRESSOR OF PATHOGENESIS-RELATED GENES1 and OsWRKY45. In contrast, BR alleviated GA-directed immune responses by interfering at multiple levels with GA metabolism, resulting in indirect stabilization of the DELLA protein and central GA repressor SLENDER RICE1 (SLR1). Collectively, these data favor a model whereby P. graminicola coopts the plant BR pathway as a decoy to antagonize effectual SA- and GA-mediated defenses. Our results highlight the importance of BRs in modulating plant immunity and uncover pathogen-mediated manipulation of plant steroid homeostasis as a core virulence strategy. PMID:22353574

  6. Brassinosteroids antagonize gibberellin- and salicylate-mediated root immunity in rice.

    Science.gov (United States)

    De Vleesschauwer, David; Van Buyten, Evelien; Satoh, Kouji; Balidion, Johny; Mauleon, Ramil; Choi, Il-Ryong; Vera-Cruz, Casiana; Kikuchi, Shoshi; Höfte, Monica

    2012-04-01

    Brassinosteroids (BRs) are a unique class of plant steroid hormones that orchestrate myriad growth and developmental processes. Although BRs have long been known to protect plants from a suite of biotic and abiotic stresses, our understanding of the underlying molecular mechanisms is still rudimentary. Aiming to further decipher the molecular logic of BR-modulated immunity, we have examined the dynamics and impact of BRs during infection of rice (Oryza sativa) with the root oomycete Pythium graminicola. Challenging the prevailing view that BRs positively regulate plant innate immunity, we show that P. graminicola exploits BRs as virulence factors and hijacks the rice BR machinery to inflict disease. Moreover, we demonstrate that this immune-suppressive effect of BRs is due, at least in part, to negative cross talk with salicylic acid (SA) and gibberellic acid (GA) pathways. BR-mediated suppression of SA defenses occurred downstream of SA biosynthesis, but upstream of the master defense regulators NONEXPRESSOR OF PATHOGENESIS-RELATED GENES1 and OsWRKY45. In contrast, BR alleviated GA-directed immune responses by interfering at multiple levels with GA metabolism, resulting in indirect stabilization of the DELLA protein and central GA repressor SLENDER RICE1 (SLR1). Collectively, these data favor a model whereby P. graminicola coopts the plant BR pathway as a decoy to antagonize effectual SA- and GA-mediated defenses. Our results highlight the importance of BRs in modulating plant immunity and uncover pathogen-mediated manipulation of plant steroid homeostasis as a core virulence strategy.

  7. Clinical phenotypes of asthma

    NARCIS (Netherlands)

    Bel, Elisabeth H.

    2004-01-01

    PURPOSE OF REVIEW: Asthma is a phenotypically heterogeneous disorder and, over the years, many different clinical subtypes of asthma have been described. A precise definition of asthma phenotypes is now becoming more and more important, not only for a better understanding of pathophysiologic

  8. Use of fission track for deciphering the dissolution mechanism of silicates glasses

    International Nuclear Information System (INIS)

    Petit, J.C.; Brousse, C.

    1985-09-01

    Polished sections of silicate glasses containing latent or pre-etched fission tracks have been subjected to corrosion in deionized water or NaCl brines at 20, 50 and 100 0 C. The evolution of glass surface helps deciphering among reported dissolution models. We show that ion-exchange is dominant in simple glasses while in complex ones, dissolution involves several steps including an in-situ transformation of the pristine material and a reprecipitation of dissolved species

  9. Little White Lies: Pericarp Color Provides Insights into the Origins and Evolution of Southeast Asian Weedy Rice

    Science.gov (United States)

    Cui, Yongxia; Song, Beng Kah; Li, Lin-Feng; Li, Ya-Ling; Huang, Zhongyun; Caicedo, Ana L.; Jia, Yulin; Olsen, Kenneth M.

    2016-01-01

    Weedy rice is a conspecific form of cultivated rice (Oryza sativa L.) that infests rice fields and results in severe crop losses. Weed strains in different world regions appear to have originated multiple times from different domesticated and/or wild rice progenitors. In the case of Malaysian weedy rice, a multiple-origin model has been proposed based on neutral markers and analyses of domestication genes for hull color and seed shattering. Here, we examined variation in pericarp (bran) color and its molecular basis to address how this trait evolved in Malaysian weeds and its possible role in weed adaptation. Functional alleles of the Rc gene confer proanthocyanidin pigmentation of the pericarp, a trait found in most wild and weedy Oryzas and associated with seed dormancy; nonfunctional rc alleles were strongly favored during rice domestication, and most cultivated varieties have nonpigmented pericarps. Phenotypic characterizations of 52 Malaysian weeds revealed that most strains are characterized by the pigmented pericarp; however, some weeds have white pericarps, suggesting close relationships to cultivated rice. Phylogenetic analyses indicate that the Rc haplotypes present in Malaysian weeds likely have at least three distinct origins: wild O. rufipogon, white-pericarp cultivated rice, and red-pericarp cultivated rice. These diverse origins contribute to high Rc nucleotide diversity in the Malaysian weeds. Comparison of Rc allelic distributions with other rice domestication genes suggests that functional Rc alleles may confer particular fitness benefits in weedy rice populations, for example, by conferring seed dormancy. This may promote functional Rc introgression from local wild Oryza populations. PMID:27729434

  10. Physical mapping of Bph3, a brown planthopper resistance locus in rice

    Directory of Open Access Journals (Sweden)

    Jirapong Jairin

    2007-09-01

    Full Text Available Resistance to brown planthopper (BPH, a destructive phloem feeding insect pest, is an important objective in rice breeding programs in Thailand. The broad-spectrum resistance gene Bph3 is one of the major BPH resistance genes identified so far in cultivated rice and has been widely used in rice improvement programs. This resistance gene has been identified and mapped on the short arm of chromosome 6. In this study, physical mapping of Bph3 was performed using a BC3F3 population derived from a cross between Rathu Heenati and KDML105. Recombinant BC3F3 individuals with the Bph3 genotype were determined by phenotypic evaluation using modified mass tiller screening at the vegetative stage of rice plants. The recombination events surrounding the Bph3 locus were used to identify the co-segregate markers. According to the genome sequence of Nipponbare, the Bph3 locus was finally localized approximately in a 190 kb interval flanked by markers RM19291 and RM8072, which contain twenty-two putative genes. Additional phenotypic experiment revealed that the resistance in Rathu Heenati was decreased by increasing nitrogen content in rice plants through remobilization of nitrogen. This phenomenon should be helpful for identifying the Bph3 gene.

  11. Asian wild rice is a hybrid swarm with extensive gene flow and feralization from domesticated rice

    OpenAIRE

    Wang, Hongru; Garrett Vieira, Filipe Jorge; Crawford, Jacob E.; Chu, Chengcai; Nielsen, Rasmus

    2017-01-01

    The domestication history of rice remains controversial, with multiple studies reaching different conclusions regarding its origin(s). These studies have generally assumed that populations of living wild rice, O. rufipogon, are descendants of the ancestral population that gave rise to domesticated rice, but relatively little attention has been paid to the origins and history of wild rice itself. Here, we investigate the genetic ancestry of wild rice by analyzing a diverse panel of rice genome...

  12. UNTAGGED MUTATION IN RICE GAL4/VP16 TRANSCRIPTIONAL ACTIVATOR FACILITATED-ENHANCER TRAP LINES

    Directory of Open Access Journals (Sweden)

    Sri Koerniati

    2013-04-01

    Full Text Available An enhancer trap system is an insertional mutagenesis based upon gene expression, instead of gene knock-out, so its insertion in genome is  expected not linked to any dramatic changes in plant phenotypes. Gene  knock-out, leading to lossof- function (LoF mutation, is a dominant  approach for rice functional genomic studies. The objective of this study was to find out whether Transcriptional Activator-Facilitated Enhancer Trap (TAFET T-DNA insertion inducing mutant phenotypes in rice TAFET population. Materials used in this experiment were T1 generation of 270 rice TAFET lines. Eight plants of each were grown in the greenhouse and observed for any mutant phenotypes. Phenotypic, histochemical, Southernblot analyses were carried out to define a mutant of pSKC66.1- 8e. Result showed that about 10% of the 270 lines produced chlorophyll-deficient  leaves, ranged from yellowish green (viridis, white stripe green zebra-like stripe to completely white (albino. Albino plants died after two weeks,  whilst white stripe or viridis mutants became normal in the next generation(T2. Another mutant was pSKC66.1-8e line which had floral dramatic phenotype change with various spikelet shapes and number of organs, and had a single twisted culm. The flower of mutant also had gus gene expression. Plants with wild type did not express gus gene and had six or more straight culms. Molecular, histochemical and phenotypic analyses of this particular line for three generations indicated that mutant phenotype was not due to the T-DNA insertion. Since there was approved that Tos17 is activated during tissue culture and induced mutant phenotype, this line might relate to Tos17 insertion, but it needs further investigation to gain such conclusion.

  13. Developing climate resilient rice through genomics assisted breeding

    Directory of Open Access Journals (Sweden)

    Valarmathi Muthu

    2017-10-01

    Full Text Available Rice is one of the major cereal food crops whose production has to be doubled to achieve the projected demand [1] and current yield trends are not sufficient to meet the projected growth in production. Increasing the rice production by 30% during 2030 needs overcoming challenges viz., yield plateau, declining land, water and labor resources and predicted effects of global climate change. Development of high performance rice genotypes with enhanced yield potential and resilience to climate change will help in sustained increase in rice production. Deployment of genomic technologies can accelerate development and delivery of improved germplasm with enhanced resilience and adaptability [2, 3]. In this context, the present study was undertaken with an aim of developing rice genotypes pyramided with QTLs/genes controlling tolerance against various biotic and abiotic stresses viz., bacterial leaf blight (xa13, Xa21, blast (Pi9, Gall midge (Gm4, drought (qDTY1.1 qDTY2.1, submergence (Sub1 and salinity (Saltol. CBMAS14065 an elite culture harboring QTLs controlling tolerance against drought, salinity and submergence was crossed with a donor harboring BLB, Blast and Gall midge resistant genes. True F1s were backcrossed with CBMAS14065 and BC1F1 progenies were subjected to foreground selection using markers linked to the target traits. Superior plants (18 of BC1F1 generation were subjected to background selection which revealed 71.42 - 86.90% recurrent parent (CBMAS14065 genome recovery. Selected BC1F1 plants were advanced to BC2F1 generation backcrossing with CBMAS14065. In BC2F1 generation, through foreground selection 6-8 QTL/gene positive plants have been selected and advanced for further evaluation. The superior lines with desired QTLs/genes will be subjected to rigorous phenotypic evaluation against target stresses and advanced further.

  14. Zinc fertilization of flooded rice

    International Nuclear Information System (INIS)

    1981-02-01

    Local scientists studied Zn fertilization of flooded rice soils in Bangladesh, India, Indonesia, the Republic of Korea, Egypt, the Philippines, Thailand and Turkey. Diagnosis of Zn deficiency was carried out for submerged rice soils. Soil maps were prepared, designating areas as low, medium and high in Zn, based on Zn extraction with DTPA and HCl solutions and on rice leaf analysis. The effectiveness of various Zn fertilizer sources and methods of application in field and greenhouse experiments was measured, using 65 Zn. The percent Zn derived from fertilizer was shown to be a much more sensitive measure of efficiency than yield or total uptake

  15. Polyploidy Enhances F1 Pollen Sterility Loci Interactions That Increase Meiosis Abnormalities and Pollen Sterility in Autotetraploid Rice.

    Science.gov (United States)

    Wu, Jinwen; Shahid, Muhammad Qasim; Chen, Lin; Chen, Zhixiong; Wang, Lan; Liu, Xiangdong; Lu, Yonggen

    2015-12-01

    Intersubspecific autotetraploid rice (Oryza sativa ssp. indica × japonica) hybrids have greater biological and yield potentials than diploid rice. However, the low fertility of intersubspecific autotetraploid hybrids, which is largely caused by high pollen abortion rates, limits their commercial utility. To decipher the cytological and molecular mechanisms underlying allelic interactions in autotetraploid rice, we developed an autotetraploid rice hybrid that was heterozygous (S(i)S(j)) at F1 pollen sterility loci (Sa, Sb, and Sc) using near-isogenic lines. Cytological studies showed that the autotetraploid had higher percentages (>30%) of abnormal chromosome behavior and aberrant meiocytes (>50%) during meiosis than did the diploid rice hybrid control. Analysis of gene expression profiles revealed 1,888 genes that were differentially expressed between the autotetraploid and diploid hybrid lines at the meiotic stage, among which 889 and 999 were up- and down-regulated, respectively. Of the 999 down-regulated genes, 940 were associated with the combined effect of polyploidy and pollen sterility loci interactions (IPE). Gene Ontology enrichment analysis identified a prominent functional gene class consisting of seven genes related to photosystem I (Gene Ontology 0009522). Moreover, 55 meiosis-related or meiosis stage-specific genes were associated with IPE in autotetraploid rice, including Os02g0497500, which encodes a DNA repair-recombination protein, and Os02g0490000, which encodes a component of the ubiquitin-proteasome pathway. These results suggest that polyploidy enhances epistatic interactions between alleles of pollen sterility loci, thereby altering the expression profiles of important meiosis-related or meiosis stage-specific genes and resulting in high pollen sterility. © 2015 American Society of Plant Biologists. All Rights Reserved.

  16. Polyploidy Enhances F1 Pollen Sterility Loci Interactions That Increase Meiosis Abnormalities and Pollen Sterility in Autotetraploid Rice1[OPEN

    Science.gov (United States)

    Wu, Jinwen; Chen, Lin; Chen, Zhixiong; Wang, Lan; Lu, Yonggen

    2015-01-01

    Intersubspecific autotetraploid rice (Oryza sativa ssp. indica × japonica) hybrids have greater biological and yield potentials than diploid rice. However, the low fertility of intersubspecific autotetraploid hybrids, which is largely caused by high pollen abortion rates, limits their commercial utility. To decipher the cytological and molecular mechanisms underlying allelic interactions in autotetraploid rice, we developed an autotetraploid rice hybrid that was heterozygous (SiSj) at F1 pollen sterility loci (Sa, Sb, and Sc) using near-isogenic lines. Cytological studies showed that the autotetraploid had higher percentages (>30%) of abnormal chromosome behavior and aberrant meiocytes (>50%) during meiosis than did the diploid rice hybrid control. Analysis of gene expression profiles revealed 1,888 genes that were differentially expressed between the autotetraploid and diploid hybrid lines at the meiotic stage, among which 889 and 999 were up- and down-regulated, respectively. Of the 999 down-regulated genes, 940 were associated with the combined effect of polyploidy and pollen sterility loci interactions (IPE). Gene Ontology enrichment analysis identified a prominent functional gene class consisting of seven genes related to photosystem I (Gene Ontology 0009522). Moreover, 55 meiosis-related or meiosis stage-specific genes were associated with IPE in autotetraploid rice, including Os02g0497500, which encodes a DNA repair-recombination protein, and Os02g0490000, which encodes a component of the ubiquitin-proteasome pathway. These results suggest that polyploidy enhances epistatic interactions between alleles of pollen sterility loci, thereby altering the expression profiles of important meiosis-related or meiosis stage-specific genes and resulting in high pollen sterility. PMID:26511913

  17. The DELLA Protein SLR1 Integrates and Amplifies Salicylic Acid- and Jasmonic Acid-Dependent Innate Immunity in Rice1

    Science.gov (United States)

    De Vleesschauwer, David; Seifi, Hamed Soren; Haeck, Ashley; Huu, Son Nguyen; Demeestere, Kristof

    2016-01-01

    Gibberellins are a class of tetracyclic plant hormones that are well known to promote plant growth by inducing the degradation of a class of nuclear growth-repressing proteins, called DELLAs. In recent years, GA and DELLAs are also increasingly implicated in plant responses to pathogen attack, although our understanding of the underlying mechanisms is still limited, especially in monocotyledonous crop plants. Aiming to further decipher the molecular underpinnings of GA- and DELLA-modulated plant immunity, we studied the dynamics and impact of GA and DELLA during infection of the model crop rice (Oryza sativa) with four different pathogens exhibiting distinct lifestyles and infection strategies. Opposite to previous findings in Arabidopsis (Arabidopsis thaliana), our findings reveal a prominent role of the DELLA protein Slender Rice1 (SLR1) in the resistance toward (hemi)biotrophic but not necrotrophic rice pathogens. Moreover, contrary to the differential effect of DELLA on the archetypal defense hormones salicylic acid (SA) and jasmonic acid (JA) in Arabidopsis, we demonstrate that the resistance-promoting effect of SLR1 is due at least in part to its ability to boost both SA- and JA-mediated rice defenses. In a reciprocal manner, we found JA and SA treatment to interfere with GA metabolism and stabilize SLR1. Together, these findings favor a model whereby SLR1 acts as a positive regulator of hemibiotroph resistance in rice by integrating and amplifying SA- and JA-dependent defense signaling. Our results highlight the differences in hormone defense networking between rice and Arabidopsis and underscore the importance of GA and DELLA in molding disease outcomes. PMID:26829979

  18. The DELLA Protein SLR1 Integrates and Amplifies Salicylic Acid- and Jasmonic Acid-Dependent Innate Immunity in Rice.

    Science.gov (United States)

    De Vleesschauwer, David; Seifi, Hamed Soren; Filipe, Osvaldo; Haeck, Ashley; Huu, Son Nguyen; Demeestere, Kristof; Höfte, Monica

    2016-03-01

    Gibberellins are a class of tetracyclic plant hormones that are well known to promote plant growth by inducing the degradation of a class of nuclear growth-repressing proteins, called DELLAs. In recent years, GA and DELLAs are also increasingly implicated in plant responses to pathogen attack, although our understanding of the underlying mechanisms is still limited, especially in monocotyledonous crop plants. Aiming to further decipher the molecular underpinnings of GA- and DELLA-modulated plant immunity, we studied the dynamics and impact of GA and DELLA during infection of the model crop rice (Oryza sativa) with four different pathogens exhibiting distinct lifestyles and infection strategies. Opposite to previous findings in Arabidopsis (Arabidopsis thaliana), our findings reveal a prominent role of the DELLA protein Slender Rice1 (SLR1) in the resistance toward (hemi)biotrophic but not necrotrophic rice pathogens. Moreover, contrary to the differential effect of DELLA on the archetypal defense hormones salicylic acid (SA) and jasmonic acid (JA) in Arabidopsis, we demonstrate that the resistance-promoting effect of SLR1 is due at least in part to its ability to boost both SA- and JA-mediated rice defenses. In a reciprocal manner, we found JA and SA treatment to interfere with GA metabolism and stabilize SLR1. Together, these findings favor a model whereby SLR1 acts as a positive regulator of hemibiotroph resistance in rice by integrating and amplifying SA- and JA-dependent defense signaling. Our results highlight the differences in hormone defense networking between rice and Arabidopsis and underscore the importance of GA and DELLA in molding disease outcomes. © 2016 American Society of Plant Biologists. All Rights Reserved.

  19. Delving deeper into technological innovations to understand differences in rice quality.

    Science.gov (United States)

    Calingacion, Mariafe; Fang, Lu; Quiatchon-Baeza, Lenie; Mumm, Roland; Riedel, Arthur; Hall, Robert D; Fitzgerald, Melissa

    2015-12-01

    Increasing demand for better quality rice varieties, which are also more suited to growth under sub-optimal cultivation conditions, is driving innovation in rice research. Here we have used a multi-disciplinary approach, involving SNP-based genotyping together with phenotyping based on yield analysis, metabolomic analysis of grain volatiles, and sensory panel analysis to determine differences between two contrasting rice varieties, Apo and IR64. Plants were grown under standard and drought-induced conditions. Results revealed important differences between the volatile profiles of the two rice varieties and we relate these differences to those perceived by the sensory panel. Apo, which is the more drought tolerant variety, was less affected by the drought condition concerning both sensory profile and yield; IR64, which has higher quality but is drought sensitive, showed greater differences in these characteristics in response to the two growth conditions. Metabolomics analyses using GCxGC-MS, followed by multivariate statistical analyses of the data, revealed a number of discriminatory compounds between the varieties, but also effects of the difference in cultivation conditions. Results indicate the complexity of rice volatile profile, even of non-aromatic varieties, and how metabolomics can be used to help link changes in aroma profile with the sensory phenotype. Our outcomes also suggest valuable multi-disciplinary approaches which can be used to help define the aroma profile in rice, and its underlying genetic background, in order to support breeders in the generation of improved rice varieties combining high yield with high quality, and tolerance of both these traits to climate change.

  20. The rice dwarf virus P2 protein interacts with ent-kaurene oxidases in vivo, leading to reduced biosynthesis of gibberellins and rice dwarf symptoms.

    Science.gov (United States)

    Zhu, Shifeng; Gao, Feng; Cao, Xuesong; Chen, Mao; Ye, Gongyin; Wei, Chunhong; Li, Yi

    2005-12-01

    The mechanisms of viral diseases are a major focus of biology. Despite intensive investigations, how a plant virus interacts with host factors to cause diseases remains poorly understood. The Rice dwarf virus (RDV), a member of the genus Phytoreovirus, causes dwarfed growth phenotypes in infected rice (Oryza sativa) plants. The outer capsid protein P2 is essential during RDV infection of insects and thus influences transmission of RDV by the insect vector. However, its role during RDV infection within the rice host is unknown. By yeast two-hybrid and coimmunoprecipitation assays, we report that P2 of RDV interacts with ent-kaurene oxidases, which play a key role in the biosynthesis of plant growth hormones gibberellins, in infected plants. Furthermore, the expression of ent-kaurene oxidases was reduced in the infected plants. The level of endogenous GA1 (a major active gibberellin in rice vegetative tissues) in the RDV-infected plants was lower than that in healthy plants. Exogenous application of GA3 to RDV-infected rice plants restored the normal growth phenotypes. These results provide evidence that the P2 protein of RDV interferes with the function of a cellular factor, through direct physical interactions, that is important for the biosynthesis of a growth hormone leading to symptom expression. In addition, the interaction between P2 and rice ent-kaurene oxidase-like proteins may decrease phytoalexin biosynthesis and make plants more competent for virus replication. Moreover, P2 may provide a novel tool to investigate the regulation of GA metabolism for plant growth and development.

  1. The Rice Dwarf Virus P2 Protein Interacts with ent-Kaurene Oxidases in Vivo, Leading to Reduced Biosynthesis of Gibberellins and Rice Dwarf Symptoms1

    Science.gov (United States)

    Zhu, Shifeng; Gao, Feng; Cao, Xuesong; Chen, Mao; Ye, Gongyin; Wei, Chunhong; Li, Yi

    2005-01-01

    The mechanisms of viral diseases are a major focus of biology. Despite intensive investigations, how a plant virus interacts with host factors to cause diseases remains poorly understood. The Rice dwarf virus (RDV), a member of the genus Phytoreovirus, causes dwarfed growth phenotypes in infected rice (Oryza sativa) plants. The outer capsid protein P2 is essential during RDV infection of insects and thus influences transmission of RDV by the insect vector. However, its role during RDV infection within the rice host is unknown. By yeast two-hybrid and coimmunoprecipitation assays, we report that P2 of RDV interacts with ent-kaurene oxidases, which play a key role in the biosynthesis of plant growth hormones gibberellins, in infected plants. Furthermore, the expression of ent-kaurene oxidases was reduced in the infected plants. The level of endogenous GA1 (a major active gibberellin in rice vegetative tissues) in the RDV-infected plants was lower than that in healthy plants. Exogenous application of GA3 to RDV-infected rice plants restored the normal growth phenotypes. These results provide evidence that the P2 protein of RDV interferes with the function of a cellular factor, through direct physical interactions, that is important for the biosynthesis of a growth hormone leading to symptom expression. In addition, the interaction between P2 and rice ent-kaurene oxidase-like proteins may decrease phytoalexin biosynthesis and make plants more competent for virus replication. Moreover, P2 may provide a novel tool to investigate the regulation of GA metabolism for plant growth and development. PMID:16299167

  2. Rice vaikib salavanglaist / Tõnis Erilaid

    Index Scriptorium Estoniae

    Erilaid, Tõnis, 1943-

    2005-01-01

    Euroopasse visiidile sõitev USA välisminister Condoleezza Rice külastab Saksamaad, Rumeeniat, Ukrainat ja Belgiat. Süüdistusi CIA lennukite maandumiste ja salavanglate kohta ei olevat tal kavas kommenteerida

  3. Red Yeast Rice: An Introduction

    Science.gov (United States)

    ... rice are used in food products in Chinese cuisine, including Peking duck. Others have been sold as ... Medicine . 2010;170(19):1722–1727. Halbert SC, French B, Gordon RY, et al. Tolerability of red ...

  4. indica rice (Oryza sativa L.)

    African Journals Online (AJOL)

    Jane

    2011-07-18

    Jul 18, 2011 ... fresh weight, regeneration, proline level and total protein content in salt sensitive indica rice cv. IR 64. For callus ... INTRODUCTION. Salinity is one of the ... Proline is reported to reduce the enzyme denaturation caused due.

  5. Detection of genomic deletions in rice using oligonucleotide microarrays

    Directory of Open Access Journals (Sweden)

    Bordeos Alicia

    2009-03-01

    Full Text Available Abstract Background The induction of genomic deletions by physical- or chemical- agents is an easy and inexpensive means to generate a genome-saturating collection of mutations. Different mutagens can be selected to ensure a mutant collection with a range of deletion sizes. This would allow identification of mutations in single genes or, alternatively, a deleted group of genes that might collectively govern a trait (e.g., quantitative trait loci, QTL. However, deletion mutants have not been widely used in functional genomics, because the mutated genes are not tagged and therefore, difficult to identify. Here, we present a microarray-based approach to identify deleted genomic regions in rice mutants selected from a large collection generated by gamma ray or fast neutron treatment. Our study focuses not only on the utility of this method for forward genetics, but also its potential as a reverse genetics tool through accumulation of hybridization data for a collection of deletion mutants harboring multiple genetic lesions. Results We demonstrate that hybridization of labeled genomic DNA directly onto the Affymetrix Rice GeneChip® allows rapid localization of deleted regions in rice mutants. Deletions ranged in size from one gene model to ~500 kb and were predicted on all 12 rice chromosomes. The utility of the technique as a tool in forward genetics was demonstrated in combination with an allelic series of mutants to rapidly narrow the genomic region, and eventually identify a candidate gene responsible for a lesion mimic phenotype. Finally, the positions of mutations in 14 mutants were aligned onto the rice pseudomolecules in a user-friendly genome browser to allow for rapid identification of untagged mutations http://irfgc.irri.org/cgi-bin/gbrowse/IR64_deletion_mutants/. Conclusion We demonstrate the utility of oligonucleotide arrays to discover deleted genes in rice. The density and distribution of deletions suggests the feasibility of a

  6. Loss of function at RAE2, a previously unidentified EPFL, is required for awnlessness in cultivated Asian rice.

    Science.gov (United States)

    Bessho-Uehara, Kanako; Wang, Diane R; Furuta, Tomoyuki; Minami, Anzu; Nagai, Keisuke; Gamuyao, Rico; Asano, Kenji; Angeles-Shim, Rosalyn B; Shimizu, Yoshihiro; Ayano, Madoka; Komeda, Norio; Doi, Kazuyuki; Miura, Kotaro; Toda, Yosuke; Kinoshita, Toshinori; Okuda, Satohiro; Higashiyama, Tetsuya; Nomoto, Mika; Tada, Yasuomi; Shinohara, Hidefumi; Matsubayashi, Yoshikatsu; Greenberg, Anthony; Wu, Jianzhong; Yasui, Hideshi; Yoshimura, Atsushi; Mori, Hitoshi; McCouch, Susan R; Ashikari, Motoyuki

    2016-08-09

    Domestication of crops based on artificial selection has contributed numerous beneficial traits for agriculture. Wild characteristics such as red pericarp and seed shattering were lost in both Asian (Oryza sativa) and African (Oryza glaberrima) cultivated rice species as a result of human selection on common genes. Awnedness, in contrast, is a trait that has been lost in both cultivated species due to selection on different sets of genes. In a previous report, we revealed that at least three loci regulate awn development in rice; however, the molecular mechanism underlying awnlessness remains unknown. Here we isolate and characterize a previously unidentified EPIDERMAL PATTERNING FACTOR-LIKE (EPFL) family member named REGULATOR OF AWN ELONGATION 2 (RAE2) and identify one of its requisite processing enzymes, SUBTILISIN-LIKE PROTEASE 1 (SLP1). The RAE2 precursor is specifically cleaved by SLP1 in the rice spikelet, where the mature RAE2 peptide subsequently induces awn elongation. Analysis of RAE2 sequence diversity identified a highly variable GC-rich region harboring multiple independent mutations underlying protein-length variation that disrupt the function of the RAE2 protein and condition the awnless phenotype in Asian rice. Cultivated African rice, on the other hand, retained the functional RAE2 allele despite its awnless phenotype. Our findings illuminate the molecular function of RAE2 in awn development and shed light on the independent domestication histories of Asian and African cultivated rice.

  7. Realistic Simulation of Rice Plant

    Directory of Open Access Journals (Sweden)

    Wei-long DING

    2011-09-01

    Full Text Available The existing research results of virtual modeling of rice plant, however, is far from perfect compared to that of other crops due to its complex structure and growth process. Techniques to visually simulate the architecture of rice plant and its growth process are presented based on the analysis of the morphological characteristics at different stages. Firstly, the simulations of geometrical shape, the bending status and the structural distortion of rice leaves are conducted. Then, by using an improved model for bending deformation, the curved patterns of panicle axis and various types of panicle branches are generated, and the spatial shape of rice panicle is therefore created. Parametric L-system is employed to generate its topological structures, and finite-state automaton is adopted to describe the development of geometrical structures. Finally, the computer visualization of three-dimensional morphologies of rice plant at both organ and individual levels is achieved. The experimental results showed that the proposed methods of modeling the three-dimensional shapes of organs and simulating the growth of rice plant are feasible and effective, and the generated three-dimensional images are realistic.

  8. Increasing rice plant growth by Trichoderma sp.

    Science.gov (United States)

    Doni, Febri; Isahak, Anizan; Zain, Che Radziah Che Mohd; Sulaiman, Norela; Fathurahman, F.; Zain, Wan Nur Syazana Wan Mohd.; Kadhimi, Ahsan A.; Alhasnawi, Arshad Naji; Anhar, Azwir; Yusoff, Wan Mohtar Wan

    2016-11-01

    Trichoderma sp. is a plant growth promoting fungi in many crops. Initial observation on the ability to enhance rice germination and vigor have been reported. In this study, the effectiveness of a local isolate Trichoderma asprellum SL2 to enhance rice seedling growth was assessed experimentally under greenhouse condition using a completely randomized design. Results showed that inoculation of rice plants with Trichoderma asprellum SL2 significantly increase rice plants height, root length, wet weight, leaf number and biomass compared to untreated rice plants (control). The result of this study can serve as a reference for further work on the application of beneficial microorganisms to enhance rice production.

  9. Storage stability of flour-blasted brown rice

    Science.gov (United States)

    Brown rice was blasted with rice flour rather than sand in a sand blaster to make microscopic nicks and cuts so that water can easily penetrate into the brown rice endosperm and cook the rice in a shorter time. The flour-blasted American Basmati brown rice, long grain brown rice, and parboiled long...

  10. Study on the Long Term Effects of Radiation on Irradiated Manawthukha Rice Grain (Mahsuri-M)

    International Nuclear Information System (INIS)

    Aye Aye Mar; Aye Aye Mon; Hnin Hnin Than; Ba Han; Tin Tin; Myint U

    2008-03-01

    Radioactivity monitoring of first and second generations Manawthukha paddy grain before cultivations were carried out. It was found out that there were no induced activity. Therefore it can be concluded that similarly it will be the same for third generation rice. The second generation rice was obtained from cultivation and harvesting of first generation [(i) non-irradiated (control), (ii) gamma-irradiated, (iii) neutron-one hour irradiated, (iv) neutron one-day irradiated rice]. Agronomical characteristics of three different types of generation of rice were studied. Morphological characteristics studies such as plant height, leaf width and panicle length,there was no large variation between three generations of rice. Phenotypes were found to be stable. Yield improvement was calculated. Nutritional values of rice generation were studied. They were (i) element analysis by different methods (NAA, EDXRF and AAS), vitamin determination and protein percent determination. There was no distinctive difference between first, second and third generation rice. In element analysis, eleven elements such as Mg, Mn, Na, K, Cl, Al, Ca, Fe, Zn, P and Cu were observed by NAA, AAS and EDXRF methods. Vitamin content (B1, B2) and protein content were also studied. Determination of amylose content, gel consistency and gelatinization temperature were involved in grain quality study. There was no large variation in three generations. Surface texture of first, second and third generation Manawthukha rice were studied by Scanning Electron Microscope (SEM). It was observed that the change of texture from generation to generation tend to become more distinctive in third generation.

  11. The role of Bh4 in parallel evolution of hull colour in domesticated and weedy rice.

    Science.gov (United States)

    Vigueira, C C; Li, W; Olsen, K M

    2013-08-01

    The two independent domestication events in the genus Oryza that led to African and Asian rice offer an extremely useful system for studying the genetic basis of parallel evolution. This system is also characterized by parallel de-domestication events, with two genetically distinct weedy rice biotypes in the US derived from the Asian domesticate. One important trait that has been altered by rice domestication and de-domestication is hull colour. The wild progenitors of the two cultivated rice species have predominantly black-coloured hulls, as does one of the two U.S. weed biotypes; both cultivated species and one of the US weedy biotypes are characterized by straw-coloured hulls. Using Black hull 4 (Bh4) as a hull colour candidate gene, we examined DNA sequence variation at this locus to study the parallel evolution of hull colour variation in the domesticated and weedy rice system. We find that independent Bh4-coding mutations have arisen in African and Asian rice that are correlated with the straw hull phenotype, suggesting that the same gene is responsible for parallel trait evolution. For the U.S. weeds, Bh4 haplotype sequences support current hypotheses on the phylogenetic relationship between the two biotypes and domesticated Asian rice; straw hull weeds are most similar to indica crops, and black hull weeds are most similar to aus crops. Tests for selection indicate that Asian crops and straw hull weeds deviate from neutrality at this gene, suggesting possible selection on Bh4 during both rice domestication and de-domestication. © 2013 The Authors. Journal of Evolutionary Biology © 2013 European Society For Evolutionary Biology.

  12. Processing Conditions, Rice Properties, Health and Environment

    Directory of Open Access Journals (Sweden)

    Nobutaka Nakamura

    2011-06-01

    Full Text Available Rice is the staple food for nearly two-thirds of the world’s population. Food components and environmental load of rice depends on the rice form that is resulted by different processing conditions. Brown rice (BR, germinated brown rice (GBR and partially-milled rice (PMR contains more health beneficial food components compared to the well milled rice (WMR. Although the arsenic concentration in cooked rice depends on the cooking methods, parboiled rice (PBR seems to be relatively prone to arsenic contamination compared to that of untreated rice, if contaminated water is used for parboiling and cooking. A change in consumption patterns from PBR to untreated rice (non-parboiled, and WMR to PMR or BR may conserve about 43–54 million tons of rice and reduce the risk from arsenic contamination in the arsenic prone area. This study also reveals that a change in rice consumption patterns not only supply more food components but also reduces environmental loads. A switch in production and consumption patterns would improve food security where food grains are scarce, and provide more health beneficial food components, may prevent some diseases and ease the burden on the Earth. However, motivation and awareness of the environment and health, and even a nominal incentive may require for a method switching which may help in building a sustainable society.

  13. Elemental composition of Malawian rice.

    Science.gov (United States)

    Joy, Edward J M; Louise Ander, E; Broadley, Martin R; Young, Scott D; Chilimba, Allan D C; Hamilton, Elliott M; Watts, Michael J

    2017-08-01

    Widespread potential dietary deficiencies of calcium (Ca), iron (Fe), iodine (I), selenium (Se) and zinc (Zn) have been identified in Malawi. Several deficiencies are likely to be compounded by high phytic acid (PA) consumption. Rice (Oryza sativa) is commonly consumed in some Malawian populations, and its mineral micronutrient content is important for food security. The considerable irrigation requirements and flooded conditions of paddy soils can also introduce or mobilise potentially toxic elements including arsenic (As), cadmium (Cd) and lead (Pb). The aim of this study was to determine the mineral composition of rice sampled from farmers' fields and markets in Malawi. Rice was sampled from 18 extension planning areas across Malawi with 21 white (i.e. polished) and 33 brown samples collected. Elemental composition was determined by inductively coupled plasma-mass spectrometry (ICP-MS). Arsenic speciation was performed using high-performance liquid chromatography (HPLC)-ICP-MS. Concentration of PA was determined using a PA-total phosphorus assay. Median total concentrations (mg kg -1 , dry weight) of elements important for human nutrition in brown and white rice, respectively, were: Ca = 66.5 and 37.8; Cu = 3.65 and 2.49; Fe = 22.1 and 7.2; I = 0.006 and rice samples, respectively, median PA concentrations were 5438 and 1906 mg kg -1 , and median PA:Zn molar ratios were 29 and 13. Concentrations of potentially toxic elements (mg kg -1 , dry weight) in brown and white rice samples, respectively, were: As = 0.030 and 0.006; Cd  ≤ 0.002 and 0.006; Pb = 0.008 and 0.008. Approximately 95 % of As was found to be inorganic As, where this could be quantified. Malawian rice, like the more widely consumed staple grain maize, contains inadequate Ca, I, Se or Zn to meet dietary requirements. Biofortification strategies could significantly increase Se and Zn concentrations and require further investigation. Concentrations of Fe in rice grain varied

  14. 75 FR 56911 - Request for Public Comment on the United States Standards for Rough Rice, Brown Rice for...

    Science.gov (United States)

    2010-09-17

    ... for Rough Rice, Brown Rice for Processing, and Milled Rice AGENCY: Grain Inspection, Packers and... reviewing the United States Standards and grading procedures for Rough Rice, Brown Rice for Processing, and Milled Rice under the Agriculture Marketing Act of 1946 (AMA). Since the standards were last revised...

  15. Effects of White Rice, Brown Rice and Germinated Brown Rice on Antioxidant Status of Type 2 Diabetic Rats

    OpenAIRE

    Imam, Mustapha Umar; Musa, Siti Nor Asma; Azmi, Nur Hanisah; Ismail, Maznah

    2012-01-01

    Oxidative stress is implicated in the pathogenesis of diabetic complications, and can be increased by diet like white rice (WR). Though brown rice (BR) and germinated brown rice (GBR) have high antioxidant potentials as a result of their bioactive compounds, reports of their effects on oxidative stress-related conditions such as type 2 diabetes are lacking. We hypothesized therefore that if BR and GBR were to improve antioxidant status, they would be better for rice consuming populations inst...

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

    Science.gov (United States)

    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 different quality traits that make up the rice grain and obtain a full picture of rice quality demographics. Rice ...

  17. DNA methyltransferase expressions in Japanese rice fish (Oryzias latipes) embryogenesis is developmentally regulated and modulated by ethanol and 5-azacytidine

    Science.gov (United States)

    We aimed to investigate the impact of the epigenome in inducting fetal alcohol spectrum disorder (FASD) phenotypes in Japanese rice fish embryogenesis. One of the significant events in epigenome is DNA methylation which is catalyzed by DNA methyl transferase (DNMT) enzymes. We analyzed DNMT enzyme m...

  18. Modulation of DNA methylation machineries in japanese rice fish (Oryzias latipes) embryogenesis by ethanol and 5-azacytidine

    Science.gov (United States)

    As a sequel of our investigations on the impact of epigenome in inducing fetal alcohol spectrum disorder (FASD) phenotypes in Japanese rice fish, we investigated on several DNA methylation machinery genes including DNA methyl transferase 3ba (dnmt3ba) and methyl binding proteins (MBPs), namely, mbdl...

  19. Rice varieties in relation to rice bread quality.

    Science.gov (United States)

    Han, Hye Min; Cho, Jun Hyeon; Kang, Hang Won; Koh, Bong Kyung

    2012-05-01

    It is difficult to predict rice bread quality only from the amylose content (AC) or dough characteristics of new lines produced by rice breeding programmes. This study investigated the AC relative to bread baking quality of rice varieties developed in Korea, and identified specific characteristics that contribute to rice bread quality. Manmibyeo, Jinsumi, Seolgaeng and Hanareumbyeo were classified as low AC, YR24088 Acp9, Suweon517, Chenmaai and Goamibyeo as intermediate AC and Milyang261 as high AC. Suweon517, Milyang261 and Manmibyeo had a high water absorption index (WAI), while Goamibyeo, YR24088 Acp9, Jinsumi, Seolgaeng, Hanareumbyeo and Chenmaai had a low WAI. The gelatinisation enthalpy of flour varied from 9.2 J g(-1) in Milyang261 to 14.8 J g(-1) in YR24088 Acp9. After 7 days of storage the rate of flour retrogradation and crumb firmness were weakly correlated, with the exception of Jinsumi. Bread volumes of Jinsumi, Chenmaai, YR24088 Acp9 and Goamibyeo were comparable to that of wheat flour, but the rest were unsuited to bread making because of their low volume and hard crumb texture. Based on volume, texture and crumb firmness ratio, Chenmaai and Goamibyeo were the most appropriate varieties for making bread. An intermediate AC and low WAI were the primary indicators of rice bread flour quality. Copyright © 2011 Society of Chemical Industry.

  20. Deciphering the clinical effect of drugs through large-scale data integration

    DEFF Research Database (Denmark)

    Kjærulff, Sonny Kim

    . This work demonstrates the power of a strategy that uses clinical data mining in association with chemical biology in order to reduce the search space and aid identification of novel drug actions. The second article described in chapter 3 outlines a high confidence side-effect-drug interaction dataset. We...... demonstrates the importance of using high-confidence drug-side-effect data in deciphering the effect of small molecules in humans. In summary, this thesis presents computational systems chemical biology approaches that can help identify clinical effects of small molecules through large-scale data integration...

  1. Effect of Cold-Water Irrigation on Grain Quality Traits in japonica Rice Varieties from Yunnan Province, China

    Directory of Open Access Journals (Sweden)

    Guo-zhen ZHAO

    2009-09-01

    Full Text Available The response of grain quality traits to cold-water irrigation and its correlation with cold tolerance were studied in 11 japonica rice varieties from Yunnan Province, China. The results indicated that the response of grain quality traits to the cold-water stress varied with rice varieties and grain quality traits. Under the cold-water stress, grain width, chalky rice rate, whiteness, 1000-grain weight, brown rice rate, taste meter value, peak viscosity, trough viscosity, breakdown viscosity and final viscosity significantly decreased, whereas grain length-width ratio, head rice rate, alkali digestion value, protein content and setback viscosity markedly increased. However, the other traits such as grain length, amylose content, milled rice rate, peak viscosity time and pasting temperature were not significantly affected by the cold-water stress. Significant correlations were discovered between phenotypic acceptability and cold response indices of taste meter value, protein content, peak viscosity and breakdown viscosity. Therefore, it would be very important to improve the cold tolerance of Yunnan rice varieties in order to stabilize and improve their eating quality.

  2. Ricebase: a breeding and genetics platform for rice, integrating individual molecular markers, pedigrees and whole-genome-based data.

    Science.gov (United States)

    Edwards, J D; Baldo, A M; Mueller, L A

    2016-01-01

    Ricebase (http://ricebase.org) is an integrative genomic database for rice (Oryza sativa) with an emphasis on combining datasets in a way that maintains the key links between past and current genetic studies. Ricebase includes DNA sequence data, gene annotations, nucleotide variation data and molecular marker fragment size data. Rice research has benefited from early adoption and extensive use of simple sequence repeat (SSR) markers; however, the majority of rice SSR markers were developed prior to the latest rice pseudomolecule assembly. Interpretation of new research using SNPs in the context of literature citing SSRs requires a common coordinate system. A new pipeline, using a stepwise relaxation of stringency, was used to map SSR primers onto the latest rice pseudomolecule assembly. The SSR markers and experimentally assayed amplicon sizes are presented in a relational database with a web-based front end, and are available as a track loaded in a genome browser with links connecting the browser and database. The combined capabilities of Ricebase link genetic markers, genome context, allele states across rice germplasm and potentially user curated phenotypic interpretations as a community resource for genetic discovery and breeding in rice. Published by Oxford University Press 2016. This work is written by US Government employees and is in the public domain in the United States.

  3. Characterization of isolates of meloidogyne from rice-wheat production fields in Nepal.

    Science.gov (United States)

    Pokharel, Ramesh R; Abawi, George S; Zhang, Ning; Duxbury, John M; Smart, Christine D

    2007-09-01

    Thirty-three isolates of root-knot nematode were recovered from soil samples from rice-wheat fields in Nepal and maintained on rice cv. BR 11. The isolates were characterized using morphology, host range and DNA sequence analyses in order to ascertain their identity. Results indicated phenotypic similarity (juvenile measurements, perennial pattern, host range and gall shape) of the Nepalese isolates with Meloidogyne graminicola, with minor variations. The rice varieties LA 110 and Labelle were susceptible to all of the Nepalese isolates, but differences in the aggressiveness of the isolates were observed. Phylogenetic analyses based on the sequences of partial internal transcribed spacer (ITS) of the rRNA genes indicated that all Nepalese isolates formed a distinct clade with known isolates of M. graminicola with high bootstrap support. Furthermore, two groups were identified within the M. graminicola clade. No correlation between ITS haplotype and aggressiveness or host range was found among the tested isolates.

  4. Study on the improvement of dinitrogen fixation on rice-bacteria associative system

    International Nuclear Information System (INIS)

    Huang Yide; Zhu Hairong; Qiu Yuansheng; Iyama, S.; Fuji, T.; Hirota, Y.

    1991-01-01

    Inoculation of improved associative diazotrophs Klebsiella oxytoca NG 13 or Enterobacter cloacae E26 was performed in association with three varietes of rice (Oryza sativa L.), namely Indica type C544, Japonica type T65 and Harebare. These improved diazotrophs carried a nifA containing plasmid pMC73A derived from Klebsiella pneumoniae M5al. In pot experiments the rice seedlings were planted in non-sterilized soil and grown under flooded conditions in the green hours. By using 15 N dilution technique it has shown that inoculation of these improved bacterial strains (NG13/pMC73A or E26/pMC73A) stimulated the growth rate and increased the nitrogen content of rice plants in comparison with that of Nif - phenotype K.oxytoca NG1389 and E.cloacae E262. The nitrogen-fixing rate was 10-35% Ndfa after 120 days cultivation

  5. Genes controlling seed dormancy and pre-harvest sprouting in a rice-wheat-barley comparison

    DEFF Research Database (Denmark)

    Li, Chengdao; Ni, Peixiang; Francki, Michael

    2004-01-01

    Pre-harvest sprouting results in significant economic loss for the grain industry around the world. Lack of adequate seed dormancy is the major reason for pre-harvest sprouting in the field under wet weather conditions. Although this trait is governed by multiple genes it is also highly heritable....... A major QTL controlling both pre-harvest sprouting and seed dormancy has been identified on the long arm of barley chromosome 5H, and it explains over 70% of the phenotypic variation. Comparative genomics approaches among barley, wheat and rice were used to identify candidate gene(s) controlling seed...... dormancy and hence one aspect of pre-harvest sprouting. The barley seed dormancy/pre-harvest sprouting QTL was located in a region that showed good synteny with the terminal end of the long arm of rice chromosome 3. The rice DNA sequences were annotated and a gene encoding GA20-oxidase was identified...

  6. Mapping of QTLs for Leaf Malondialdehyde Content Associated with Stress Tolerance in Rice

    Directory of Open Access Journals (Sweden)

    Jing JIANG

    2009-03-01

    Full Text Available Malondialdehyde (MDA is the final product of lipid peroxidation, and MDA content can reflect the stress tolerance of plants. To map QTLs conditioning the MDA content in rice leaves, a recombinant inbred line (RIL population with 247 lines derived from an indica-indica cross Zhenshan 97B×Milyang 46, and a linkage map consisting of 207 DNA markers were used. The RIL population showed a transgressive segregation in the MDA content of rice leaves. Two QTLs for the MDA content in rice leaves were detected in the intervals RG532–RG811 and RG381–RG236 on chromosome 1, with the additive effects from maternal and paternal parents, accounting for 4.33% and 4.62% of phenotype variations, respectively.

  7. Deciphering energy

    International Nuclear Information System (INIS)

    Dessus, Benjamin

    2014-01-01

    In this book, the author aims at giving some explanations about the various terms regarding energy which are present in our everyday life, in speeches, in papers and magazines, on the air, in our energy bills, for instance: energy poverty, price of a barrel of oil, resources and proved reserves, intermittency and energy storage, fossil and renewable energies, and so on. In a first part, the author addresses issues ranging from the development needs of a society to the energy assessment of a country, i.e.: nature and quantity of needs in services provided by energy, analysis of the required quantity of energy products needed to satisfy these needs, stages between primary resources and service delivery, description of the French consumption of available final energy products (per product and per economic sector). In the second part, he addresses energy supply, energy sectors and environmental issues, thus focusing on the front end of the energy system, i.e. ways of production from primary energy resources to final energy products: main physical characteristics and description of the different fissile, fossil and renewable energies, description of the main sectors of production of final energy products (fuels, electricity, heat) with a specific attention to electricity. In this part, local, regional and global environmental issues related to the exploitation of these energy sectors are discussed: sources of atmospheric pollution related to energy, relationship between energy and global warming, role of the different greenhouse gases emitted by these sectors, and quantitative analysis of these emissions. The third part addresses the economy of energy systems. The author proposes a cost assessment method which can be used for the production analysis as well as the economic analysis of a specific energy product. He also described external costs and profits, and methods to take those hidden costs and profits into account. Other economic tools are discussed and compared which can be used to define and assess energy policies. The last part (Prospective and energy transition) recalls the evolution of concepts and concerns which have been at the origin of world and national energy prospective scenarios for the last thirty years and resulted in the emergence of the notion of energy transition with its different interpretations by the different actors of the energy sector

  8. A Rice Immunophilin Gene, OsFKBP16-3, Confers Tolerance to Environmental Stress in Arabidopsis and Rice

    Directory of Open Access Journals (Sweden)

    Jun Cheul Ahn

    2013-03-01

    Full Text Available The putative thylakoid lumen immunophilin, FKBP16-3, has not yet been characterized, although this protein is known to be regulated by thioredoxin and possesses a well-conserved CxxxC motif in photosynthetic organisms. Here, we characterized rice OsFKBP16-3 and examined the role of this gene in the regulation of abiotic stress in plants. FKBP16-3s are well conserved in eukaryotic photosynthetic organisms, including the presence of a unique disulfide-forming CxxxC motif in their N-terminal regions. OsFKBP16-3 was mainly expressed in rice leaf tissues and was upregulated by various abiotic stresses, including salt, drought, high light, hydrogen peroxide, heat and methyl viologen. The chloroplast localization of OsFKBP16-3-GFP was confirmed through the transient expression of OsFKBP16-3 in Nicotiana benthamiana leaves. Transgenic Arabidopsis and transgenic rice plants that constitutively expressed OsFKBP16-3 exhibited increased tolerance to salinity, drought and oxidative stresses, but showed no change in growth or phenotype, compared with vector control plants, when grown under non-stressed conditions. This is the first report to demonstrate the potential role of FKBP16-3 in the environmental stress response, which may be regulated by a redox relay process in the thylakoid lumen, suggesting that artificial regulation of FKBP16-3 expression is a candidate for stress-tolerant crop breeding.

  9. A Non-destructive and Continuous Measurement of Gelatinization of Rice in Rice Cooking Process

    OpenAIRE

    Hagura, Yoshio; Suzuki, Kanichi

    2002-01-01

    A non-destructive and continuous method to measure gelatinization of rice samples in a rice-water system during rice cooking process was examined. An aluminum pot and a lid of a rice cooker were used as two electrode plates, and changes in dielectric properties (capacitance : C, and dielectric dissipation factor : tan δ) of the samples in the rice cooking process were measured by a capacitance meter. Differential scanning calorimetry (DSC) was used to measure gelatinization enthalpy and to de...

  10. Effect of Rice bran on the Quality of Rice Flour Breads (Gluten-free)

    OpenAIRE

    仲上, 晴世; 矢部, えん; Haruyo, Nakagami; En, Yabe

    2016-01-01

    Over recent years progress has been made in the development of substitute foods for allergy patients. One such is rice flour bread. However, typically rice flour bread uses polysaccharide thickener in substitution for the gluten in wheat. Most polysaccharide thickeners are of dietary fiber origin, and the nutritive value is poor. Therefore, in this study, I made rice flour bread adding rice bran in place of polysaccharide thickener. Various nutrients are included in rice bran, including vitam...

  11. FLUORIDE LEVELS IN COMMERCIALLY AVAILABLE RICE IN ...

    African Journals Online (AJOL)

    Preferred Customer

    2013-05-05

    May 5, 2013 ... Rice is one of the commonly consumed cereals for more than half of the ... also used as flour, for making rice wine, as ingredient for beer and liquor, ... Fluoride is a necessary element to human health, and a moderate amount of fluoride intake ... For Ethiopian red rice (ERR) Fogera was selected to collect.

  12. Impact of bio-processing on rice

    Directory of Open Access Journals (Sweden)

    ANCA NICOLAU

    2011-07-01

    Full Text Available The usual way of preparing rice is boiling, thermal process that gives it a lower digestibility as compared to instantiation, extrusion or expandation. Having in view this fact, the possibility to biotechnologically improve the boiled rice digestibility was investigated in a laboratory study. In this respect, boiled rice wassolid state fermented using a strain of Saccharomycopsis fibuligera, an amylase producing yeast originating from ragi. Fermented rice was then analyzed from the point of view of its content in easily assimilable sugars, protein, amino-acids, phosphorus and vitamins from B group. Biochemical analyses revealed that the fermented rice has a ten times higher content of reducing sugars than boiled rice, due to starch hydrolysis, while chromatographic studies proved that the fermented rice contains glucose, maltose, maltotriose and maltotetrose that are easily assimilable carbohydrates.Fermented rice has a protein content that is two times higher than that of boiled rice because it contains the yeast biomass, and is enriched in vitamins from B group (B1, B2, and B6 that are synthesized by the yeast. Inorganic phosphorus present in rice doubles its concentration in fermented rice, which means thatphosphorus bioavailability is increased.The sensorial profile of boiled rice is also improved by fermentation.This study proves the possibility to have a processing method which is relatively cheap, practical and of which the resulting product has good nutritive qualities and does not pose safety problems due to pure culture utilization as starter.

  13. PICTORIAL INTERLUDES Flake-shaped rice bodies

    African Journals Online (AJOL)

    removing the rice bodies and the bursa.3. In summary: rice bodies can occur without underlying systemic disorder, have different shapes and sizes, and have specific signal characteristics on. MRI that allow discrimination from synovial chondromatosis. 1. Cheung HS, Ryan LM, Kozin F, McCarty DJ. Synovial origins of rice ...

  14. New market opportunities for rice grains

    Science.gov (United States)

    Breeding efforts for rice have been focusing on increasing yield and improving quality (milling yield and grain quality), while maintaining cooked rice sensory properties to meet consumer preferences. These breeding targets will no doubt continue as the main foci for the rice industry. However, the ...

  15. Arsenic in rice: A cause for concern

    DEFF Research Database (Denmark)

    Hojsak, Iva; Braegger, Christian; Bronsky, Jiri

    2015-01-01

    Inorganic arsenic intake is likely to affect long-term health. High concentrations are found in some rice-based foods and drinks widely used in infants and young children. In order to reduce exposure we recommend avoidance of rice drinks for infants and young children. For all rice products, stri...

  16. Consumer preference mapping for rice product concepts

    NARCIS (Netherlands)

    Suwannaporn, P.; Linnemann, A.R.; Chaveesuk, R.

    2008-01-01

    Purpose - Rice consumption per capita in many Asian countries is decreasing constantly, but American and European citizens are eating more rice nowadays. A preference study among consumers was carried out with the aim of determining new rice product characteristics in order to support export of Thai

  17. Asian wild rice is a hybrid swarm with extensive gene flow and feralization from domesticated rice.

    Science.gov (United States)

    Wang, Hongru; Vieira, Filipe G; Crawford, Jacob E; Chu, Chengcai; Nielsen, Rasmus

    2017-06-01

    The domestication history of rice remains controversial, with multiple studies reaching different conclusions regarding its origin(s). These studies have generally assumed that populations of living wild rice, O. rufipogon , are descendants of the ancestral population that gave rise to domesticated rice, but relatively little attention has been paid to the origins and history of wild rice itself. Here, we investigate the genetic ancestry of wild rice by analyzing a diverse panel of rice genomes consisting of 203 domesticated and 435 wild rice accessions. We show that most modern wild rice is heavily admixed with domesticated rice through both pollen- and seed-mediated gene flow. In fact, much presumed wild rice may simply represent different stages of feralized domesticated rice. In line with this hypothesis, many presumed wild rice varieties show remnants of the effects of selective sweeps in previously identified domestication genes, as well as evidence of recent selection in flowering genes possibly associated with the feralization process. Furthermore, there is a distinct geographical pattern of gene flow from aus , indica , and japonica varieties into colocated wild rice. We also show that admixture from aus and indica is more recent than gene flow from japonica , possibly consistent with an earlier spread of japonica varieties. We argue that wild rice populations should be considered a hybrid swarm, connected to domesticated rice by continuous and extensive gene flow. © 2017 Wang et al.; Published by Cold Spring Harbor Laboratory Press.

  18. Effects of Extraction Methods on Phytochemicals of Rice Bran Oils Produced from Colored Rice.

    Science.gov (United States)

    Mingyai, Sukanya; Srikaeo, Khongsak; Kettawan, Aikkarach; Singanusong, Riantong; Nakagawa, Kiyotaka; Kimura, Fumiko; Ito, Junya

    2018-02-01

    Rice bran oil (RBO) especially from colored rice is rich in phytochemicals and has become popular in food, cosmetic, nutraceutical and pharmaceutical applications owing to its offering health benefits. This study determined the contents of phytochemicals including oryzanols, phytosterols, tocopherols (Toc) and tocotrienols (T3) in RBOs extracted using different methods namely cold-press extraction (CPE), solvent extraction (SE) and supercritical CO 2 extraction (SC-CO 2 ). Two colored rice, Red Jasmine rice (RJM, red rice) and Hom-nin rice (HN, black rice), were studied in comparison with the popular Thai fragrant rice Khao Dawk Mali 105 (KDML 105, white rice). RBOs were found to be the rich source of oryzanols, phytosterols, Toc and T3. Rice varieties had a greater effect on the phytochemicals concentrations than extraction methods. HN rice showed the significantly highest concentration of all phytochemicals, followed by RJM and KDML 105 rice, indicating that colored rice contained high concentration of phytochemicals in the oil than non-colored rice. The RBO samples extracted by the CPE method had a greater concentration of the phytochemicals than those extracted by the SC-CO 2 and SE methods, respectively. In terms of phytochemical contents, HN rice extracted using CPE method was found to be the best.

  19. COPD: Definition and Phenotypes

    DEFF Research Database (Denmark)

    Vestbo, J.

    2014-01-01

    particles or gases. Exacerbations and comorbidities contribute to the overall severity in individual patients. The evolution of this definition and the diagnostic criteria currently in use are discussed. COPD is increasingly divided in subgroups or phenotypes based on specific features and association...

  20. Phenotypic Resistance to Antibiotics

    Directory of Open Access Journals (Sweden)

    Jose L. Martinez

    2013-04-01

    Full Text Available The development of antibiotic resistance is usually associated with genetic changes, either to the acquisition of resistance genes, or to mutations in elements relevant for the activity of the antibiotic. However, in some situations resistance can be achieved without any genetic alteration; this is called phenotypic resistance. Non-inherited resistance is associated to specific processes such as growth in biofilms, a stationary growth phase or persistence. These situations might occur during infection but they are not usually considered in classical susceptibility tests at the clinical microbiology laboratories. Recent work has also shown that the susceptibility to antibiotics is highly dependent on the bacterial metabolism and that global metabolic regulators can modulate this phenotype. This modulation includes situations in which bacteria can be more resistant or more susceptible to antibiotics. Understanding these processes will thus help in establishing novel therapeutic approaches based on the actual susceptibility shown by bacteria during infection, which might differ from that determined in the laboratory. In this review, we discuss different examples of phenotypic resistance and the mechanisms that regulate the crosstalk between bacterial metabolism and the susceptibility to antibiotics. Finally, information on strategies currently under development for diminishing the phenotypic resistance to antibiotics of bacterial pathogens is presented.

  1. Different types of inks having certain medicolegal importance: Deciphering the faded and physically erased handwriting

    Directory of Open Access Journals (Sweden)

    Manal Abd-ElAziz Abd-ElZaher

    2014-06-01

    Full Text Available Disappearing ink is a type of ink which could be used to forge documents as it will fade away without any trace within 40–65 h. Erasable ink is another type of ink easily removed by certain rubbers incorporated in each pen. Both types of inks were applied separately on different types of papers (checks, standard white foolscap, and plain white A4 paper. For vanishing ink, it was observed visually in the first 6 h and then every 6 h. It was found that the vanishing ink disappeared completely within 2 h on checks, 36 h on standard white foolscap paper, and 40 h on plain white A4 paper. For erasable ink, the written strokes were manipulated manually using the incorporated eraser. Deciphering the faded writing failed by the conventional methods, but oblique light can reveal the indentation marks. The faded writing became visible when treated with weak alkaline (NaOH solutions. Erasable ink was deciphered with the aid of infra-red radiation combined with VSC-6000 as clear white traces against red fluorescence. It was concluded that the use of a weak (NaOH solution is an effective method for revealing the faded writing, and the infra-red illumination is also effective.

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

    Science.gov (United States)

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

    2014-02-01

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

  3. Isotope studies on rice fertilization

    International Nuclear Information System (INIS)

    1978-01-01

    The aim of the report is to provide practical information on the efficient utilization of nitrogen fertilizers in rice production. Results obtained from field investigations during the years 1970 to 1974 in ten countries (Bangladesh, Burma, Indonesia, Republic of Korea, Sri Lanka, Taiwan, Thailand, Vietnam, India, Philippines), using 15 N-labelled nitrogen fertilizers (ammonium sulfate, urea) are given. The experiments, which were conducted both during the dry and wet seasons, included comparison of varieties, effect of placement, source and time of nitrogen fertilizer application on the yield and quality of rice. The data from the project is presented in table form. In most of the experiments, the addition of nitrogen increased the rice grain yield. The role of soil nitrogen vs. fertilizer nitrogen is compared, and it is concluded that the physiological growth stage at which fertilizer-derived nitrogen is absorbed is of great importance

  4. Iron biofortification of Myanmar rice

    Directory of Open Access Journals (Sweden)

    May Sann Aung

    2013-05-01

    Full Text Available Iron (Fe deficiency causes elevates human mortality rates, especially in developing countries. In Myanmar, the prevalence of Fe-deficient anemia in children and pregnant women are 75% and 71%, respectively. Myanmar people have one of the highest per capita rice consumption rates globally. Consequently, production of Fe-biofortified rice would likely contribute to solving the Fe-deficiency problem in this human population. To produce Fe-biofortified Myanmar rice by transgenic methods, we first analyzed callus induction and regeneration efficiencies in 15 varieties that are presently popular because of their high yields and/or qualities. Callus formation and regeneration efficiency in each variety was strongly influenced by types of culture media containing a range of 2,4-dichlorophenoxyacetic acid concentrations. The Paw San Yin variety, which has a high Fe content in polished seeds, performed well in callus induction and regeneration trials. Thus, we transformed this variety using a gene expression cassette that enhanced Fe transport within rice plants through overexpression of the nicotianamine synthase gene HvNAS1, Fe flow to the endosperm through the Fe(II-nicotianamine transporter gene OsYSL2, and Fe accumulation in endosperm by the Fe storage protein gene SoyferH2. A line with a transgene insertion was successfully obtained. Enhanced expressions of the introduced genes OsYSL2, HvNAS1, and SoyferH2 occurred in immature T2 seeds. The transformants accumulated 3.4-fold higher Fe concentrations, and also 1.3-fold higher zinc concentrations in T2 polished seeds compared to levels in non-transgenic rice. This Fe-biofortified rice has the potential to reduce Fe-deficiency anemia in millions of Myanmar people without changing food habits and without introducing additional costs.

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

    Science.gov (United States)

    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.

  6. Comparison of Effect of Brassinosteroid and Gibberellin Biosynthesis Inhibitors on Growth of Rice Seedlings

    OpenAIRE

    Matusmoto, Tadashi; Yamada, Kazuhiro; Yoshizawa, Yuko; Oh, Keimei

    2016-01-01

    Brassinosteroid (BR) and gibberellin (GA) are two predominant plant hormones that regulate plant cell elongation. Mutants disrupt the biosynthesis of these hormones and display different degrees of dwarf phenotypes in rice. Although the role of each plant hormone in promoting the longitudinal growth of plants has been extensively studied using genetic methods, their relationship is still poorly understood. In this study, we used two specific inhibitors targeting BR and GA biosynthesis to inve...

  7. Dolce Vita in the Rice Paddy - Characterization of weedy rice groups in Northern Italy and investigation of their evolutionary origins

    OpenAIRE

    Grimm, Annabelle

    2014-01-01

    The thesis deals with the topic of the invasive rice form called weedy rice or red rice. Studies focused on the geographical area of Italy. Different populations of weedy rice in Italy were genetically characterized. The evolutionary origins of different weedy rice groups were investigated using molecular, morphological and physiological methods. Invasion of wild rice as well as de-domestication of cultivars could be identified as evolutionary sources of weedy rice in Northern Italy.

  8. Similar traits, different genes? Examining convergent evolution in related weedy rice populations.

    Science.gov (United States)

    Thurber, Carrie S; Jia, Melissa H; Jia, Yulin; Caicedo, Ana L

    2013-02-01

    Convergent phenotypic evolution may or may not be associated with convergent genotypic evolution. Agricultural weeds have repeatedly been selected for weed-adaptive traits such as rapid growth, increased seed dispersal and dormancy, thus providing an ideal system for the study of convergent evolution. Here, we identify QTL underlying weedy traits and compare their genetic architecture to assess the potential for convergent genetic evolution in two distinct populations of weedy rice. F(2) offspring from crosses between an indica cultivar and two individuals from genetically differentiated U.S. weedy rice populations were used to map QTL for four quantitative (heading date, seed shattering, plant height and growth rate) and two qualitative traits. We identified QTL on nine of the twelve rice chromosomes, yet most QTL locations do not overlap between the two populations. Shared QTL among weed groups were only seen for heading date, a trait for which weedy groups have diverged from their cultivated ancestors and from each other. Sharing of some QTL with wild rice also suggests a possible role in weed evolution for genes under selection during domestication. The lack of overlapping QTL for the remaining traits suggests that, despite a close evolutionary relationship, weedy rice groups have adapted to the same agricultural environment through different genetic mechanisms. © 2012 Blackwell Publishing Ltd.

  9. Objective evaluation of whiteness of cooked rice and rice cakes using a portable spectrophotometer.

    Science.gov (United States)

    Goto, Hajime; Asanome, Noriyuki; Suzuki, Keitaro; Sano, Tomoyoshi; Saito, Hiroshi; Abe, Yohei; Chuba, Masaru; Nishio, Takeshi

    2014-03-01

    The whiteness of cooked rice and rice cakes was evaluated using a portable spectrophotometer with a whiteness index (WI). Also, by using boiled rice for measurement of Mido values by Mido Meter, it was possible to infer the whiteness of cooked rice without rice cooking. In the analysis of varietal differences of cooked rice, 'Tsuyahime', 'Koshihikari' and 'Koshinokaori' showed high whiteness, while 'Satonoyuki' had inferior whiteness. The whiteness of rice cakes made from 'Koyukimochi' and 'Dewanomochi' was higher than the whiteness of those made from 'Himenomochi' and 'Koganemochi'. While there was a significant correlation (r = 0.84) between WI values and whiteness scores of cooked rice by the sensory test, no correlation was detected between the whiteness scores and Mido values, indicating that the values obtained by a spectrophotometer differ from those obtained by a Mido Meter. Thus, a spectrophotometer may be a novel device for measurement of rice eating quality.

  10. RiceAtlas, a spatial database of global rice calendars and production.

    Science.gov (United States)

    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.

  11. Labelling of rice seedlings and rice plants with 32P

    International Nuclear Information System (INIS)

    Achmad Nasroh, K.

    1989-01-01

    Labelling of rice seedlings and rice plants with 32 P. Labelled rice seedlings can be used to tag insect pests that feed on. Radioactivity counting of 32 P in the endosperm and in the shoot of rice seeds that soaked for 72 hours in KH 2 32 PO 4 solution of 1 μCi/ml were 29,300 and 9,500 cpm respectively. When these labelled seedlings were grown in unlabelled medium the radioactivity in the shoot increased. It was due to the 32 P that was translocated to the shoot from the endosperm. The 32 P translocation reached maximum about one week after the seedling were grown in the unlabelled medium. Labelled seedlings could also be produced by growing 5, 10 and 15 days old seedlings hydroponically in Kimura B solution containing 32 P. Ten days after growing, the radioactivity concentration of the seedlings stem reached about 115,000; 85,000 and 170,000 cpm/mg dry weight for the 5, 10 and 15 days old seedlings respectively. For the implementation of this method, 20 ml labelled Kimura B was needed for labelling of one seedling. The seedlings should be prepared in tap water. During the growth the 32 P in the labelled seedlings was distributed throughout the plant, so that new leaves and tillers became also radioactive. (author). 5 refs

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

    Directory of Open Access Journals (Sweden)

    Manoj Kumar Yadav

    Full Text Available 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.

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

    Science.gov (United States)

    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.

  14. Sustainable rice production in Malaysia beyond 2000

    International Nuclear Information System (INIS)

    Nashriyah Mat; Ho Nai Kin; Ismail Sahid; Ahyaudin Ali; Lum Keng Yeang; Mashhor Mansor

    2002-01-01

    This book is a compendium of works carried out by various institutions on subjects related to sustainable rice production. The institutions comprise Department of Agriculture, Malaysian Agricultural Research and Development Institute, Malaysian Institute for Nuclear Technology Research, Muda Agricultural Development Authority, Universiti Kebangsaan Malaysia, Universiti Putra Malaysia, Universiti Sains Malaysia, International Islamic University of Malaysia and the Agrochemical Company Mosanto. Integrated Biodiversity Management parallel with the Integrated Weed / Pest / Disease Management, rice-fish farming networking, agrochemical residue monitoring in rice and marine ecosystems, and application of biotechnology in rice productivity are taken as the future direction towards achieving sustainable rice production beyond 2000. Challenges from social and technical agroecosystem constraints, agricultural input management and maintenance of agroecosystem biodiversity are highlighted. It is imperative that the challenges are surmounted to attain the target that would be reflected by tangible rice output of 10 t/ha, and at the same time maintaining the well-being of rice-farmers. (Author)

  15. Transcriptional Network Analysis Reveals Drought Resistance Mechanisms of AP2/ERF Transgenic Rice

    Directory of Open Access Journals (Sweden)

    Hongryul Ahn

    2017-06-01

    Full Text Available This study was designed to investigate at the molecular level how a transgenic version of rice “Nipponbare” obtained a drought-resistant phenotype. Using multi-omics sequencing data, we compared wild-type rice (WT and a transgenic version (erf71 that had obtained a drought-resistant phenotype by overexpressing OsERF71, a member of the AP2/ERF transcription factor (TF family. A comprehensive bioinformatics analysis pipeline, including TF networks and a cascade tree, was developed for the analysis of multi-omics data. The results of the analysis showed that the presence of OsERF71 at the source of the network controlled global gene expression levels in a specific manner to make erf71 survive longer than WT. Our analysis of the time-series transcriptome data suggests that erf71 diverted more energy to survival-critical mechanisms related to translation, oxidative response, and DNA replication, while further suppressing energy-consuming mechanisms, such as photosynthesis. To support this hypothesis further, we measured the net photosynthesis level under physiological conditions, which confirmed the further suppression of photosynthesis in erf71. In summary, our work presents a comprehensive snapshot of transcriptional modification in transgenic rice and shows how this induced the plants to acquire a drought-resistant phenotype.

  16. Integrated physiological, biochemical and molecular analysis identifies important traits and mechanisms associated with differential response of rice genotypes to elevated temperature

    Directory of Open Access Journals (Sweden)

    Boghireddy eSailaja

    2015-11-01

    Full Text Available In changing climate, heat stress caused by high temperature poses a serious threat to rice cultivation. A multiple organizational analysis at physiological, biochemical and molecular level is required to fully understand the impact of elevated temperature in rice. This study was aimed at deciphering the elevated temperature response in eleven popular and mega rice cultivars widely grown in India. Physiological and biochemical traits specifically membrane thermostability (MTS, antioxidants, and photosynthesis were studied at vegetative and reproductive phases which were used to establish a correlation with grain yield under stress. Several useful traits in different genotypes were identified which will be important resource to develop high temperature tolerant rice cultivars. Interestingly, Nagina22 emerged as best performer in terms of yield as well as expression of physiological and biochemical traits at elevated temperature. It showed lesser relative injury, lesser reduction in chlorophyll content, increased super oxide dismutase, catalase and peroxidase activity, lesser reduction in net photosynthetic rate (PN, high transpiration rate (E and other photosynthetic/ fluorescence parameters contributing to least reduction in spikelet fertility and grain yield at elevated temperature. Further, expression of 14 genes including heat shock transcription factors and heat shock proteins was analyzed in Nagina22 (tolerant and Vandana (susceptible at flowering phase, strengthening the fact that N22 performs better at molecular level also during elevated temperature. This study shows that elevated temperature response is complex and involves multiple biological processes which are needed to be characterized to address the challenges of future climate extreme conditions.

  17. The mitochondrial gene orfH79 plays a critical role in impairing both male gametophyte development and root growth in CMS-Honglian rice.

    Science.gov (United States)

    Peng, Xiaojue; Wang, Kun; Hu, Chaofeng; Zhu, Youlin; Wang, Ting; Yang, Jing; Tong, Jiping; Li, Shaoqing; Zhu, Yingguo

    2010-06-24

    Cytoplasmic male sterility (CMS) has often been associated with abnormal mitochondrial open reading frames. The mitochondrial gene orfH79 is a candidate gene for causing the CMS trait in CMS-Honglian (CMS-HL) rice. However, whether the orfH79 expression can actually induce CMS in rice remains unclear. Western blot analysis revealed that the ORFH79 protein is mainly present in mitochondria of CMS-HL rice and is absent in the fertile line. To investigate the function of ORFH79 protein in mitochondria, this gene was fused to a mitochondrial transit peptide sequence and used to transform wild type rice, where its expression induced the gametophytic male sterile phenotype. In addition, excessive accumulation of reactive oxygen species (ROS) in the microspore, a reduced ATP/ADP ratio, decreased mitochondrial membrane potential and a lower respiration rate in the transgenic plants were found to be similar to those in CMS-HL rice. Moreover, retarded growth of primary and lateral roots accompanied by abnormal accumulation of ROS in the root tip was observed in both transgenic rice and CMS-HL rice (YTA). These results suggest that the expression of orfH79 in mitochondria impairs mitochondrial function, which affects the development of both male gametophytes and the roots of CMS-HL rice.

  18. Genetic Control of a Transition from Black to Straw-White Seed Hull in Rice Domestication1[C][W][OA

    Science.gov (United States)

    Zhu, Bo-Feng; Si, Lizhen; Wang, Zixuan; Jingjie Zhu, Yan Zhou; Shangguan, Yingying; Lu, Danfeng; Fan, Danlin; Li, Canyang; Lin, Hongxuan; Qian, Qian; Sang, Tao; Zhou, Bo; Minobe, Yuzo; Han, Bin

    2011-01-01

    The genetic mechanism involved in a transition from the black-colored seed hull of the ancestral wild rice (Oryza rufipogon and Oryza nivara) to the straw-white seed hull of cultivated rice (Oryza sativa) during grain ripening remains unknown. We report that the black hull of O. rufipogon was controlled by the Black hull4 (Bh4) gene, which was fine-mapped to an 8.8-kb region on rice chromosome 4 using a cross between O. rufipogon W1943 (black hull) and O. sativa indica cv Guangluai 4 (straw-white hull). Bh4 encodes an amino acid transporter. A 22-bp deletion within exon 3 of the bh4 variant disrupted the Bh4 function, leading to the straw-white hull in cultivated rice. Transgenic study indicated that Bh4 could restore the black pigment on hulls in cv Guangluai 4 and Kasalath. Bh4 sequence alignment of all taxa with the outgroup Oryza barthii showed that the wild rice maintained comparable levels of nucleotide diversity that were about 70 times higher than those in the cultivated rice. The results from the maximum likelihood Hudson-Kreitman-Aguade test suggested that the significant reduction in nucleotide diversity in rice cultivars could be caused by artificial selection. We propose that the straw-white hull was selected as an important visual phenotype of nonshattered grains during rice domestication. PMID:21263038

  19. Transgene Flow from Glufosinate-Resistant Rice to Improved and Weedy Rice in China

    Directory of Open Access Journals (Sweden)

    Yong-liang LU

    2014-09-01

    Full Text Available The development of transgenic rice with novel traits in China can increase rice productivity, but transgene flow to improved or weedy rice has become a major concern. We aimed to evaluate the potential maximum frequencies of transgene flow from glufosinate-resistant rice to improved rice cultivars and weedy rice. Treatments were arranged in randomized complete blocks with three replicates. Experiments were conducted between 2009 and 2010 at the Center for Environmental Safety Supervision and Inspection for Genetically Modified Plants, China National Rice Research Institute, Hangzhou, China. Glufosinate-resistant japonica rice 99-1 was the pollen donor. The pollen recipients were two inbred japonica rice (Chunjiang 016 and Xiushui 09, two inbred indica rice (Zhongzu 14 and Zhongzao 22, two indica hybrid rice (Zhongzheyou 1 and Guodao 1, and one weedy indica rice (Taizhou weedy rice. The offspring of recipients were planted in the field and sprayed with a commercial dose of glufosinate. Leaf tissues of survivors were analyzed by polymerase chain reaction to detect the presence of the transgene. The frequency of gene flow ranged from 0 to 0.488%. In 2009, the order of gene flow frequency was as follows: weedy rice > Chunjiang 016 > Xiushui 09 and Zhongzu 14 > Guodao 1, Zhongzheyou 1 and Zhongzao 22. Gene flow frequencies were generally higher in 2009 than in 2010, but did not differ significantly among rice materials. Gene flow frequency was the highest in weedy rice followed by the inbred japonica rice. The risk of gene flow differed significantly between years and year-to-year variance could mask risk differences among pollen recipients. Gene flow was generally lesser in taller pollen recipients than in shorter ones, but plant height only accounted for about 30% of variation in gene flow. When flowering synchrony was maximized, as in this study, low frequencies of gene flow occurred from herbicide-resistant japonica rice to other cultivars and

  20. Evaluation of tall rice mutant

    International Nuclear Information System (INIS)

    Hakim, L.; Azam, M.A.; Miah, A.J.; Mansur, M.A.; Akanda, H.R.

    1989-01-01

    One tall mutant (Mut NS1) of rice variety Nizersail was put to multilocation on-farm trial. It showed improvement over the parent in respect of by earlier maturity and higher grain yield at all locations and thus it appears as an improved mutant of Nizersail. (author). 6 refs

  1. ART Or AGR: Deciphering Which Reserve Program is Best Suited for Today’s Total Force Structure

    Science.gov (United States)

    2016-02-01

    AIR COMMAND AND STAFF COLLEGE AIR UNIVERSITY ART OR AGR: DECIPHERING WHICH RESERVE PROGRAM IS BEST SUITED FOR TODAY’S TOTAL FORCE STRUCTURE...4 ART Program...time workforce, which are the ART and AGR programs, by comparing each and highlighting the differences, advantages and disadvantages they present to

  2. Deciphering the complete mitochondrial genome and phylogeny of the extinct cave bear in the Paleolithic painted cave of Chauvet

    NARCIS (Netherlands)

    Bon, Céline; Caudy, Nicolas; De Dieuleveult, Maud; Fosse, Philippe; Philippe, Michel; Maksud, Frédéric; Beraud-Colomb, Éliane; Bouzaid, Eric; Kefi, Rym; Laugier, Christelle; Rousseau, Bernard; Casane, Didier; Van Der Plicht, Johannes; Elalouf, Jean-Marc

    2008-01-01

    Retrieving a large amount of genetic information from extinct species was demonstrated feasible, but complete mitochondrial genome sequences have only been deciphered for the moa, a bird that became extinct a few hundred years ago, and for Pleistocene species, such as the woolly mammoth and the

  3. Induced Mutations in Thai Rice

    International Nuclear Information System (INIS)

    Klakhaeng, Kanchana

    2014-01-01

    Rice is the primary source of food for more than half of the world's population. It benefits greatly from technological inputs in the area of breeding such as induced mutation. Induced mutation can produce mutants with significant improvement in plant type, maturity, yields and protein ratio when compared to the parent. These improved traits enable the mutants to fit into farming systems with either shorter or longer growing seasons. Three induced mutant rice varieties, including RD6, RD10 and RD15, are well accepted by farmers and consumers in Thailand. RD6 and RD15 were aromatic, photosensitive varieties which were derived from KDML105 by acute irradiation of 20 and 15 kilorad gamma ray, respectively. After induced mutation, pedigree selection was applied. RD6 showed drought tolerance and also good grain quality including softness and good aroma with a higher average yield than the famous glutinous variety, San-Pah-Tong. Additionally, it was resistant to blast and brown spot diseases with an average yield of 4.19 tons/ha. RD15 showed drought tolerance and resistance to brown spot disease with the highest yield of 3.5 tons/ha. These two mutant varieties are currently the most famous aromatic rice varieties in Thailand. On the other hand, RD10 is a glutinous, photoperiod insensitive rice variety which was derived from RD1 by irradiation of 1 kilorad fast neutrons. RD10 showed good grain quality such as softness and stickiness with the yield of 4.25 tons/ha. As an on-going project, recommended rice varieties were irradiated with electron beam for anaerobic germination ability, submergence tolerance, stagnant-flood tolerance and also internode elongation.

  4. [Effects of fish on field resource utilization and rice growth in rice-fish coculture].

    Science.gov (United States)

    Zhang, Jian; Hu, Liang Liang; Ren, Wei Zheng; Guo, Liang; Wu, Min Fang; Tang, Jian Jun; Chen, Xin

    2017-01-01

    Rice field can provide habitat for fish and other aquatic animals. Rice-fish coculture can increase rice yield and simultaneously reduce the use of chemicals through reducing rice pest occurrence and nutrient complementary use. However, how fish uses food sources (e.g. phytoplankton, weeds, duckweed, macro-algal and snail) from rice field, and whether the nutrients releasing from those food sources due to fish transforming can improve rice growth are still unknown. Here, we conducted two field experiments to address these questions. One was to investigate the pattern of fish activity in the field using the method of video recording. The other was to examine the utilization of field resources by fish using stable isotope technology. Rice growth and rice yield were also exa-mined. Results showed that fish tended to be more active and significantly expanded the activity range in the rice-fish coculture compared to fish monoculture (fish not living together with rice plants). The contributions of 3 potential aquatic organisms (duckweed, phytoplankton and snail) to fish dietary were 22.7%, 34.8% and 30.0% respectively under rice-fish coculture without feed. Under the treatment with feed, however, the contributions of these 3 aquatic organisms to the fish die-tary were 8.9%, 5.9% and 1.6% respectively. The feed contribution was 71.0%. Rice-fish coculture significantly increased the nitrogen concentration in rice leaves, prolonged tillering stage by 10-12 days and increased rice spike rate and yield. The results suggested that raising fish in paddy field may transform the nutrients contained in field resources to bioavailable for rice plants through fish feeding activity, which can improve rice growth and rice yield.

  5. [Nitrogen cycling in rice-duck mutual ecosystem during double cropping rice growth season].

    Science.gov (United States)

    Zhang, Fan; Chen, Yuan-Quan; Sui, Peng; Gao, Wang-Sheng

    2012-01-01

    Raising duck in paddy rice field is an evolution of Chinese traditional agriculture. In May-October 2010, a field experiment was conducted in a double cropping rice region of Hunan Province, South-central China to study the nitrogen (N) cycling in rice-duck mutual ecosystem during early rice and late rice growth periods, taking a conventional paddy rice field as the control. Input-output analysis method was adopted. The N output in the early rice-duck mutual ecosystem was 239.5 kg x hm(-2), in which, 12.77 kg x hm(-2) were from ducks, and the N output in the late rice-duck mutual ecosystem was 338.7 kg x hm(-2), in which, 23.35 kg x hm(-2) were from ducks. At the present N input level, there existed soil N deficit during the growth seasons of both early rice and late rice. The N input from duck sub-system was mainly from the feed N, and the cycling rate of the duck feces N recycled within the system was 2.5% during early rice growth season and 3.5% during late rice growth season. After late rice harvested, the soil N sequestration was 178.6 kg x hm(-2).

  6. A comparative study of competitiveness between different genotypes of weedy rice (Oryza sativa) and cultivated rice.

    Science.gov (United States)

    Dai, Lei; Dai, Weimin; Song, Xiaoling; Lu, Baorong; Qiang, Sheng

    2014-01-01

    Competition from weedy rice can cause serious yield losses to cultivated rice. However, key traits that facilitate competitiveness are still not well understood. To explore the mechanisms behind the strong growth and competitive ability, replacement series experiments were established with six genotypes of weedy rice from different regions and one cultivated rice cultivar. (1) Weedy rice from southern China had the greatest impact on growth and yield of cultivated rice throughout the entire growing season. Weedy rice from the northeast was very competitive during the early vegetative stage while the competitive effects of eastern weedy rice were more detrimental at later crop-growth stages. (2) As the proportion of weedy rice increased, plant height, tillers, above-ground biomass, and yield of cultivated rice significantly declined; the crop always being at disadvantage regardless of proportion. (3) Weedy biotypes with greater diversity as estimated by their Shannon indexes were more detrimental to the growth and yield of cultivated rice. Geographic origin (latitude) of weedy rice biotype, its mixture proportion under competition with the crop and its genetic diversity are determinant factors of the outcome of competition and the associated decline in the rice crop yield. © 2013 Society of Chemical Industry. © 2013 Society of Chemical Industry.

  7. Metabolomics to Decipher the Chemical Defense of Cereals against Fusarium graminearum and Deoxynivalenol Accumulation

    Directory of Open Access Journals (Sweden)

    Léa Gauthier

    2015-10-01

    Full Text Available Fusarium graminearum is the causal agent of Fusarium head blight (FHB and Gibberella ear rot (GER, two devastating diseases of wheat, barley, and maize. Furthermore, F. graminearum species can produce type B trichothecene mycotoxins that accumulate in grains. Use of FHB and GER resistant cultivars is one of the most promising strategies to reduce damage induced by F. graminearum. Combined with genetic approaches, metabolomic ones can provide powerful opportunities for plant breeding through the identification of resistant biomarker metabolites which have the advantage of integrating the genetic background and the influence of the environment. In the past decade, several metabolomics attempts have been made to decipher the chemical defense that cereals employ to counteract F. graminearum. By covering the major classes of metabolites that have been highlighted and addressing their potential role, this review demonstrates the complex and integrated network of events that cereals can orchestrate to resist to F. graminearum.

  8. Spectral Barcoding of Quantum Dots: Deciphering Structural Motifs from the Excitonic Spectra

    International Nuclear Information System (INIS)

    Mlinar, V.; Zunger, A.

    2009-01-01

    Self-assembled semiconductor quantum dots (QDs) show in high-resolution single-dot spectra a multitude of sharp lines, resembling a barcode, due to various neutral and charged exciton complexes. Here we propose the 'spectral barcoding' method that deciphers structural motifs of dots by using such barcode as input to an artificial-intelligence learning system. Thus, we invert the common practice of deducing spectra from structure by deducing structure from spectra. This approach (i) lays the foundation for building a much needed structure-spectra understanding for large nanostructures and (ii) can guide future design of desired optical features of QDs by controlling during growth only those structural motifs that decide given optical features.

  9. Deciphering molecular circuits from genetic variation underlying transcriptional responsiveness to stimuli.

    Science.gov (United States)

    Gat-Viks, Irit; Chevrier, Nicolas; Wilentzik, Roni; Eisenhaure, Thomas; Raychowdhury, Raktima; Steuerman, Yael; Shalek, Alex K; Hacohen, Nir; Amit, Ido; Regev, Aviv

    2013-04-01

    Individual genetic variation affects gene responsiveness to stimuli, often by influencing complex molecular circuits. Here we combine genomic and intermediate-scale transcriptional profiling with computational methods to identify variants that affect the responsiveness of genes to stimuli (responsiveness quantitative trait loci or reQTLs) and to position these variants in molecular circuit diagrams. We apply this approach to study variation in transcriptional responsiveness to pathogen components in dendritic cells from recombinant inbred mouse strains. We identify reQTLs that correlate with particular stimuli and position them in known pathways. For example, in response to a virus-like stimulus, a trans-acting variant responds as an activator of the antiviral response; using RNA interference, we identify Rgs16 as the likely causal gene. Our approach charts an experimental and analytic path to decipher the mechanisms underlying genetic variation in circuits that control responses to stimuli.

  10. DECIPHERING THE FINEST IMPRINT OF GLACIAL EROSION: OBJECTIVE ANALYSIS OF STRIAE PATTERNS ON BEDROCK

    Directory of Open Access Journals (Sweden)

    Piet Stroeven

    2011-05-01

    Full Text Available The aim of this study is to compare the efficiency of different mathematical and statistical geometrical methods applied to characterise the orientation distribution of striae on bedrock for deciphering the finest imprint of glacial erosion. The involved methods include automatic image analysis techniques of Fast Fourier Transform (FFT, and the experimental investigations by means of Saltikov's directed secants analysis (rose of intersection densities, applied to digital and analogue images of the striae pattern, respectively. In addition, the experimental data were compared with the modelling results made on the basis of Underwood's concept of linear systems in a plane. The experimental and modelling approaches in the framework of stereology yield consistent results. These results reveal that stereological methods allow a reliable and efficient delineation of different families of glacial striae from a complex record imprinted in bedrock.

  11. Metabolomics to Decipher the Chemical Defense of Cereals against Fusarium graminearum and Deoxynivalenol Accumulation

    Science.gov (United States)

    Gauthier, Léa; Atanasova-Penichon, Vessela; Chéreau, Sylvain; Richard-Forget, Florence

    2015-01-01

    Fusarium graminearum is the causal agent of Fusarium head blight (FHB) and Gibberella ear rot (GER), two devastating diseases of wheat, barley, and maize. Furthermore, F. graminearum species can produce type B trichothecene mycotoxins that accumulate in grains. Use of FHB and GER resistant cultivars is one of the most promising strategies to reduce damage induced by F. graminearum. Combined with genetic approaches, metabolomic ones can provide powerful opportunities for plant breeding through the identification of resistant biomarker metabolites which have the advantage of integrating the genetic background and the influence of the environment. In the past decade, several metabolomics attempts have been made to decipher the chemical defense that cereals employ to counteract F. graminearum. By covering the major classes of metabolites that have been highlighted and addressing their potential role, this review demonstrates the complex and integrated network of events that cereals can orchestrate to resist to F. graminearum. PMID:26492237

  12. Four Versions of the Christus by the Massys: Deciphering the Meaning of the Letters

    Directory of Open Access Journals (Sweden)

    Vicente Jara Vera

    2017-02-01

    Full Text Available The Flemish painters Quentin Massys and his son Jan Massys appear to be the authors of four works with a very similar motif, the bust of Jesus Christ. These canvasses can be found in different locations today: the Prado Museum in Madrid (Spain, the RKD Netherlands Institute for Art History of The Hague (Netherlands, the Kunstmuseum Winterthur (Switzerland, and another one in a private collection. Written on the edge of the robe around the neck, these canvasses display a series of Hebrew or pseudo-Hebrew letters. We offer the complete solution deciphered, until today incomplete, for three of them, with a very similar letter sequence. Finally, we resolve completely one of the canvasses, which, until today, had no known solution.

  13. Rice production in relation to soil quality under different rice-based cropping systems

    Science.gov (United States)

    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

  14. Aerobic rice mechanization: techniques for crop establishment

    Science.gov (United States)

    Khusairy, K. M.; Ayob, H.; Chan, C. S.; Fauzi, M. I. Mohamed; Mohamad Fakhrul, Z. O.; Shahril Shah, G. S. M.; Azlan, O.; Rasad, M. A.; Hashim, A. M.; Arshad, Z.; E, E. Ibrahim; Saifulizan, M. N.

    2015-12-01

    Rice being the staple food crops, hundreds of land races in it makes the diversity of rice crops. Aerobic rice production was introduced which requires much less water input to safeguard and sustain the rice production and conserve water due to decreasing water resources, climatic changes and competition from urban and industrial users. Mechanization system plays an important role for the success of aerobic rice cultivation. All farming activities for aerobic rice production are run on aerobic soil conditions. Row seeder mechanization system is developed to replace conventional seeding technique on the aerobic rice field. It is targeted for small and the large scale aerobic rice farmers. The aero - seeder machine is used for the small scale aerobic rice field, while the accord - seeder is used for the large scale aerobic rice field. The use of this mechanization machine can eliminate the tedious and inaccurate seeding operations reduce labour costs and increases work rate. The machine is easy to operate and it can increase crop establishment rate. It reduce missing hill, increasing planting and crop with high yield can be produce. This machine is designed for low costs maintenance and it is easy to dismantle and assemble during maintenance and it is safe to be used.

  15. Rice agroecosystem and the maintenance of biodiversity

    International Nuclear Information System (INIS)

    Ahyaudin Ali

    2002-01-01

    Rice fields are a special type of wetland. They are shallow, constantly disturbed and experience extremes in temperature and dissolved oxygen content. They receive nutrients in the form of fertilizers during rice cultivation. Rice fields; support a variety of flora and fauna that have adapted and adjusted themselves to the extreme conditions. Since rice fields also support populations of wild fish, rice?fish integration should be done in order to optimize land use and provide supplementary income to farmers. Rice?fish farming encourages farmers to judiciously apply pesticides and herbicides in their fields thus helping to control excessive and unwarranted use of these chemicals. Rice fields also support many migratory and nonmigratory bird species and provides habitat for small mammals. Thus the rice agroecosystem helps to maintain aquatic biodiversity. The Muda rice agroecosystem consists of a troika of interconnected ecosystems. The troika consisting of reservoirs, the connecting network of canals and the rice fields; should be investigated further. This data is needed for informed decision-making concerning development and management of the system so that productivity and biodiversity can be maintained and sustained. (Author)

  16. Deciphering Egyptian Hieroglyphs: Towards a New Strategy for Navigation in Museums

    Directory of Open Access Journals (Sweden)

    Jaime Duque-Domingo

    2017-03-01

    Full Text Available This work presents a novel strategy to decipher fragments of Egyptian cartouches identifying the hieroglyphs of which they are composed. A cartouche is a drawing, usually inside an oval, that encloses a group of hieroglyphs representing the name of a monarch. Aiming to identify these drawings, the proposed method is based on several techniques frequently used in computer vision and consists of three main stages: first, a picture of the cartouche is taken as input and its contour is localized. In the second stage, each hieroglyph is individually extracted and identified. Finally, the cartouche is interpreted: the sequence of the hieroglyphs is established according to a previously generated benchmark. This sequence corresponds to the name of the king. Although this method was initially conceived to deal with both high and low relief writing in stone, it can be also applied to painted hieroglyphs. This approach is not affected by variable lighting conditions, or the intensity and the completeness of the objects. This proposal has been tested on images obtained from the Abydos King List and other Egyptian monuments and archaeological excavations. The promising results give new possibilities to recognize hieroglyphs, opening a new way to decipher longer texts and inscriptions, being particularly useful in museums and Egyptian environments. Additionally, devices used for acquiring visual information from cartouches (i.e., smartphones, can be part of a navigation system for museums where users are located in indoor environments by means of the combination of WiFi Positioning Systems (WPS and depth cameras, as unveiled at the end of the document.

  17. Deciphering Late-Pleistocence landscape evolution: linking proxies by combining pedo-stratigraphy and luminescence dating

    Science.gov (United States)

    Kreutzer, Sebastian; Meszner, Sascha; Faust, Dominik; Fuchs, Markus

    2014-05-01

    Interpreting former landscape evolution asks for understanding the processes that sculpt such landforms by means of deciphering complex systems. For reconstructing terrestrial Quaternary environments based on loess archives this might be considered, at least, as a three step process: (1) Identifying valuable records in appropriate morphological positions in a previously defined research area, (2) analysing the profiles by field work and laboratory methods and finally (3) linking the previously considered pseudo-isolated systems to set up a comprehensive picture. Especially the first and the last step might bring some pitfalls, as it is tempting to specify single records as pseudo-isolated, closed systems. They might be, with regard to their preservation in their specific morphological position, but in fact they are part of a complex, open system. Between 2008 and 2013, Late-Pleistocene loess archives in Saxony have been intensively investigated by field and laboratory methods. Linking pedo- and luminescence dating based chronostratigraphies, a composite profile for the entire Saxonian Loess Region has been established. With this, at least, two-fold approach we tried to avoid misinterpretations that might appear when focussing on one standard profile in an open morphological system. Our contribution focuses on this multi-proxy approach to decipher the Late-Pleistocene landscape evolution in the Saxonian Loess Region. Highlighting the challenges and advantages of combining different methods, we believe that (1) this multi-proxy approach is without alternative, (2) the combination of different profiles may simplify the more complex reality, but it may be a useful generalisation to understand and reveal the stratigraphical significance of the landscape evolution in this region.

  18. Assessment of Rice Associated Bacterial Ability to Enhance Rice Seed Germination and Rice Growth Promotion

    Directory of Open Access Journals (Sweden)

    R. Gholamalizadeh

    2017-08-01

    Full Text Available ABSTRACT The application of beneficial bacteria has recently been used for sustainable agriculture. In current research, 71 bacterial isolates were obtained from rice plant and the rhizosphere soil of different paddy fields in Guilan province, Iran. After primitive investigation, 40 bacteria with typical predominant characteristics were selected. By PCR-RFLP of their 16S r-DNA gene, 8 Operational Taxonomic Units (OTUs totally consisted of 33 isolates were obtained. From all of them, 8 isolates were selected for rice seed germination experiment, then, effective isolates were used for pot experiment to evaluate their ability for promoting rice growth. All of them were able to increase rice growth and yield, but in different potential. These tested isolates were identified as Alcaligenes faecalis (DEp8, O1R4, Pantoea ananatis (AEn1, Bacillus vietnamensis (MR5, Bacillus idriensis (MR2 and Stenotrophomonas maltophilia by partial sequencing of their 16S r-DNA gene. Among them, AEn1 and MR5 produced indole-3- acetic acid (IAA in larger amounts than the other isolates and the isolates AEn1 and O1R4 were able to solubilize phosphate in higher amounts. According to the results obtained, it can be concluded that AEn1, O1R4 and MR5 can be considered as bacterial inoculants to use as alternatives for chemical fertilizers.

  19. Genome-Wide Association Study for Traits Related to Plant and Grain Morphology, and Root Architecture in Temperate Rice Accessions.

    Science.gov (United States)

    Biscarini, Filippo; Cozzi, Paolo; Casella, Laura; Riccardi, Paolo; Vattari, Alessandra; Orasen, Gabriele; Perrini, Rosaria; Tacconi, Gianni; Tondelli, Alessandro; Biselli, Chiara; Cattivelli, Luigi; Spindel, Jennifer; McCouch, Susan; Abbruscato, Pamela; Valé, Giampiero; Piffanelli, Pietro; Greco, Raffaella

    2016-01-01

    In this study we carried out a genome-wide association analysis for plant and grain morphology and root architecture in a unique panel of temperate rice accessions adapted to European pedo-climatic conditions. This is the first study to assess the association of selected phenotypic traits to specific genomic regions in the narrow genetic pool of temperate japonica. A set of 391 rice accessions were GBS-genotyped yielding-after data editing-57000 polymorphic and informative SNPS, among which 54% were in genic regions. In total, 42 significant genotype-phenotype associations were detected: 21 for plant morphology traits, 11 for grain quality traits, 10 for root architecture traits. The FDR of detected associations ranged from 3 · 10-7 to 0.92 (median: 0.25). In most cases, the significant detected associations co-localised with QTLs and candidate genes controlling the phenotypic variation of single or multiple traits. The most significant associations were those for flag leaf width on chromosome 4 (FDR = 3 · 10-7) and for plant height on chromosome 6 (FDR = 0.011). We demonstrate the effectiveness and resolution of the developed platform for high-throughput phenotyping, genotyping and GWAS in detecting major QTLs for relevant traits in rice. We identified strong associations that may be used for selection in temperate irrigated rice breeding: e.g. associations for flag leaf width, plant height, root volume and length, grain length, grain width and their ratio. Our findings pave the way to successfully exploit the narrow genetic pool of European temperate rice and to pinpoint the most relevant genetic components contributing to the adaptability and high yield of this germplasm. The generated data could be of direct use in genomic-assisted breeding strategies.

  20. Genome-Wide Association Study for Traits Related to Plant and Grain Morphology, and Root Architecture in Temperate Rice Accessions.

    Directory of Open Access Journals (Sweden)

    Filippo Biscarini

    Full Text Available In this study we carried out a genome-wide association analysis for plant and grain morphology and root architecture in a unique panel of temperate rice accessions adapted to European pedo-climatic conditions. This is the first study to assess the association of selected phenotypic traits to specific genomic regions in the narrow genetic pool of temperate japonica. A set of 391 rice accessions were GBS-genotyped yielding-after data editing-57000 polymorphic and informative SNPS, among which 54% were in genic regions.In total, 42 significant genotype-phenotype associations were detected: 21 for plant morphology traits, 11 for grain quality traits, 10 for root architecture traits. The FDR of detected associations ranged from 3 · 10-7 to 0.92 (median: 0.25. In most cases, the significant detected associations co-localised with QTLs and candidate genes controlling the phenotypic variation of single or multiple traits. The most significant associations were those for flag leaf width on chromosome 4 (FDR = 3 · 10-7 and for plant height on chromosome 6 (FDR = 0.011.We demonstrate the effectiveness and resolution of the developed platform for high-throughput phenotyping, genotyping and GWAS in detecting major QTLs for relevant traits in rice. We identified strong associations that may be used for selection in temperate irrigated rice breeding: e.g. associations for flag leaf width, plant height, root volume and length, grain length, grain width and their ratio. Our findings pave the way to successfully exploit the narrow genetic pool of European temperate rice and to pinpoint the most relevant genetic components contributing to the adaptability and high yield of this germplasm. The generated data could be of direct use in genomic-assisted breeding strategies.

  1. Correlation exploration of metabolic and genomic diversity in rice

    Directory of Open Access Journals (Sweden)

    Shinozaki Kazuo

    2009-12-01

    Full Text Available Abstract Background It is essential to elucidate the relationship between metabolic and genomic diversity to understand the genetic regulatory networks associated with the changing metabolo-phenotype among natural variation and/or populations. Recent innovations in metabolomics technologies allow us to grasp the comprehensive features of the metabolome. Metabolite quantitative trait analysis is a key approach for the identification of genetic loci involved in metabolite variation using segregated populations. Although several attempts have been made to find correlative relationships between genetic and metabolic diversity among natural populations in various organisms, it is still unclear whether it is possible to discover such correlations between each metabolite and the polymorphisms found at each chromosomal location. To assess the correlative relationship between the metabolic and genomic diversity found in rice accessions, we compared the distance matrices for these two "omics" patterns in the rice accessions. Results We selected 18 accessions from the world rice collection based on their population structure. To determine the genomic diversity of the rice genome, we genotyped 128 restriction fragment length polymorphism (RFLP markers to calculate the genetic distance among the accessions. To identify the variations in the metabolic fingerprint, a soluble extract from the seed grain of each accession was analyzed with one dimensional 1H-nuclear magnetic resonance (NMR. We found no correlation between global metabolic diversity and the phylogenetic relationships among the rice accessions (rs = 0.14 by analyzing the distance matrices (calculated from the pattern of the metabolic fingerprint in the 4.29- to 0.71-ppm 1H chemical shift and the genetic distance on the basis of the RFLP markers. However, local correlation analysis between the distance matrices (derived from each 0.04-ppm integral region of the 1H chemical shift against genetic

  2. Tier I Rice Model - Version 1.0 - Guidance for Estimating Pesticide Concentrations in Rice Paddies

    Science.gov (United States)

    Describes a Tier I Rice Model (Version 1.0) for estimating surface water exposure from the use of pesticides in rice paddies. The concentration calculated can be used for aquatic ecological risk and drinking water exposure assessments.

  3. significance of rice sheath photosynthesis: yield determination by c ...

    African Journals Online (AJOL)

    ACSS

    1State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha 410125, P.R. China. 2School of ... for contribution rates of sheath photosynthesis to economical yield. ..... related processes during ripening in rice plants.

  4. Perceived factors limiting rice production in Pategi Local ...

    African Journals Online (AJOL)

    user

    perceived limiting factors in rice production include lack of rice processing ... This production increase has not been enough to meet the consumption demand of ... of Kwara State, Nigeria seeks to determine some of the factors limiting rice ...

  5. potential for biological control of rice yellow mottle virus vectors

    African Journals Online (AJOL)

    Administrator

    Insect pests and disease infestations are the primary constraints in rice (Oryza sativa) production .... Asia. Of all the rice diseases, the one caused by the rice yellow mottle virus (RYMV), first reported ..... yellow mottle virus in Central Africa.

  6. Effect of Interplanting with Zero Tillage and Straw Manure on Rice Growth and Rice Quality

    Directory of Open Access Journals (Sweden)

    Shi-ping LIU

    2007-09-01

    Full Text Available The interplanting with zero-tillage of rice, i.e. direct sowing rice 10–20 days before wheat harvesting, and remaining about 30-cm high stubble after cutting wheat or rice with no tillage, is a new cultivation technology in wheat-rice rotation system. To study the effects of interplanting with zero tillage and straw manure on rice growth and quality, an experiment was conducted in a wheat-rotation rotation system. Four treatments, i.e. ZIS (Zero-tillage, straw manure and rice interplanting, ZI (Zero-tillage, no straw manure and rice interplanting, PTS (Plowing tillage, straw manure and rice transplanting, and PT (Plowing tillage, no straw manure and rice transplanting, were used. ZIS reduced plant height, leaf area per plant and the biomass of rice plants, but the biomass accumulation of rice at the late stage was quicker than that under conventional transplanting cultivation. In the first year (2002, there was no significant difference in rice yield among the four treatments. However, rice yield decreased in interplanting with zero-tillage in the second year (2003. Compared with the transplanting treatments, the number of filled grains per panicle decreased but 1000-grain weight increased in interplanting with zero-tillage, which were the main factors resulting in higher yield. Interplanting with zero-tillage improved the milling and appearance qualities of rice. The rates of milled and head rice increased while chalky rice rate and chalkiness decreased in interplanting with zero-tillage. Zero-tillage and interplanting also affected rice nutritional and cooking qualities. In 2002, ZIS showed raised protein content, decreased amylose content, softer gel consistency, resulting in improved rice quality. In 2003, zero-tillage and interplanting decreased protein content and showed similar amylose content as compared with transplanting treatments. Moreover, protein content in PTS was obviously increased in comparison with the other three treatments

  7. Assessing the impacts of climate change on rice yields in the main rice areas of China

    Energy Technology Data Exchange (ETDEWEB)

    Yao, Fengmei [College of Earth Sciences, The Graduate University of the Chinese Academy of Sciences, 19A, Yuquan Road, Beijing, 100049 (China); Xu, Yinglong; Lin, Erda [Agricultural Environment and Sustainable Development Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081 (China); Yokozawa, Masayuki [National Institute for Agro-environmental Sciences, Tsukuba 305-8604 (Japan); Zhang, Jiahua [Chinese Academy of Meteorological Sciences, Beijing, 100081 (China)

    2007-02-15

    This paper assesses the impact of climate change on irrigated rice yield using B2 climate change scenario from the Regional Climate Model (RCM) and CERES-rice model during 2071--2090. Eight typical rice stations ranging in latitude, longitude, and elevation that are located in the main rice ecological zones of China are selected for impact assessment. First, Crop Estimation through Resource and Environment Synthesis (CERES)-rice model is validated using farm experiment data in selected stations. The simulated results represent satisfactorily the trend of flowering duration and yields. The deviation of simulation within {+-} 10% of observed flowering duration and {+-} 15% of observed yield. Second, the errors of the outputs of RCM due to the difference of topography between station point and grid point is corrected. The corrected output of the RCM used for simulating rice flowering duration and yield is more reliable than the not corrected. Without CO2 direct effect on crop, the results from the assessment explore that B2 climate change scenario would have a negative impact on rice yield at most rice stations and have little impacts at Fuzhou and Kunming. To find the change of inter-annual rice yield, a preliminary assessment is made based on comparative cumulative probability at low and high yield and the coefficient variable of yield between the B2 scenario and baseline. Without the CO2 direct effect on rice yield, the result indicates that frequency for low yield would increase and it reverses for high yield, and the variance for rice yield would increase. It is concluded that high frequency at low yield and high variances of rice yield could pose a threat to rice yield at most selected stations in the main rice areas of China. With the CO2 direct effect on rice yield, rice yield increase in all selected stations.

  8. Assessing the impacts of climate change on rice yields in the main rice areas of China

    International Nuclear Information System (INIS)

    Yao, Fengmei; Xu, Yinglong; Lin, Erda; Yokozawa, Masayuki; Zhang, Jiahua

    2007-01-01

    This paper assesses the impact of climate change on irrigated rice yield using B2 climate change scenario from the Regional Climate Model (RCM) and CERES-rice model during 2071--2090. Eight typical rice stations ranging in latitude, longitude, and elevation that are located in the main rice ecological zones of China are selected for impact assessment. First, Crop Estimation through Resource and Environment Synthesis (CERES)-rice model is validated using farm experiment data in selected stations. The simulated results represent satisfactorily the trend of flowering duration and yields. The deviation of simulation within ± 10% of observed flowering duration and ± 15% of observed yield. Second, the errors of the outputs of RCM due to the difference of topography between station point and grid point is corrected. The corrected output of the RCM used for simulating rice flowering duration and yield is more reliable than the not corrected. Without CO2 direct effect on crop, the results from the assessment explore that B2 climate change scenario would have a negative impact on rice yield at most rice stations and have little impacts at Fuzhou and Kunming. To find the change of inter-annual rice yield, a preliminary assessment is made based on comparative cumulative probability at low and high yield and the coefficient variable of yield between the B2 scenario and baseline. Without the CO2 direct effect on rice yield, the result indicates that frequency for low yield would increase and it reverses for high yield, and the variance for rice yield would increase. It is concluded that high frequency at low yield and high variances of rice yield could pose a threat to rice yield at most selected stations in the main rice areas of China. With the CO2 direct effect on rice yield, rice yield increase in all selected stations

  9. Introgression of Blast Resistance Genes (Putative Pi-b and Pi-kh) into Elite Rice Cultivar MR219 through Marker-Assisted Selection

    Science.gov (United States)

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

    2015-01-01

    Blast is the most common biotic stress leading to the reduction of rice yield in many rice-growing areas of the world, including Malaysia. Improvement of blast resistance of rice varieties cultivated in blast endemic areas is one of the most important objectives of rice breeding programs. In this study, the marker-assisted backcrossing strategy was applied to improve the blast resistance of the most popular Malaysian rice variety MR219 by introgressing blast resistance genes from the Pongsu Seribu 2 variety. Two blast resistance genes, Pi-b and Pi-kh, were pyramided into MR219. Foreground selection coupled with stringent phenotypic selection identified 15 plants homozygous for the Pi-b and Pi-kh genes, and background selection revealed more than 95% genome recovery of MR219 in advanced blast resistant lines. Phenotypic screening against blast disease indicated that advanced homozygous blast resistant lines were strongly resistant against pathotype P7.2 in the blast disease endemic areas. The morphological, yield, grain quality, and yield-contributing characteristics were significantly similar to those of MR219. The newly developed blast resistant improved lines will retain the high adoptability of MR219 by farmers. The present results will also play an important role in sustaining the rice production of Malaysia. PMID:26734013

  10. Rice Seedling Substrate Produced by Coal Gangue

    Directory of Open Access Journals (Sweden)

    SHAO Yu-fei

    2017-10-01

    Full Text Available Peats are the mostly used material in making rice seedling substrate. However, mining peats could cause environmental problems. In order to reduce or replace peats in rice seedling substrate industry, this paper studied suitable way to configure rice seedling. The coal gangue was used to experiment cultivating rice. Four rice seeding experiments were carried out based on physical and chemical properties of materials attributes. The results showed:(1 Coal gangue was feasible for rice seedling; (2 The maximum adding amount of coal gangue was 80%(volume ratio though the coal gangue need to be activated; (3 In the case of no activated treatment only 38%(volume ratio of coal gangue could be added to the substrate.

  11. Improvement of rice starch by gamma irradiation

    International Nuclear Information System (INIS)

    Duan Zhiying; Wu Dianxing; Shen Shengquan; Han Juanying; Xia Yingwu

    2003-01-01

    Three types of rice cultivars, Indica, Japonica and hybrid rice, with similar intermediate apparent amylose content (AAC) as well as early Indica rice cultivars with different amounts of AAC were selected for studying the effects of gamma irradiation on starch viscosity, physico-chemical properties and starch granule structure. Four major parameters of RVA profile, peak viscosity (PKV), hot paste viscosity (HPV), cool paste viscosity (CPV), setback viscosity (SBV) and consistence viscosity (CSV) were considerably decreased with increasing dose levels. Gamma irradiation reduced the amylose contents in the cultivars with low AAC, intermediate AAC, and glutinous rice, but had no effects on the high AAC cultivar. No visible changes in alkali spreading value (ASV) were detected after irradiation, but the peak time (PKT) were reduced with the dose level. Gel consistency (GC) were significantly increased in the tested cultivars, especially in the high AAC Indica rice, suggesting that it is promising to use gamma irradiation to improve eating and cooking quality of rice

  12. RiceAtlas, a spatial database of global rice calendars and production

    NARCIS (Netherlands)

    Laborte, Alice G.; Gutierrez, Mary Anne; Balanza, Jane Girly; Saito, Kazuki; Zwart, Sander; Boschetti, Mirco; Murty, M. V.R.; Villano, Lorena; Aunario, Jorrel Khalil; Reinke, Russell; Koo, Jawoo; Hijmans, Robert J.; Nelson, Andrew

    2017-01-01

    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

  13. DETERMINATION OF SPATIAL INTEGRATION AND SUBSTITUTION OF FOREIGN RICE FOR LOCAL RICE IN GHANA

    Directory of Open Access Journals (Sweden)

    Philip Kofi ADOM

    2014-11-01

    Full Text Available This study tested for spatial integration in the rice market and the substitution of imported rice for local rice in Ghana. It is established that the markets for domestic imported rice are well-integrated, but not complete. The imperfect spatial integration of domestic foreign rice markets implies that the market provides opportunities for arbitrage. Price leadership roles are found to be determined by the kind of sub-inter-regional-trade network defined. However, in all, the Accra market emerged as a dominant market leader in the domestic foreign rice market. There is evidence of significant regional substitution of foreign rice for local rice in the long run, but the result is mixed in the short run. The result that local rice is not a perfect substitute for imported rice implies that price disincentive measures such as increasing the import tariffs on foreign rice will only produce a mild effect on increasing the producer price faced by local rice farmers, but aggravate the burden on households’ budget.

  14. Soil to rice transfer factors for 210Pb: a study on rice grown in India

    International Nuclear Information System (INIS)

    Karunakara, N.; Rao, Chetan; Ujwal, P.; Yashodhara, I.; Sudeep Kumara; Somashekarappa, H.M.; Bhaskara Shenoy, K.; Ravi, P.M.

    2013-01-01

    India is the second largest producer of rice (Oryza sativa L.) in the world and rice is the essential component of the diet for the majority of the population of India. However, detailed studies aimed at evaluation of radionuclide transfer factors (F v ) for rice grown in India are almost non-existent. This paper presents soil to rice transfer factors for 210 Pb for rice grown in natural field conditions on the West Coast of India. A rice field was developed very close to the Kaiga nuclear power plant for the field studies. For a comparative study of radionuclide transfer factors, rice samples were also collected from the rice fields of nearby villages. The soil to un-hulled rice grain 210 Pb varied in the range <1.2 x10 -2 to 8.1 x 10 -1 with a mean of 1.4 x 10 -1 . The mean values of un-hulled grain to white rice processing retention factors (F r ) was 0.03 for 210 Pb. Using the processing retention factors the soil to white rice transfer factor was estimated and found to have the mean value of 4.2 x 10 -3 . The study has shown that the transfer of 210 Pb was retained in the root and its transfer to above ground organs of rice plant is significantly lower. (author)

  15. An Economic Risk Analysis of Weed Suppressive Rice Cultivars in Rice Production

    Science.gov (United States)

    Weeds are a major constraint to rice production. In the United States, most rice cultivars are not inherently weed-suppressive and require substantial herbicide inputs to achieve agronomic and economic viability. Intensive herbicide application in rice also has many potential drawbacks, resulting in...

  16. Salinity alters the protein composition of rice endosperm and the physicochemical properties of rice flour.

    Science.gov (United States)

    Baxter, Graeme; Zhao, Jian; Blanchard, Christopher

    2011-09-01

    Salinity is one of the major threats to production of rice and other agricultural crops worldwide. Although numerous studies have shown that salinity can severely reduce rice yield, little is known about its impact on the chemical composition, processing and sensory characteristics of rice. The objective of the current study was to investigate the effect of salinity on the pasting and textural properties of rice flour as well as on the protein content and composition of rice endosperm. Rice grown under saline conditions had significantly lower yields but substantially higher protein content. The increase in protein content was mainly attributed to increases in the amount of glutelin, with lesser contributions from albumin. Salinity also altered the relative proportions of the individual peptides within the glutelin fraction. Flours obtained from rice grown under saline conditions showed significantly higher pasting temperatures, but lower peak and breakdown viscosities. Rice gels prepared from the flour showed significantly higher hardness and adhesiveness values, compared to the freshwater controls. Salinity can significantly affect the pasting and textural characteristics of rice flour. Although some of the effects could be attributed to changes in protein content of the rice flour, especially the increased glutelin level, the impact of salinity on the physicochemical properties of rice is rather complex and may involve the interrelated effects of other rice components such as starch and lipids. Copyright © 2011 Society of Chemical Industry.

  17. Medicinal and nutritional importance of rice bran

    International Nuclear Information System (INIS)

    Ahmad, R.; Salim, M.; Rauf, R.; Baloach, M.K.

    2005-01-01

    Rice-bran is produced from the outer layer of brown rice and is stabilized through steam-heating. The rice-bran and its products are safe for human and animal consumption. The microbiological safety and rigorous quality-control practices merits its use as nutritional and dietary supplement for overall health-maintenance and as a part of a healthy diet and life-style, as it contributes to the reduction of certain diseases and health-related conditions. Stabilized rice-barn contain 15% of high nutritional- value protein, 20% of high-quality fat with Omega-3 and Omega-6 fatty acids, and nutritional dietary fiber. In addition to several phytonutrients, rice-bran contains vitamins and minerals, while over 100 potent antioxidants have been identified to date. Several scientific papers have reported the analysis and bioavailibility of rice-bran nutrients. Various chemical studies demonstrated the biological effects of the nutrients found in rice-bran. So far, more than 250 scientific publications are available on rice-bran, establishing the striking medicinal properties of rice-bran products. The oil-fraction of rice-bran has concentrated all tire fat-soluble phytonutrient in it, making itself an excellent health-promoting edible oil, as well as message oil The fiber-fraction of rice-bran has a profound effect on the gastrointestinal health, and improves bowel function. Rice-bran fiber along with phytonutrients was found to reduce cholesterol and lipid levels and maintain cardiovascular function. It has beneficial effect on tire kidney and urinary tract health and is helpful in weight-management and fiber replacement diets. (author)

  18. A Chromosome Segment Substitution Library of Weedy Rice for Genetic Dissection of Complex Agronomic and Domestication Traits.

    Directory of Open Access Journals (Sweden)

    Prasanta K Subudhi

    Full Text Available Chromosome segment substitution lines (CSSLs are a powerful alternative for locating quantitative trait loci (QTL, analyzing gene interactions, and providing starting materials for map-based cloning projects. We report the development and characterization of a CSSL library of a U.S. weedy rice accession 'PSRR-1' with genome-wide coverage in an adapted rice cultivar 'Bengal' background. The majority of the CSSLs carried a single defined weedy rice segment with an average introgression segment of 2.8 % of the donor genome. QTL mapping results for several agronomic and domestication traits from the CSSL population were compared with those obtained from two recombinant inbred line (RIL populations involving the same weedy rice accession. There was congruence of major effect QTLs between both types of populations, but new and additional QTLs were detected in the CSSL population. Although, three major effect QTLs for plant height were detected on chromosomes 1, 4, and 8 in the CSSL population, the latter two escaped detection in both RIL populations. Since this was observed for many traits, epistasis may play a major role for the phenotypic variation observed in weedy rice. High levels of shattering and seed dormancy in weedy rice might result from an accumulation of many small effect QTLs. Several CSSLs with desirable agronomic traits (e.g. longer panicles, longer grains, and higher seed weight identified in this study could be useful for rice breeding. Since weedy rice is a reservoir of genes for many weedy and agronomic attributes, the CSSL library will serve as a valuable resource to discover latent genetic diversity for improving crop productivity and understanding the plant domestication process through cloning and characterization of the underlying genes.

  19. Rice breeding with induced mutations

    Energy Technology Data Exchange (ETDEWEB)

    1968-06-01

    The Joint FAO/IAEA Division of Atomic Energy in Food and Agriculture decided in 1964 to organize a co-ordinated research programme on the use of induced mutations in rice breeding. The programme was organized within the framework of activities of the International Rice Commission. This is a report of the Third Co-ordination Meeting of the participants, which was held in Taipei, 5-9 June 1967. As the projects, which together make up the co-ordinated programme, are at different stages of progress, the report contains a variety of papers including completed studies, field and progress reports, and highlights of the discussions with some additional recommendations prepared by the participants. Refs, figs and tabs.

  20. Bioethanol production from rice straw residues

    Directory of Open Access Journals (Sweden)

    Elsayed B. Belal

    2013-01-01

    Full Text Available A rice straw -cellulose utilizing mold was isolated from rotted rice straw residues. The efficient rice straw degrading microorganism was identified as Trichoderma reesei. The results showed that different carbon sources in liquid culture such as rice straw, carboxymethyl cellulose, filter paper, sugar cane bagasse, cotton stalk and banana stalk induced T. reesei cellulase production whereas glucose or Potato Dextrose repressed the synthesis of cellulase. T. reesei cellulase was produced by the solid state culture on rice straw medium. The optimal pH and temperature for T. reesei cellulase production were 6 and 25 ºC, respectively. Rice straw exhibited different susceptibilities towards cellulase to their conversion to reducing sugars. The present study showed also that, the general trend of rice straw bioconversion with cellulase was more than the general trend by T. reesei. This enzyme effectively led to enzymatic conversion of acid, alkali and ultrasonic pretreated cellulose from rice straw into glucose, followed by fermentation into ethanol. The combined method of acid pretreatment with ultrasound and subsequent enzyme treatment resulted the highest conversion of lignocellulose in rice straw to sugar and consequently, highest ethanol concentration after 7 days fermentation with S. cerevisae yeast. The ethanol yield in this study was about 10 and 11 g.L-1.

  1. Response Of Lowland Rice To Soil Compaction

    International Nuclear Information System (INIS)

    Idawati; Haryanto

    2000-01-01

    Soil compaction, as a new tillage practice for paddy soil, is to substitute pudding in order to reduce land preparation cost. To study response of lowland rice to soil compaction, a pot experiment has been conducted which took place in the greenhouse of P3TIR-BATAN. Soil for experiment was taken from pusakanegara. Two factors (degree of soil compaction and rice variety) were combined. Degree of compaction was split into 3 levels (DI = normal; D215% more compact than normal; 30 % more compact than normal), and rice variety into 2 levels (IR64 and Atomita IV). KH 2 32 PO 4 solution was injected into the soil surrounding rice clump to test the root activity at blooming stage of rice plant. Data resulted from this experiment is presented together with additional data from some other experiments of fertilization in the research s erie to study soil compaction. Some information's from experiment results are as following. Both rice varieties tested gave the same response to soil compaction. Root activity, according to data of 32 P absorbed by plant, was not harmed by soil compaction at the degree tested in the experiment. This prediction is supported by the growth by rice observed at generative growth stage, in pot experiment as well as in field experiment, which showed that soil compaction tested did not decrease rice yield but in opposite in tended to increase the yield. In practising soil compaction in land preparation, fertilizers should be applied by deep placement to have higher increasing is rice yield

  2. Enzymatic hydrolsis of pretreated rice straw

    Energy Technology Data Exchange (ETDEWEB)

    Vlasenko, E.Y.; Shoemaker, S.P. [California Inst. of Food and Agricultural Research, Davis, CA (United States); Ding, H. [California Univ., Davis (Canada). Dept. of Food Science and Technology; Labavitch, J.M. [California Univ., Davis, CA (United States). Dept. of Pomology

    1997-02-01

    California rice straw is being evaluated as a feedstock for production of power and fuel. This paper examines the initial steps in the process: pretreatment of rice straw and enzymatic hydrolysis of the polysaccharides in the pretreated material to soluble sugars. Rice straw was subjected to three distinct pretreatment procedures: acid-catalyzed steam explosion (Swan Biomass Company), acid hydrolysis (U.S. DOE National Renewable Energy Laboratory), and ammonia fiber explosion or AFEX (Texas A and M University). Standard conditions for each pretreatment were used, but none was optimized for rice straw specifically. Six commercial cellulases, products of Genencor International (USA), Novo (Denmark), Iogen (Canada) and Fermtech (Russia) were used for hydrolysis. The Swan- and the acid-pretreatments effectively removed hemicellulose from rice straw, providing high yields of fermentable sugars. The AFEX-pretreatment was distinctly different from other pretreatments in that it did not significantly solubilize hemicellulose. All three pretreatment procedures substantially increased enzymatic digestibility of rice straw. Three commercial Trichoderma-reesei-derived enzyme preparations: Cellulase 100L (Iogen), Spezyme CP (Genencor), and Al (Fermtech), were more active on pretreated rice straw compared than others tested. Conditions for hydrolysis of rice straw using Cellulase 100L were evaluated. The supplementation of this enzyme preparation with cellobiase (Novozyme 188) significantly improved the parameters of hydrolysis for the Swan- and the acid-pretreated materials, but did not affect the hydrolysis of the AFEX-pretreated rice straw. (Author)

  3. Compressive Load Resistance Characteristics of Rice Grain

    OpenAIRE

    Sumpun Chaitep; Chaiy R. Metha Pathawee; Pipatpong Watanawanyoo

    2008-01-01

    Investigation was made to observe the compressive load property of rice gain both rough rice and brown grain. Six rice varieties (indica and japonica) were examined with the moisture content at 10-12%. A compressive load with reference to a principal axis normal to the thickness of the grain were conducted at selected inclined angles of 0°, 15°, 30°, 45°, 60° and 70°. The result showed the compressive load resistance of rice grain based on its characteristic of yield s...

  4. High level expression of Acidothermus cellulolyticus β-1, 4-endoglucanase in transgenic rice enhances the hydrolysis of its straw by cultured cow gastric fluid

    Energy Technology Data Exchange (ETDEWEB)

    Chou, Hong L.; Dai, Ziyu; Hsieh, Chia W.; Ku, Maurice S.

    2011-12-10

    Large-scale production of effective cellulose hydrolytic enzymes is the key to the bioconversion of agricultural residues to ethanol. The goal of this study was to develop a rice plant as a bioreactor for the large-scale production of cellulose hydrolytic enzymes via genetic transformation, and to simultaneously improve rice straw as an efficient biomass feedstock for conversion of cellulose to glucose. In this study, the cellulose hydrolytic enzyme {beta}-1, 4-endoglucanase (E1) from the thermophilic bacterium Acidothermus cellulolyticus was overexpressed in rice through Agrobacterium-mediated transformation. The expression of the bacterial gene in rice was driven by the constitutive Mac promoter, a hybrid promoter of Ti plasmid mannopine synthetase promoter and cauliflower mosaic virus 35S promoter enhancer with the signal peptide of tobacco pathogenesis-related protein for targeting the protein to the apoplastic compartment for storage. A total of 52 transgenic rice plants from six independent lines expressing the bacterial enzyme were obtained, which expressed the gene at high levels with a normal phenotype. The specific activities of E1 in the leaves of the highest expressing transgenic rice lines were about 20 fold higher than those of various transgenic plants obtained in previous studies and the protein amounts accounted for up to 6.1% of the total leaf soluble protein. Zymogram and temperature-dependent activity analyses demonstrated the thermostability of the enzyme and its substrate specificity against cellulose, and a simple heat treatment can be used to purify the protein. In addition, hydrolysis of transgenic rice straw with cultured cow gastric fluid yielded almost twice more reducing sugars than wild type straw. Taken together, these data suggest that transgenic rice can effectively serve as a bioreactor for large-scale production of active, thermostable cellulose hydrolytic enzymes. As a feedstock, direct expression of large amount of cellulases in

  5. Molecular Breeding of Rice Restorer Lines and Hybrids for Brown Planthopper (BPH) Resistance Using the Bph14 and Bph15 Genes.

    Science.gov (United States)

    Wang, Hongbo; Ye, Shengtuo; Mou, Tongmin

    2016-12-01

    The development of hybrid rice is a practical approach for increasing rice production. However, the brown planthopper (BPH), Nilaparvata lugens Stål, causes severe yield loss of rice (Oryza sativa L.) and can threaten food security. Therefore, breeding hybrid rice resistant to BPH is the most effective and economical strategy to maintain high and stable production. Fortunately, numerous BPH resistance genes have been identified, and abundant linkage markers are available for molecular marker-assisted selection (MAS) in breeding programs. Hence, we pyramided two BPH resistance genes, Bph14 and Bph15, into a susceptive CMS restorer line Huahui938 and its derived hybrids using MAS to improve the BPH resistance of hybrid rice. Three near-isogenic lines (NILs) with pyramided Bph14 and Bph15 were obtained by molecular marker-assisted backcross (MAB) and phenotypic selection. The genomic components of these NILs were detected using the whole-genome SNP (Single nucleotide polymorphism) array, RICE6K, suggesting that the recurrent parent genome (RPG) recovery of the NILs was 87.88, 87.70 and 86.62 %, respectively. BPH bioassays showed that the improved NILs and their derived hybrids carrying homozygous Bph14 and Bph15 were resistant to BPH. However, the hybrids with heterozygous Bph14 and Bph15 remained susceptible to BPH. The developed NILs showed no significant differences in major agronomic traits and rice qualities compared with the recurrent parent. Moreover, the improved hybrids derived from the NILs exhibited better agronomic performance and rice quality compared with the controls under natural field conditions. This study demonstrates that it is essential to stack Bph14 and Bph15 into both the maternal and paternal parents for developing BPH-resistant hybrid rice varieties. The SNP array with abundant DNA markers is an efficient tool for analyzing the RPG recovery of progenies and can be used to monitor the donor segments in NILs, thus being extremely important

  6. Elemental composition of Malawian rice.

    OpenAIRE

    Joy, EJM; Louise Ander, E; Broadley, MR; Young, SD; Chilimba, AD; Hamilton, EM; Watts, MJ

    2016-01-01

    Widespread potential dietary deficiencies of calcium (Ca), iron (Fe), iodine (I), selenium (Se) and zinc (Zn) have been identified in Malawi. Several deficiencies are likely to be compounded by high phytic acid (PA) consumption. Rice (Oryza sativa) is commonly consumed in some Malawian populations, and its mineral micronutrient content is important for food security. The considerable irrigation requirements and flooded conditions of paddy soils can also introduce or mobilise potentially toxic...

  7. Highly variable penetrance of abnormal phenotypes in embryonic lethal knockout mice

    Science.gov (United States)

    Wilson, Robert; Geyer, Stefan H.; Reissig, Lukas; Rose, Julia; Szumska, Dorota; Hardman, Emily; Prin, Fabrice; McGuire, Christina; Ramirez-Solis, Ramiro; White, Jacqui; Galli, Antonella; Tudor, Catherine; Tuck, Elizabeth; Mazzeo, Cecilia Icoresi; Smith, James C.; Robertson, Elizabeth; Adams, David J.; Mohun, Timothy; Weninger, Wolfgang J.

    2017-01-01

    Background: Identifying genes that are essential for mouse embryonic development and survival through term is a powerful and unbiased way to discover possible genetic determinants of human developmental disorders. Characterising the changes in mouse embryos that result from ablation of lethal genes is a necessary first step towards uncovering their role in normal embryonic development and establishing any correlates amongst human congenital abnormalities. Methods: Here we present results gathered to date in the Deciphering the Mechanisms of Developmental Disorders (DMDD) programme, cataloguing the morphological defects identified from comprehensive imaging of 220 homozygous mutant and 114 wild type embryos from 42 lethal and subviable lines, analysed at E14.5. Results: Virtually all mutant embryos show multiple abnormal phenotypes and amongst the 42 lines these affect most organ systems. Within each mutant line, the phenotypes of individual embryos form distinct but overlapping sets. Subcutaneous edema, malformations of the heart or great vessels, abnormalities in forebrain morphology and the musculature of the eyes are all prevalent phenotypes, as is loss or abnormal size of the hypoglossal nerve. Conclusions: Overall, the most striking finding is that no matter how profound the malformation, each phenotype shows highly variable penetrance within a mutant line. These findings have challenging implications for efforts to identify human disease correlates. PMID:27996060

  8. Deciphering the distance to antibiotic resistance for the pneumococcus using genome sequencing data

    NARCIS (Netherlands)

    Mobegi, Fredrick M; Cremers, Amelieke J H; de Jonge, Marien I; Bentley, Stephen D; van Hijum, Sacha A F T; Zomer, Aldert|info:eu-repo/dai/nl/304642754

    2017-01-01

    Advances in genome sequencing technologies and genome-wide association studies (GWAS) have provided unprecedented insights into the molecular basis of microbial phenotypes and enabled the identification of the underlying genetic variants in real populations. However, utilization of genome sequencing

  9. Gamma irradiation of rice grains

    International Nuclear Information System (INIS)

    Roy, M.K.; Ghosh, S.K.; Chatterjee, S.R.

    1991-01-01

    Rice grains of the variety, Pusa-33, at 12.0% moisture, were irradiated with doses of 0-150 kGy. The crystallinity of starch, soluble amylose and yellowness of treated grains increased with increment in the dose of radiation but water absorption and volume expansion on cooling decreased. irradiation at doses of 3-5 kGy increased imperceptibly the hardening of rice cooled after cooking, but had no effect on edibility. The off-aroma in irradiated grains was perceptible at doses higher than 5 kGy. The changes in colour and aroma persisted also on cooking. Upto a dose of 5 kGy, the sensory scores of rice, both cooked and uncooked, were at or above acceptable limit of score (5,5). The doses of 3 and 5 kGy were highly effective in reducing fungal population in irradiated grains, but in view of the changes in colour and cooking qualities, 3 kGy is the preferred dose-limit of irradiation. (author). 17 refs., 5 tabs., 1 fig

  10. Proteomics of Rice Seed Germination

    Directory of Open Access Journals (Sweden)

    Dongli eHe

    2013-07-01

    Full Text Available Seed is a condensed form of plant. Under suitable environmental conditions, it can resume the metabolic activity from physiological quiescent status, and mobilize the reserves, biosynthesize new proteins, regenerate organelles and cell membrane, eventually protrude the radicle and enter into seedling establishment. So far, how these activities are regulated in a coordinated and sequential manner is largely unknown. With the availability of more and more genome sequence information and the development of mass spectrometry (MS technology, proteomics has been widely applied in analyzing the mechanisms of different biological processes, and proved to be very powerful. Regulation of rice seed germination is critical for rice cultivation. In recent years, a lot of proteomic studies have been conducted in exploring the gene expression regulation, reserves mobilization and metabolisms reactivation, which brings us new insights on the mechanisms of metabolism regulation during this process. Nevertheless, it also invokes a lot of questions. In this mini-review, we summarized the progress in the proteomic studies of rice seed germination. The current challenges and future perspectives were also discussed, which might be helpful for the following studies.

  11. Clustering of 18 Local Black Rice Base on Total Anthocyanin

    Directory of Open Access Journals (Sweden)

    Kristamtini Kristamtini

    2017-10-01

    Full Text Available Black rice has a high anthocyanin content in the pericarp layer, which provides a dark purple color. Anthocyanin serve as an antioxidant that control cholesterol level in the blood, prevent anemia, potentially improve the body's resistance to disease, improve damage to liver cells (hepatitis and chirrosis, prevent impaired kidney function, prevent cancer/tumors, slows down antiaging, and prevent atherosclerosis and cardiovascular disease. Exploration results at AIAT Yogyakarta, Indonesia from 2011 to 2014 obtained 18 cultivar of local black rice Indonesia. The names of the rice are related to the color (black, red or purple formed by anthocyanin deposits in the pericarp layer, seed coat or aleuron. The objective of the study was to classify several types of local black rice from explorations based on the total anthocyanin content. The study was conducted by clustering analyzing the total anthocyanin content of 18 local black rice cultivars in Indonesia. Cluster analysis of total anthocyanin content were done using SAS ver. 9.2. Clustering dendogram shows that there were 4 groups of black rice cultivars based on the total anthocyanin content. Group I consists of Melik black rice, Patalan black rice, Yunianto black rice, Muharjo black rice, Ngatijo black rice, short life of Tugiyo black rice, Andel hitam 1, Jlitheng, and Sragen black rice. Group II consists of Pari ireng, Magelang black hairy rice, Banjarnegara-Wonosobo black rice, and Banjarnegara black rice. Group III consists of NTT black rice, Magelang non hairy black rice, Sembada hitam, and longevity Tugiyo black rice. Group IV consist only one type of black rice namely Cempo ireng. The grouping result indicate the existence of duplicate names among the black rice namely Patalan with Yunianto black rice, and short life Tugiyo with Andel hitam 1 black rice.

  12. Gibberellin regulates pollen viability and pollen tube growth in rice.

    Science.gov (United States)

    Chhun, Tory; Aya, Koichiro; Asano, Kenji; Yamamoto, Eiji; Morinaka, Yoichi; Watanabe, Masao; Kitano, Hidemi; Ashikari, Motoyuki; Matsuoka, Makoto; Ueguchi-Tanaka, Miyako

    2007-12-01

    Gibberellins (GAs) play many biological roles in higher plants. We collected and performed genetic analysis on rice (Oryza sativa) GA-related mutants, including GA-deficient and GA-insensitive mutants. Genetic analysis of the mutants revealed that rice GA-deficient mutations are not transmitted as Mendelian traits to the next generation following self-pollination of F1 heterozygous plants, although GA-insensitive mutations are transmitted normally. To understand these differences in transmission, we examined the effect of GA on microsporogenesis and pollen tube elongation in rice using new GA-deficient and GA-insensitive mutants that produce semifertile flowers. Phenotypic analysis revealed that the GA-deficient mutant reduced pollen elongation1 is defective in pollen tube elongation, resulting in a low fertilization frequency, whereas the GA-insensitive semidominant mutant Slr1-d3 is mainly defective in viable pollen production. Quantitative RT-PCR revealed that GA biosynthesis genes tested whose mutations are transmitted to the next generation at a lower frequency are preferentially expressed after meiosis during pollen development, but expression is absent or very low before the meiosis stage, whereas GA signal-related genes are actively expressed before meiosis. Based on these observations, we predict that the transmission of GA-signaling genes occurs in a sporophytic manner, since the protein products and/or mRNA transcripts of these genes may be introduced into pollen-carrying mutant alleles, whereas GA synthesis genes are transmitted in a gametophytic manner, since these genes are preferentially expressed after meiosis.

  13. From metabolome to phenotype

    DEFF Research Database (Denmark)

    Khakimov, Bekzod; Rasmussen, Morten Arendt; Kannangara, Rubini Maya

    2017-01-01

    for ideal vegetable protein production and for augmented β-glucan production. Seeds from three barley lines (Bomi, lys3.a and lys5.f) were sampled eight times during grain filling and analysed for metabolites using gas chromatography-mass spectrometry (GC-MS). The lys3.a mutation disrupts a regulator gene...... their successful application to link genetic and environmental factors with the seed phenotype of unique and agro-economically important barley models for optimal vegetable protein and dietary fibre production......., causing an increase in proteins rich in the essential amino acid lysine, while lys5.f carries a mutation in an ADP-glucose transporter gene leading to a significant increase in production of mixed-linkage β-glucan at the expense of α-glucan. Unique metabolic patterns associated with the tricarboxylic acid...

  14. Leaf development of cultivated rice and weedy red rice under elevated temperature scenarios

    OpenAIRE

    Streck,Nereu A.; Uhlmann,Lilian O.; Gabriel,Luana F.

    2013-01-01

    The objective of this study was to simulate leaf development of cultivated rice genotypes and weedy red rice biotypes in climate change scenarios at Santa Maria, RS, Brazil. A leaf appearance (LAR) model adapted for rice was used to simulate the accumulated leaf number, represented by the Haun Stage, from crop emergence to flag leaf appearance (EM-FL). Three cultivated rice genotypes and two weedy red rice biotypes in six emergence dates were used. The LAR model was run for each emergence dat...

  15. Deep Learning for Plant Phenotyping

    OpenAIRE

    Mori, Matteo

    2016-01-01

    Plant Phenotyping is an emerging science which provides us the knowledge to better understand plants. Indeed, the study of the link between genetic background and environment in which plants develop can help us to determine cures for plants’ sicknesses and new ways to improve yields using limited resources. In this regard, one of the main aspects of Plant Phenotyping that were studied in the past, was Root Phenotyping, which is based on the study of the root architectures. In particular, toda...

  16. Quantitative Trait Loci for Mercury Tolerance in Rice Seedlings

    Directory of Open Access Journals (Sweden)

    Chong-qing WANG

    2013-05-01

    Full Text Available Mercury (Hg is one of the most toxic heavy metals to living organisms and its conspicuous effect is the inhibition of root growth. However, little is known about the molecular genetic basis for root growth under excess Hg2+ stress. To map quantitative trait loci (QTLs in rice for Hg2+ tolerance, a population of 120 recombinant inbred lines derived from a cross between two japonica cultivars Yuefu and IRAT109 was grown in 0.5 mmol/L CaCl2 solution. Relative root length (RRL, percentage of the seminal root length in +HgCl2 to –HgCl2, was used for assessing Hg2+ tolerance. In a dose-response experiment, Yuefu had a higher RRL than IRAT109 and showed the most significant difference at the Hg2+ concentration of 1.5 μmol/L. Three putative QTLs for RRL were detected on chromosomes 1, 2 and 5, and totally explained about 35.7% of the phenotypic variance in Hg2+ tolerance. The identified QTLs for RRL might be useful for improving Hg2+ tolerance of rice by molecular marker-assisted selection.

  17. Long-term balancing selection at the Phosphorus Starvation Tolerance 1 (PSTOL1) locus in wild, domesticated and weedy rice (Oryza).

    Science.gov (United States)

    Vigueira, Cynthia C; Small, Linda L; Olsen, Kenneth M

    2016-04-22

    The ability to grow in phosphorus-depleted soils is an important trait for rice cultivation in many world regions, especially in the tropics. The Phosphorus Starvation Tolerance 1 (PSTOL1) gene has been identified as underlying the ability of some cultivated rice varieties to grow under low-phosphorus conditions; however, the gene is absent from other varieties. We assessed PSTOL1 presence/absence in a geographically diverse sample of wild, domesticated and weedy rice and sequenced the gene in samples where it is present. We find that the presence/absence polymorphism spans cultivated, weedy and wild Asian rice groups. For the subset of samples that carry PSTOL1, haplotype sequences suggest long-term selective maintenance of functional alleles, but with repeated evolution of loss-of-function alleles through premature stops and frameshift mutations. The loss-of-function alleles have evolved convergently in multiple rice species and cultivated rice varieties. Greenhouse assessments of plant growth under low- and high-phosphorus conditions did not reveal significant associations with PSTOL1 genotype variation; however, the striking signature of balancing selection at this locus suggests that further phenotypic characterizations of PSTOL1 allelic variants is warranted and may be useful for crop improvement. These findings suggest balancing selection for both functional and non-functional PSTOL1 alleles that predates and transcends Asian rice domestication, a pattern that may reflect fitness tradeoffs associated with geographical variation in soil phosphorus content.

  18. Micronutrient-fortified rice can increase hookworm infection risk

    DEFF Research Database (Denmark)

    de Gier, Brechje; Campos Ponce, Maiza; Perignon, Marlene

    2016-01-01

    or inflammation after iron supplementation. OBJECTIVE: To study effects of micronutrient-fortified rice on hookworm infection in Cambodian schoolchildren. METHODS: A double-blinded, cluster-randomized trial was conducted in 16 Cambodian primary schools partaking in the World Food Program school meal program....... Three types of multi-micronutrient fortified rice were tested against placebo rice within the school meal program: UltraRice_original, UltraRice_improved and NutriRice. Four schools were randomly assigned to each study group (placebo n = 492, UltraRice_original n = 479, UltraRice_improved n = 500, NutriRice.......6%, but differed considerably among schools (range 0%- 48.1%).Micronutrient-fortified rice significantly increased risk of new hookworm infection. This effect was modified by baseline hookworm prevalence at the school; hookworm infection risk was increased by all three types of fortified rice in schools where...

  19. Nutrient management for rice production

    International Nuclear Information System (INIS)

    Khan, A.R.; Chandra, D.; Nanda, P.; Singh, S.S.; Singh, S.R.; Ghorai, A.K.

    2002-06-01

    The nutrient removed by the crops far exceeds the amounts replenished through fertilizer, causing a much greater strain on the native soil reserves. The situation is further aggravated in countries like India, where sub-optimal fertilizer used by the farmers is a common phenomenon rather than an exception. The total consumption of nutrients of all crops in India, even though reached 15 million tons in 1997, remains much below the estimated nutrient removal of 25 million tons (Swarup and Goneshamurthy, 1998). The gap between nutrient removal supplied through fertilizer has widened further in 2000 to 34 million tons of plant nutrients from the soil against an estimated fertilizer availability of 18 million tons (Singh and Dwivedi, 1996). Nitrogen is the nutrient which limits the most the rice production worldwide. In Asia, where more than 90 percent of the world's rice is produced, about 60 percent of the N fertilizer consumed is used on rice (Stangel and De Dutta, 1985). Conjunctive use of organic material along with fertilizer has been proved an efficient source of nitrogen. Organic residue recycling is becoming an increasingly important aspect of environmentally sound sustainable agriculture. Returning residues like green manure to the soil is necessary for maintaining soil organic matter, which is important for favourable soil structure, soil water retention and soil microbial flora and fauna activities. Use of organic manures in conjunction or as an alternative to chemical fertilizer is receiving attention. Green manure, addition to some extent, helps not only in enhancing the yield but also in improving the physical and chemical nature of soils. The excessive application of chemical fertilizers made it imperative that a part of inorganic fertilizer may be substituted with the recycling of organic wastes. Organic manure has been recorded to enhance the efficiency and reduce the requirement of chemical fertilizers. Partial nitrogen substitution through organic

  20. Benthic macroinvertebrates in Italian rice fields

    Directory of Open Access Journals (Sweden)

    Daniela Lupi

    2013-02-01

    Full Text Available Rice fields can be considered man-managed temporary wetlands. Five rice fields handled with different management strategies, their adjacent channels, and a spring were analysed by their benthic macroinvertebrate community to i evaluate the role of rice agroe- cosystem in biodiversity conservation; ii find indicator species which can be used to compare the ecological status of natural wetlands with rice agroecosystems; and iii find the influence of environmental variables on biodiversity. Different methods of data analysis with increasing degree of complexity – from diversity index up to sophisticated multivariate analysis – were used. The investigation provided a picture of benthic macroinvertebrates inhabiting rice agroecosystems where 173 taxa were identified, 89 of which detected in rice paddies. Among them, 4 phyla (Mollusca, Annelida, Nematomorpha, and Arthropoda, 8 classes (Bivalvia, Gastropoda, Oligochaeta, Hirudinea, Gordioida, Insecta, Branchiopoda, and Malacostraca, 24 orders, 68 families, 127 genera and 159 species have been found. Ten threatened and 3 invasive species were detected in the habitats examined. The information obtained by the different methods of data analysis allowed a more comprehensive view on the value of the components of rice agroecosystems. Data analyses highlighted significant differences between habitats (feeding channel and rice field, with higher diversity observed in channels, and emphasised the role of the water chemical-physical parameters. The period of water permanence in rice fields resulted to be only one of the factors influencing the community of benthic macroinvertebrates. The presence of rare/endangered species allowed characterising some stations, but it was less informative about management strategies in rice paddies because most of these species were absent in rice fields.

  1. Overexpression of Rice Wall-Associated Kinase 25 (OsWAK25) Alters Resistance to Bacterial and Fungal Pathogens

    Science.gov (United States)

    Harkenrider, Mitch; Sharma, Rita; De Vleesschauwer, David; Tsao, Li; Zhang, Xuting; Chern, Mawsheng; Canlas, Patrick; Zuo, Shimin; Ronald, Pamela C.

    2016-01-01

    Wall-associated kinases comprise a sub-family of receptor-like kinases that function in plant growth and stress responses. Previous studies have shown that the rice wall-associated kinase, OsWAK25, interacts with a diverse set of proteins associated with both biotic and abiotic stress responses. Here, we show that wounding and BTH treatments induce OsWAK25 transcript expression in rice. We generated OsWAK25 overexpression lines and show that these lines exhibit a lesion mimic phenotype and enhanced expression of rice NH1 (NPR1 homolog 1), OsPAL2, PBZ1 and PR10. Furthermore, these lines show resistance to the hemibiotrophic pathogens, Xanthomonas oryzae pv. oryzae (Xoo) and Magnaporthe oryzae, yet display increased susceptibility to necrotrophic fungal pathogens, Rhizoctonia solani and Cochliobolus miyabeanus. PMID:26795719

  2. Arsenic accumulation in rice: Consequences of rice genotypes and management practices to reduce human health risk.

    Science.gov (United States)

    Islam, Shofiqul; Rahman, Mohammad Mahmudur; Islam, M R; Naidu, Ravi

    2016-11-01

    Rice is an essential staple food and feeds over half of the world's population. Consumption of rice has increased from limited intake in Western countries some 50years ago to major dietary intake now. Rice consumption represents a major route for inorganic arsenic (As) exposure in many countries, especially for people with a large proportion of rice in their daily diet as much as 60%. Rice plants are more efficient in assimilating As into its grains than other cereal crops and the accumulation may also adversely affect the quality of rice and their nutrition. Rice is generally grown as a lowland crop in flooded soils under reducing conditions. Under these conditions the bioavailability of As is greatly enhanced leading to excessive As bioaccumulation compared to that under oxidizing upland conditions. Inorganic As species are carcinogenic to humans and even at low levels in the diet pose a considerable risk to humans. There is a substantial genetic variation among the rice genotypes in grain-As accumulation as well as speciation. Identifying the extent of genetic variation in grain-As concentration and speciation of As compounds are crucial to determining the rice varieties which accumulate low inorganic As. Varietal selection, irrigation water management, use of fertilizer and soil amendments, cooking practices etc. play a vital role in reducing As exposure from rice grains. In the meantime assessing the bioavailability of As from rice is crucial to understanding human health exposure and reducing the risk. Copyright © 2016 Elsevier Ltd. All rights reserved.

  3. An overview of the sustainability of rice agroecosystem through rice-fish integration

    International Nuclear Information System (INIS)

    Ahyaudin Ali

    2002-01-01

    Rice-fish integration in the rice agroecosystem has been introduced and is expanding in Malaysia. This type of farm integration has resulted in land optimization, thus enabling farmers to grow both fish and rice in one farming system. Introducing fish into the ricefield has also increased seasonal income as well as reduced pesticide use. Although basic ecological knowledge on rice-fish integration has allowed rice-fish integration to be introduced, further research is required to allow for fine tuning of the methodologies used. Thus research on the ecology, management, production methods and the characterization of rice-fish farming system of Malaysia is needed. Further characterization and description is needed on the ecology of the rice-fish farming system of Malaysia in terms of production, food webs, nutrient flow and system diversity. To increase the sustainability efficiency and productivity of the system, implementation of management techniques formulated through research is required. (Author)

  4. Residues and accumulation of molinate in rice crops and aquatic weeds in the MUDA rice agroecosystem

    International Nuclear Information System (INIS)

    Nashriyah Mat; Sabri Junoh; Nuriati Nurdin; Ramli Ishak

    2002-01-01

    Plant and soil residue levels and its accumulation in rice crops and rice aquatic weed plants were studied. Molinate residue levels in rice, weeds and soil were not significantly different between the recycled and the non-recycled area, even though they were higher in the non-recycled area. In the rice plant, the residue level at 10 DAT (days after treatment) was significantly higher than 30 DAT in the recycled area. In rice aquatic weed plants, the residue level was significantly higher at 10 DAT as compared to 30 DAT in the non-recycled area. Molinate residue levels in soil at 10 DAT and 30 DAT were similar. Molinate accumulated (ratio of molinate concentration in plant over soil) more in the rice crop as compared to rice aquatic weeds at 10 DAT, in both the recycled and the non-recycled areas. (Author)

  5. Functional analysis of rice HOMEOBOX4 (Oshox4) gene reveals a negative function in gibberellin responses.

    Science.gov (United States)

    Dai, Mingqiu; Hu, Yongfeng; Ma, Qian; Zhao, Yu; Zhou, Dao-Xiu

    2008-02-01

    The homeodomain-leucine zipper (HD-Zip) putative transcription factor genes are divided into 4 families. In this work, we studied the function of a rice HD-Zip I gene, H OME O BO X4 (Oshox4). Oshox4 transcripts were detected in leaf and floral organ primordia but excluded from the shoot apical meristem and the protein was nuclear localized. Over-expression of Oshox4 in rice induced a semi-dwarf phenotype that could not be complemented by applied GA3. The over-expression plants accumulated elevated levels of bioactive GA, while the GA catabolic gene GA2ox3 was upregulated in the transgenic plants. In addition, over-expression of Oshox4 blocked GA-dependent alpha-amylase production. However, down-regulation of Oshox4 in RNAi transgenic plants induced no phenotypic alteration. Interestingly, the expression of YAB1 that is involved in the negative feedback regulation of the GA biosynthesis was upregulated in the Oshox4 over-expressing plants. One-hybrid assays showed that Oshox4 could interact with YAB1 promoter in yeast. In addition, Oshox4 expression was upregulated by GA. These data together suggest that Oshox4 may be involved in the negative regulation of GA signalling and may play a role to fine tune GA responses in rice.

  6. Tocopherol-deficient rice plants display increased sensitivity to photooxidative stress.

    Science.gov (United States)

    Chen, Defu; Chen, Haiwei; Zhang, Luhua; Shi, Xiaoli; Chen, Xiwen

    2014-06-01

    Tocopherols are lipophilic antioxidants that are synthesized exclusively in photosynthetic organisms. Despite extensive in vivo characterization of tocopherol functions in plants, their functions in the monocot model plant, rice, remain to be determined. In this study, transgenic rice plants constitutively silenced for homogentisate phytyltransferase (HPT) and tocopherol cyclase (TC) activity were generated. Silencing of HPT and TC resulted in up to a 98 % reduction in foliar tocopherol content relative to the control plants, which was also confirmed by transcript level analysis. When grown under normal conditions, HPT and TC transgenics showed no distinctive phenotype relative to the control plants, except a slight reduction in plant height and a slight decrease in the first leaf length. However, when exposed to high light at low temperatures, HPT and TC transgenics had a significantly higher leaf yellowing index than the control plants. The tocopherol-deficient plants decreased their total individual chlorophyll levels, their chlorophyll a/b ratio, and the maximum photochemical efficiency of photosystem II, whereas increased lipid peroxidation levels relative to the control plants. Tocopherol deficiency had no effect on ascorbate biosynthesis, but induced glutathione, antheraxanthin, and particularly zeaxanthin biosynthesis for compensation under stressful conditions. However, despite these compensation mechanisms, HPT and TC transgenics still exhibited altered phenotypes under high light at low temperatures. Therefore, it is suggested that tocopherols cannot be replaced and play an indispensable role in photoprotection in rice.

  7. GOLD HULL AND INTERNODE2 encodes a primarily multifunctional cinnamyl-alcohol dehydrogenase in rice.

    Science.gov (United States)

    Zhang, Kewei; Qian, Qian; Huang, Zejun; Wang, Yiqin; Li, Ming; Hong, Lilan; Zeng, Dali; Gu, Minghong; Chu, Chengcai; Cheng, Zhukuan

    2006-03-01

    Lignin content and composition are two important agronomic traits for the utilization of agricultural residues. Rice (Oryza sativa) gold hull and internode phenotype is a classical morphological marker trait that has long been applied to breeding and genetics study. In this study, we have cloned the GOLD HULL AND INTERNODE2 (GH2) gene in rice using a map-based cloning approach. The result shows that the gh2 mutant is a lignin-deficient mutant, and GH2 encodes a cinnamyl-alcohol dehydrogenase (CAD). Consistent with this finding, extracts from roots, internodes, hulls, and panicles of the gh2 plants exhibited drastically reduced CAD activity and undetectable sinapyl alcohol dehydrogenase activity. When expressed in Escherichia coli, purified recombinant GH2 was found to exhibit strong catalytic ability toward coniferaldehyde and sinapaldehyde, while the mutant protein gh2 completely lost the corresponding CAD and sinapyl alcohol dehydrogenase activities. Further phenotypic analysis of the gh2 mutant plants revealed that the p-hydroxyphenyl, guaiacyl, and sinapyl monomers were reduced in almost the same ratio compared to the wild type. Our results suggest GH2 acts as a primarily multifunctional CAD to synthesize coniferyl and sinapyl alcohol precursors in rice lignin biosynthesis.

  8. GOLD HULL AND INTERNODE2 Encodes a Primarily Multifunctional Cinnamyl-Alcohol Dehydrogenase in Rice1

    Science.gov (United States)

    Zhang, Kewei; Qian, Qian; Huang, Zejun; Wang, Yiqin; Li, Ming; Hong, Lilan; Zeng, Dali; Gu, Minghong; Chu, Chengcai; Cheng, Zhukuan

    2006-01-01

    Lignin content and composition are two important agronomic traits for the utilization of agricultural residues. Rice (Oryza sativa) gold hull and internode phenotype is a classical morphological marker trait that has long been applied to breeding and genetics study. In this study, we have cloned the GOLD HULL AND INTERNODE2 (GH2) gene in rice using a map-based cloning approach. The result shows that the gh2 mutant is a lignin-deficient mutant, and GH2 encodes a cinnamyl-alcohol dehydrogenase (CAD). Consistent with this finding, extracts from roots, internodes, hulls, and panicles of the gh2 plants exhibited drastically reduced CAD activity and undetectable sinapyl alcohol dehydrogenase activity. When expressed in Escherichia coli, purified recombinant GH2 was found to exhibit strong catalytic ability toward coniferaldehyde and sinapaldehyde, while the mutant protein gh2 completely lost the corresponding CAD and sinapyl alcohol dehydrogenase activities. Further phenotypic analysis of the gh2 mutant plants revealed that the p-hydroxyphenyl, guaiacyl, and sinapyl monomers were reduced in almost the same ratio compared to the wild type. Our results suggest GH2 acts as a primarily multifunctional CAD to synthesize coniferyl and sinapyl alcohol precursors in rice lignin biosynthesis. PMID:16443696

  9. The rice YABBY1 gene is involved in the feedback regulation of gibberellin metabolism.

    Science.gov (United States)

    Dai, Mingqiu; Zhao, Yu; Ma, Qian; Hu, Yongfeng; Hedden, Peter; Zhang, Qifa; Zhou, Dao-Xiu

    2007-05-01

    Gibberellin (GA) biosynthesis is regulated by feedback control providing a mechanism for GA homeostasis in plants. However, regulatory elements involved in the feedback control are not known. In this report, we show that a rice (Oryza sativa) YABBY1 (YAB1) gene had a similar expression pattern as key rice GA biosynthetic genes GA3ox2 and GA20ox2. Overexpression of YAB1 in transgenic rice resulted in a semidwarf phenotype that could be fully rescued by applied GA. Quantification of the endogenous GA content revealed increases of GA(20) and decreases of GA(1) levels in the overexpression plants, in which the transcripts of the biosynthetic gene GA3ox2 were decreased. Cosuppression of YAB1 in transgenic plants induced expression of GA3ox2. The repression of GA3ox2 could be obtained upon treatment by dexamethasone of transgenic plants expressing a YAB1-glucocorticoid receptor fusion. Importantly, we show that YAB1 bound to a GA-responsive element within the GA3ox2 promoter. In addition, the expression of YAB1 was deregulated in GA biosynthesis and signaling mutants and could be either transiently induced by GA or repressed by a GA inhibitor. Finally, either overexpression or cosuppression of YAB1 impaired GA-mediated repression of GA3ox2. These data together suggest that YAB1 is involved in the feedback regulation of GA biosynthesis in rice.

  10. Methods of developing core collections based on the predicted genotypic value of rice ( Oryza sativa L.).

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

  12. Genetic mapping of the rice resistance-breaking gene of the brown planthopper Nilaparvata lugens.

    Science.gov (United States)

    Kobayashi, Tetsuya; Yamamoto, Kimiko; Suetsugu, Yoshitaka; Kuwazaki, Seigo; Hattori, Makoto; Jairin, Jirapong; Sanada-Morimura, Sachiyo; Matsumura, Masaya

    2014-07-22

    Host plant resistance has been widely used for controlling the major rice pest brown planthopper (BPH, Nilaparvata lugens). However, adaptation of the wild BPH population to resistance limits the effective use of resistant rice varieties. Quantitative trait locus (QTL) analysis was conducted to identify resistance-breaking genes against the anti-feeding mechanism mediated by the rice resistance gene Bph1. QTL analysis in iso-female BPH lines with single-nucleotide polymorphism (SNP) markers detected a single region on the 10th linkage group responsible for the virulence. The QTL explained from 57 to 84% of the total phenotypic variation. Bulked segregant analysis with next-generation sequencing in F2 progenies identified five SNPs genetically linked to the virulence. These analyses showed that virulence to Bph1 was controlled by a single recessive gene. In contrast to previous studies, the gene-for-gene relationship between the major resistance gene Bph1 and virulence gene of BPH was confirmed. Identified markers are available for map-based cloning of the major gene controlling BPH virulence to rice resistance. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

  13. Characterisation of the microbiota of rice sourdoughs and description of Lactobacillus spicheri sp. nov.

    Science.gov (United States)

    Meroth, Christiane B; Hammes, Walter P; Hertel, Christian

    2004-03-01

    The microbiota of two industrially processed rice sourdoughs was characterised by bacteriological culture in combination with PCR-denaturing gradient gel electrophoresis (DGGE) and 16S/28S rDNA sequence analysis. Rice sourdough I was continuously propagated for several years by back-slopping every week, whereas sourdough II was processed by using a commercial starter culture and back-slopping daily for three days. In rice sourdough II Candida krusei and Saccharomyces cerevisiae as well as Lactobacillus fermentum, Lactobacillus gallinarum, Lactobacillus kimchii, Lactobacillus plantarum, and Lactobacillus pontis dominated at the first day of fermentation. RAPD analysis of lactobacilli revealed identical profiles for each of the species except for L. fermentum and L. pontis indicating the presence of different strains. Fluctuations within the LAB community during fermentation were monitored by PCR-DGGE. L. pontis decreased in numbers over time and L. curvatus became dominant after 3 days of fermentation. Rice sourdough I contained S. cerevisiae, Lactobacillus paracasei (present with three different RAPD types), Lactobacillus paralimentarius, and a Lactobacillus strain which could not be allotted to any valid species. Phylogenetic analysis based on 16S rDNA sequences revealed Lactobacillus brevis as the closest relative (97.3% sequence similarity). Differences in some phenotypic characteristics and DNA-DNA relatedness indicated that the strain represents a new Lactobacillus species, for which the name Lactobacillus spicheri is proposed.

  14. Laccase-13 Regulates Seed Setting Rate by Affecting Hydrogen Peroxide Dynamics and Mitochondrial Integrity in Rice

    Directory of Open Access Journals (Sweden)

    Yang Yu

    2017-07-01

    Full Text Available Seed setting rate is one of the most important components of rice grain yield. To date, only several genes regulating setting rate have been identified in plant. In this study, we showed that laccase-13 (OsLAC13, a member of laccase family genes which are known for their roles in modulating phenylpropanoid pathway and secondary lignification in cell wall, exerts a regulatory function in rice seed setting rate. OsLAC13 expressed in anthers and promotes hydrogen peroxide production both in vitro and in the filaments and anther connectives. Knock-out of OsLAC13 showed significantly increased seed setting rate, while overexpression of this gene exhibited induced mitochondrial damage and suppressed sugar transportation in anthers, which in turn affected seed setting rate. OsLAC13 also induced H2O2 production and mitochondrial damage in the root tip cells which caused the lethal phenotype. We also showed that high abundant of OsmiR397, the suppressor of OsLAC13 mRNA, increased the seed setting rate of rice plants, and restrains H2O2 accumulation in roots during oxidative stress. Our results suggested a novel regulatory role of OsLAC13 gene in regulating seed setting rate by affecting H2O2 dynamics and mitochondrial integrity in rice.

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

    Directory of Open Access Journals (Sweden)

    Gopala Krishnan S

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

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

    Science.gov (United States)

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

    2014-01-01

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

  17. QTL Analysis of Anoxic Tolerance at Seedling Stage in Rice

    Directory of Open Access Journals (Sweden)

    Yang WANG

    2010-09-01

    Full Text Available Coleoptile lengths of 7-day-old seedlings under anoxic stress and normal conditions were investigated in two permanently segregated populations and their parents in rice (Oryza sativa L.. Using anoxic response index, a ratio of coleoptile length under anoxic stress to coleoptile length under normal conditions, as an indicator of seedling anoxic tolerance (SAT, QTLs for SAT were detected. Two loci controlling SAT, designated as qSAT-2-R and qSAT-7-R, were detected in a recombinant inbred line (RIL population (247 lines derived from a cross between Xiushui 79 (japonica variety and C Bao (japonica restorer line. qSAT-2-R, explaining 8.7% of the phenotype variation, was tightly linked with the SSR marker RM525. qSAT-7-R, explaining 9.8% of the phenotype variation, was tightly linked with the marker RM418. The positive alleles of the two loci came from C Bao. Six loci controlling SAT, designated as qSAT-2-B, qSAT-3-B, qSAT-5-B, qSAT-8-B, qSAT-9-B and qSAT-12-B, were detected in a backcross inbred line (BIL population (98 lines derived from a backcross of Nipponbare (japonica/Kasalath (indica//Nipponbare (japonica. The positive alleles of qSAT-2-B, qSAT-3-B and qSAT-9-B, which explained 16.2%, 11.4% and 9.5% of the phenotype variation, respectively, came from Nipponbare. Besides, the positive alleles of qSAT-5-B, qSAT-8-B and qSAT-12-B, which explained 7.3%, 5.8% and 14.0% of the phenotype variation, respectively, were from Kasalath.

  18. Novel gene expression tools for rice biotechnology

    Science.gov (United States)

    Biotechnology is an effective and important method of improving both quality and agronomic traits in rice. We are developing novel molecular tools for genetic engineering, with a focus on developing novel transgene expression control elements (i.e. promoters) for rice. A suite of monocot grass promo...

  19. Recent advances on bioactivities of black rice.

    Science.gov (United States)

    Dias, Aécio L de S; Pachikian, Barbara; Larondelle, Yvan; Quetin-Leclercq, Joëlle

    2017-11-01

    Black rice has been consumed for centuries in Asian countries such as China, Korea or Japan. Nowadays, extracts and derivatives are considered as beneficial functional foods because of their high content in several bioactive molecules such as anthocyanins, other phenolics and terpenoids. The purpose of this review is to summarize and discuss recent developments on black rice bioactivities. Some sterols and triterpenoids with potential anticancer properties already tested in vitro and in vivo have been isolated and identified from bran extracts of black rice. Protection against osteoporosis has been suggested for the first time for black rice extracts. Because of its antioxidant and anti-inflammatory properties, black rice also protects liver and kidney from injuries. One clinical study reported the interest of black rice in case of alcohol withdrawal. Several advances have been recently achieved on the understanding of the potential biological effects of black rice and its derivatives. They further confirm that black rice should be considered as a promising source of health-promoting functional foods targeting a large set of noninfectious diseases. However, more clinical studies are needed to support the findings highlighted in this review.

  20. Functional genomics strategies with transposons in rice

    NARCIS (Netherlands)

    Greco, R.

    2003-01-01

    Rice is a major staple food crop and a recognizedmonocotylenedousmodel plant from which gene function discovery is projected to contribute to improvements in a variety of cereals like wheat and maize. The recent release of rough drafts of the rice genome sequence for public

  1. Grain Unloading Of Arsenic Species In Rice

    Science.gov (United States)

    Rice (Oryza sativa) is the staple food for over half the world's population yet may represent a significant dietary source of inorganic arsenic (As), a nonthreshold, class 1 human carcinogen. Rice grain As is dominated by the inorganic species, and the organic species dim...

  2. 33 CFR 117.324 - Rice Creek.

    Science.gov (United States)

    2010-07-01

    ... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Rice Creek. 117.324 Section 117.324 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY BRIDGES DRAWBRIDGE OPERATION REGULATIONS Specific Requirements Florida § 117.324 Rice Creek. The CSX Railroad Swingbridge, mile...

  3. Soil quality assessment in rice production systems

    NARCIS (Netherlands)

    Rodrigues de Lima, A.C.

    2007-01-01

    In the state of Rio Grande do Sul, Brazil, rice production is one of the most important regional activities. Farmers are concerned that the land use practices for rice production in the Camaquã region may not be sustainable because of detrimental effects on soil quality. The study presented in this

  4. Land Titles and Rice Production in Vietnam

    DEFF Research Database (Denmark)

    Van Den Broeck, Katleen; Newman, Carol; Tarp, Finn

    analysis of plot level rice yields that land titles are indeed important. Only exclusively held titles have the expected positive effects, and the positive effect on yields is found in male headed households. Furthermore, a household level rice yield function reveals that exclusive user rights...

  5. Adoption of Recommended Rice Production Practices among ...

    African Journals Online (AJOL)

    User

    rice production practices by women farmers in Nasarawa State. A total of 203 women rice farmers were selected for the study using multi- ... RRPPs were unavailability of credit facilities, poor marketing system and ... economy which provides employment opportunity for about 70-80 percent of the total ..... shown in Table 1.

  6. Deciphering spreading mechanisms in amyotrophic lateral sclerosis: clinical evidence and potential molecular processes.

    Science.gov (United States)

    Pradat, Pierre-François; Kabashi, Edor; Desnuelle, Claude

    2015-10-01

    The aim of this review is to refer to recent arguments supporting the existence of specific propagation mechanisms associated with spreading of neuron injury in amyotrophic lateral sclerosis (ALS). Misfolded ALS-linked protein accumulation can induce aggregation of their native equivalent isoforms through a mechanism analogous to the infectious prion proteins initiation and its propagation. Although ALS is clinically heterogeneous, a shared characteristic is the focal onset and the progressive extension to all body regions. Being viewed until now as just summation of the increased number of affected neurons, dispersion is now rather considered as the result of a seeded self-propagating process. A sequential regional spreading pattern is supported by the distribution of TDP-43 aggregates in ALS autopsy cases. Electrophysiology and advanced neuroimaging methods also recently provided some evidence for propagation of lesions both in the brain and spinal cord, more longitudinal studies being still needed. Lesions are supposed to spread cell-to-cell regionally or through connected neuronal pathway. At the molecular level, the prion-like spreading is an emerging mechanism hypothesis, but other machineries such as those that are in charge of dealing with misfolded proteins and secretion of deleterious peptides may be involved in the propagation of neuron loss. Deciphering the mechanisms underlying spreading of ALS symptoms is of crucial importance to better understand this neurodegenerative disease, build new and appropriate animal models and to define novel therapeutic targets.

  7. The race to decipher the top secrets of TOP mRNAs.

    Science.gov (United States)

    Meyuhas, Oded; Kahan, Tamar

    2015-07-01

    Cells encountering hostile growth conditions, like those residing in the middle of a newly developing solid tumor, conserve resources and energy by downregulating protein synthesis. One mechanism in this response is the translational repression of multiple mRNAs that encode components of the translational apparatus. This coordinated translational control is carried through a common cis-regulatory element, the 5' Terminal OligoPyrimidine motif (5'TOP), after which these mRNAs are referred to as TOP mRNAs. Subsequent to the initial structural and functional characterization of members of this family, the research of TOP mRNAs has progressed in three major directions: a) delineating the landscape of the family; b) establishing the pathways that transduce stress cues into selective translational repression; and c) attempting to decipher the most proximal trans-acting factor(s) and defining its mode of action--a repressor or activator. The present chapter critically reviews the development in these three avenues of research with a special emphasis on the two "top secrets" of the TOP mRNA family: the scope of its members and the identity of the proximal cellular regulator(s). This article is part of a Special Issue entitled: Translation and Cancer. Copyright © 2014 Elsevier B.V. All rights reserved.

  8. Deciphering the Mechanism of Action of Wrightia tinctoria for Psoriasis Based on Systems Pharmacology Approach.

    Science.gov (United States)

    Sundarrajan, Sudharsana; Lulu, Sajitha; Arumugam, Mohanapriya

    2017-11-01

    Psoriasis is a chronic immune-mediated disorder of the skin. The disease manifests itself with red or silvery scaly plaques distributing over the lower back, scalp, and extensor aspects of limbs. Several medications are available for the treatment of psoriasis; however, high rates of remission and side-effects still persist as a major concern. Siddha, one of the traditional systems of Indian medicine offers cure to many dermatological conditions, including psoriasis. The oil prepared from the leaves of Wrightia tinctoria is prescribed by many healers for the treatment of psoriasis. This work aims to decipher the mechanism of action of the W. tinctoria in curing psoriasis and its associated comorbidities. The work integrates various pharmacology approaches such as drug-likeness evaluation, oral bioavailability predictions, and network pharmacology approaches to understand the roles of various bioactive components of the herb. This work identified 67 compounds of W. tinctoria interacting with 238 protein targets. The compounds were found to act through synergistic mechanism in reviving the disrupted process in the diseased state. The results of this work not only shed light on the pharmacological action of the herb but also validate the usage of safe herbal drugs.

  9. Rating the raters in a mixed model: An approach to deciphering the rater reliability

    Science.gov (United States)

    Shang, Junfeng; Wang, Yougui

    2013-05-01

    Rating the raters has attracted extensive attention in recent years. Ratings are quite complex in that the subjective assessment and a number of criteria are involved in a rating system. Whenever the human judgment is a part of ratings, the inconsistency of ratings is the source of variance in scores, and it is therefore quite natural for people to verify the trustworthiness of ratings. Accordingly, estimation of the rater reliability will be of great interest and an appealing issue. To facilitate the evaluation of the rater reliability in a rating system, we propose a mixed model where the scores of the ratees offered by a rater are described with the fixed effects determined by the ability of the ratees and the random effects produced by the disagreement of the raters. In such a mixed model, for the rater random effects, we derive its posterior distribution for the prediction of random effects. To quantitatively make a decision in revealing the unreliable raters, the predictive influence function (PIF) serves as a criterion which compares the posterior distributions of random effects between the full data and rater-deleted data sets. The benchmark for this criterion is also discussed. This proposed methodology of deciphering the rater reliability is investigated in the multiple simulated and two real data sets.

  10. Deciphering the Dynamic Interaction Profile of an Intrinsically Disordered Protein by NMR Exchange Spectroscopy.

    Science.gov (United States)

    Delaforge, Elise; Kragelj, Jaka; Tengo, Laura; Palencia, Andrés; Milles, Sigrid; Bouvignies, Guillaume; Salvi, Nicola; Blackledge, Martin; Jensen, Malene Ringkjøbing

    2018-01-24

    Intrinsically disordered proteins (IDPs) display a large number of interaction modes including folding-upon-binding, binding without major structural transitions, or binding through highly dynamic, so-called fuzzy, complexes. The vast majority of experimental information about IDP binding modes have been inferred from crystal structures of proteins in complex with short peptides of IDPs. However, crystal structures provide a mainly static view of the complexes and do not give information about the conformational dynamics experienced by the IDP in the bound state. Knowledge of the dynamics of IDP complexes is of fundamental importance to understand how IDPs engage in highly specific interactions without concomitantly high binding affinity. Here, we combine rotating-frame R 1ρ , Carr-Purcell-Meiboom Gill relaxation dispersion as well as chemical exchange saturation transfer to decipher the dynamic interaction profile of an IDP in complex with its partner. We apply the approach to the dynamic signaling complex formed between the mitogen-activated protein kinase (MAPK) p38α and the intrinsically disordered regulatory domain of the MAPK kinase MKK4. Our study demonstrates that MKK4 employs a subtle combination of interaction modes in order to bind to p38α, leading to a complex displaying significantly different dynamics across the bound regions.

  11. Deciphering Corporate Governance and Environmental Commitments among Southeast Asian Transnationals: Uptake of Sustainability Certification

    Directory of Open Access Journals (Sweden)

    Jean-Marc Roda

    2015-04-01

    Full Text Available Promoting tropical forest sustainability among corporate players is a major challenge. Many tools have been developed, but without much success. Southeast Asia has become a laboratory of globalization processes, where the development and success of agribusiness transnationals raises questions about their commitment to environmental concerns. An abundance of literature discusses what determines the behavior of Asian corporations, with a particular emphasis on cultural factors. Our hypothesis is that financial factors, such as ownership structure, may also have a fundamental role. We analyzed the audited accounts of four major Asian agribusiness transnationals. Using network analysis, we deciphered how the 931 companies relate to each other and determine the behavior of the transnationals to which they belong. We compared various metrics with the environmental commitment of these transnationals. We found that ownership structures reflect differences in flexibility, control and transaction costs, but not in ethnicities. Capital and its control, ownership structure, and flexibility explain 97% of the environmental behavior. It means that existing market-based tools to promote environmental sustainability do not engage transnationals at the scale where most of their behavior is determined. For the first time, the inner mechanisms of corporate governance are unraveled in agricultural and forest sustainability. New implications such as the convergence of environmental sustainability with family business sustainability emerged.

  12. Deciphering a unique biotin scavenging pathway with redundant genes in the probiotic bacterium Lactococcus lactis.

    Science.gov (United States)

    Zhang, Huimin; Wang, Qingjing; Fisher, Derek J; Cai, Mingzhu; Chakravartty, Vandana; Ye, Huiyan; Li, Ping; Solbiati, Jose O; Feng, Youjun

    2016-05-10

    Biotin protein ligase (BPL) is widespread in the three domains of the life. The paradigm BPL is the Escherichia coli BirA protein, which also functions as a repressor for the biotin biosynthesis pathway. Here we report that Lactococcus lactis possesses two different orthologues of birA (birA1_LL and birA2_LL). Unlike the scenario in E. coli, L. lactis appears to be auxotrophic for biotin in that it lacks a full biotin biosynthesis pathway. In contrast, it retains two biotin transporter-encoding genes (bioY1_LL and bioY2_LL), suggesting the use of a scavenging strategy to obtain biotin from the environment. The in vivo function of the two L. lactis birA genes was judged by their abilities to complement the conditional lethal E. coli birA mutant. Thin-layer chromatography and mass spectroscopy assays demonstrated that these two recombinant BirA proteins catalyze the biotinylation reaction of the acceptor biotin carboxyl carrier protein (BCCP), through the expected biotinoyl-AMP intermediate. Gel shift assays were used to characterize bioY1_LL and BirA1_LL. We also determined the ability to uptake (3)H-biotin by L. lactis. Taken together, our results deciphered a unique biotin scavenging pathway with redundant genes present in the probiotic bacterium L. lactis.

  13. Deciphering the genetic regulatory code using an inverse error control coding framework.

    Energy Technology Data Exchange (ETDEWEB)

    Rintoul, Mark Daniel; May, Elebeoba Eni; Brown, William Michael; Johnston, Anna Marie; Watson, Jean-Paul

    2005-03-01

    We have found that developing a computational framework for reconstructing error control codes for engineered data and ultimately for deciphering genetic regulatory coding sequences is a challenging and uncharted area that will require advances in computational technology for exact solutions. Although exact solutions are desired, computational approaches that yield plausible solutions would be considered sufficient as a proof of concept to the feasibility of reverse engineering error control codes and the possibility of developing a quantitative model for understanding and engineering genetic regulation. Such evidence would help move the idea of reconstructing error control codes for engineered and biological systems from the high risk high payoff realm into the highly probable high payoff domain. Additionally this work will impact biological sensor development and the ability to model and ultimately develop defense mechanisms against bioagents that can be engineered to cause catastrophic damage. Understanding how biological organisms are able to communicate their genetic message efficiently in the presence of noise can improve our current communication protocols, a continuing research interest. Towards this end, project goals include: (1) Develop parameter estimation methods for n for block codes and for n, k, and m for convolutional codes. Use methods to determine error control (EC) code parameters for gene regulatory sequence. (2) Develop an evolutionary computing computational framework for near-optimal solutions to the algebraic code reconstruction problem. Method will be tested on engineered and biological sequences.

  14. Tillering and panicle branching genes in rice.

    Science.gov (United States)

    Liang, Wei-hong; Shang, Fei; Lin, Qun-ting; Lou, Chen; Zhang, Jing

    2014-03-01

    Rice (Oryza sativa L.) is one of the most important staple food crops in the world, and rice tillering and panicle branching are important traits determining grain yield. Since the gene MONOCULM 1 (MOC 1) was first characterized as a key regulator in controlling rice tillering and branching, great progress has been achieved in identifying important genes associated with grain yield, elucidating the genetic basis of yield-related traits. Some of these important genes were shown to be applicable for molecular breeding of high-yielding rice. This review focuses on recent advances, with emphasis on rice tillering and panicle branching genes, and their regulatory networks. Copyright © 2013 Elsevier B.V. All rights reserved.

  15. A spectral analysis of rice grains

    International Nuclear Information System (INIS)

    McIlvaine, M.S.; Cua, F.T.; Navarro, E.F.

    1976-06-01

    With the advent of extensive nuclear testing and the development and use of highly potent pesticides and fertilizers, the hazardous threats of radioactive contamination due to fallout and to the absorption of pesticide residues have been given due consideration. Among the many forms of life exposed to these threats are food crops and among these is rice. Several rice grain samples - Japanese rice samples ''A'' and ''B'' submitted by the National Grains Authority (NGA) for analysis, random samples of rice being sold to the public at local markets, and ''black rice'' which were picked from along the shores of a Mindoro town were subjected to spectral analysis. Results revealed the presence of trace elements normally found in plants, such as; K-42, I-124, Cl-38, Na-24, Br-82, and Mn-56. No mercury was detected in the sample specimen analyzed

  16. Mutation in Rice Abscisic Acid2 Results in Cell Death, Enhanced Disease-Resistance, Altered Seed Dormancy and Development

    Directory of Open Access Journals (Sweden)

    Yongxiang Liao

    2018-03-01

    Full Text Available Lesion mimic mutants display spontaneous cell death, and thus are valuable for understanding the molecular mechanism of cell death and disease resistance. Although a lot of such mutants have been characterized in rice, the relationship between lesion formation and abscisic acid (ABA synthesis pathway is not reported. In the present study, we identified a rice mutant, lesion mimic mutant 9150 (lmm9150, exhibiting spontaneous cell death, pre-harvest sprouting, enhanced growth, and resistance to rice bacterial and blast diseases. Cell death in the mutant was accompanied with excessive accumulation of H2O2. Enhanced disease resistance was associated with cell death and upregulation of defense-related genes. Map-based cloning identified a G-to-A point mutation resulting in a D-to-N substitution at the amino acid position 110 of OsABA2 (LOC_Os03g59610 in lmm9150. Knock-out of OsABA2 through CRISPR/Cas9 led to phenotypes similar to those of lmm9150. Consistent with the function of OsABA2 in ABA biosynthesis, ABA level in the lmm9150 mutant was significantly reduced. Moreover, exogenous application of ABA could rescue all the mutant phenotypes of lmm9150. Taken together, our data linked ABA deficiency to cell death and provided insight into the role of ABA in rice disease resistance.

  17. Mutation in Rice Abscisic Acid2 Results in Cell Death, Enhanced Disease-Resistance, Altered Seed Dormancy and Development.

    Science.gov (United States)

    Liao, Yongxiang; Bai, Que; Xu, Peizhou; Wu, Tingkai; Guo, Daiming; Peng, Yongbin; Zhang, Hongyu; Deng, Xiaoshu; Chen, Xiaoqiong; Luo, Ming; Ali, Asif; Wang, Wenming; Wu, Xianjun

    2018-01-01

    Lesion mimic mutants display spontaneous cell death, and thus are valuable for understanding the molecular mechanism of cell death and disease resistance. Although a lot of such mutants have been characterized in rice, the relationship between lesion formation and abscisic acid (ABA) synthesis pathway is not reported. In the present study, we identified a rice mutant, lesion mimic mutant 9150 ( lmm9150 ), exhibiting spontaneous cell death, pre-harvest sprouting, enhanced growth, and resistance to rice bacterial and blast diseases. Cell death in the mutant was accompanied with excessive accumulation of H 2 O 2 . Enhanced disease resistance was associated with cell death and upregulation of defense-related genes. Map-based cloning identified a G-to-A point mutation resulting in a D-to-N substitution at the amino acid position 110 of OsABA2 (LOC_Os03g59610) in lmm9150 . Knock-out of OsABA2 through CRISPR/Cas9 led to phenotypes similar to those of lmm9150 . Consistent with the function of OsABA2 in ABA biosynthesis, ABA level in the lmm9150 mutant was significantly reduced. Moreover, exogenous application of ABA could rescue all the mutant phenotypes of lmm9150 . Taken together, our data linked ABA deficiency to cell death and provided insight into the role of ABA in rice disease resistance.

  18. Fluoride levels in commercially available rice in Ethiopia | Tegegne ...

    African Journals Online (AJOL)

    Alkaline fusion was used for sample preparation of six varieties for both the raw rice and rice cooked with tap water and fluoridated water. Fluoride levels ranged from 0.1-5.5 mg/kg in raw rice sample. Rice which was cooked with different fluoride levels of water showed increment depending on the method of cooking.

  19. Signatures of adaptation in the weedy rice genome

    Science.gov (United States)

    Weedy rice is a common problem of by product of domestication that has evolved multiple times from cultivated and wild rice relatives. Here we use whole genome sequences to examine the origin and adaptation of the two major US weedy red rice strains, with a comparison to Chinese weedy red rice. We f...

  20. The economic power of the Golden Rice opposition

    NARCIS (Netherlands)

    Wesseler, J.H.H.; Zilberman, D.

    2014-01-01

    Vitamin A enriched rice (Golden Rice) is a cost-efficient solution that can substantially reduce health costs. Despite Golden Rice being available since early 2000, this rice has not been introduced in any country. Governments must perceive additional costs that overcompensate the benefits of the

  1. Significance of rice sheath photosynthesis: Yield determination by ...

    African Journals Online (AJOL)

    Using high-yielding hybrid rice Liangyopeijiu (LYP9), its male parent 9311 and hybrid rice Shanyou 63 (SY63) as the experimental materials, the photosynthesis of rice sheath was studied by 14C radio-autography. The results showed that rice sheath could trap sunlight and produce photosynthates, and these ...

  2. Genomic diversity among Basmati rice ( Oryza sativa L) mutants ...

    African Journals Online (AJOL)

    Mutation breeding can be considered successful in obtaining new cultivars and broadening the genetic base of rice crop. In order to obtain new varieties of rice with improved agronomic and grain characteristics, gamma radiation (60Co) has been used to generate novel mutants of the Basmati rice. In this study rice cultivars ...

  3. 7 CFR 868.301 - Definition of milled rice.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 7 2010-01-01 2010-01-01 false Definition of milled rice. 868.301 Section 868.301... FOR CERTAIN AGRICULTURAL COMMODITIES United States Standards for Milled Rice Terms Defined § 868.301 Definition of milled rice. Whole or broken kernels of rice (Oryza sativa L.) from which the hulls and at...

  4. 7 CFR 868.201 - Definition of rough rice.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 7 2010-01-01 2010-01-01 false Definition of rough rice. 868.201 Section 868.201... FOR CERTAIN AGRICULTURAL COMMODITIES United States Standards for Rough Rice Terms Defined § 868.201 Definition of rough rice. Rice (Oryza sativa L.) which consists of 50 percent or more of paddy kernels (see...

  5. 21 CFR 573.160 - Ammoniated rice hulls.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 6 2010-04-01 2010-04-01 false Ammoniated rice hulls. 573.160 Section 573.160... Additive Listing § 573.160 Ammoniated rice hulls. The food additive ammoniated rice hulls may be safely... obtained by the treatment of ground rice hulls with monocalcium phosphate and anhydrous ammonia at a...

  6. Rice field for the treatment of pond aquaculture effluents | Wang ...

    African Journals Online (AJOL)

    We conducted an experiment to evaluate the efficiency of rice fields in treating pond aquaculture effluent and its responses to different fertilizer treatments. Four treatments was considered in the experiment: no rice planted as the control (CT); rice planted and no fertilizer input (RE); rice planted and a rate of approximately ...

  7. Questioning triple rice intensification on the Vietnamese mekong delta floodplains

    NARCIS (Netherlands)

    Tran, Dung Duc; Halsema, van Gerardo; Hellegers, Petra J.G.J.; Ludwig, Fulco; Wyatt, Andrew

    2018-01-01

    Large areas of the Vietnamese Mekong Delta floodplains (VMDF) are protected by high dikes to facilitate three rice crops per year. While this has increased rice production, there is evidence that triple rice systems have negative long-term effects, both environmental and economic. Double rice

  8. Does African catfish ( Clarias gariepinus ) affect rice in integrated ...

    African Journals Online (AJOL)

    An experiment was conducted for 98 days in the Lake Victoria Basin to investigate the interactions of fish and rice growth performance in rice paddies. The experiment was laid out in a split-plot design, with rice cultivar as the main plot and method of rice-fish culture as the sub-plot. Treatments consisted of two levels of ...

  9. Plant Phenotype Characterization System

    Energy Technology Data Exchange (ETDEWEB)

    Daniel W McDonald; Ronald B Michaels

    2005-09-09

    This report is the final scientific report for the DOE Inventions and Innovations Project: Plant Phenotype Characterization System, DE-FG36-04GO14334. The period of performance was September 30, 2004 through July 15, 2005. The project objective is to demonstrate the viability of a new scientific instrument concept for the study of plant root systems. The root systems of plants are thought to be important in plant yield and thus important to DOE goals in renewable energy sources. The scientific study and understanding of plant root systems is hampered by the difficulty in observing root activity and the inadequacy of existing root study instrumentation options. We have demonstrated a high throughput, non-invasive, high resolution technique for visualizing plant root systems in-situ. Our approach is based upon low-energy x-ray radiography and the use of containers and substrates (artificial soil) which are virtually transparent to x-rays. The system allows us to germinate and grow plant specimens in our containers and substrates and to generate x-ray images of the developing root system over time. The same plant can be imaged at different times in its development. The system can be used for root studies in plant physiology, plant morphology, plant breeding, plant functional genomics and plant genotype screening.

  10. Sex hormone binding globulin phenotypes

    DEFF Research Database (Denmark)

    Cornelisse, M M; Bennett, Patrick; Christiansen, M

    1994-01-01

    Human sex hormone binding globulin (SHBG) is encoded by a normal and a variant allele. The resulting SHBG phenotypes (the homozygous normal SHBG, the heterozygous SHBG and the homozygous variant SHBG phenotype) can be distinguished by their electrophoretic patterns. We developed a novel detection....... This method of detection was used to determine the distribution of SHBG phenotypes in healthy controls of both sexes and in five different pathological conditions characterized by changes in the SHBG level or endocrine disturbances (malignant and benign ovarian neoplasms, hirsutism, liver cirrhosis...... on the experimental values. Differences in SHBG phenotypes do not appear to have any clinical significance and no sex difference was found in the SHBG phenotype distribution....

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

    Science.gov (United States)

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

    2017-01-25

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

  12. Physicochemical and Antioxidant Properties of Rice Bran Oils Produced from Colored Rice Using Different Extraction Methods.

    Science.gov (United States)

    Mingyai, Sukanya; Kettawan, Aikkarach; Srikaeo, Khongsak; Singanusong, Riantong

    2017-06-01

    This study investigated the physicochemical and antioxidant properties of rice bran oil (RBO) produced from the bran of three rice varities; Khao Dawk Mali 105 (white rice), Red Jasmine rice (red rice) and Hom-nin rice (black rice) using three extraction methods including cold-press extraction (CPE), solvent extraction (SE) and supercritical CO 2 extraction (SC-CO 2 ). Yields, color, acid value (AV), free fatty acid (FFA), peroxide value (PV), iodine value (IV), total phenolic compound (TPC), γ-oryzanol, α-tocopherol and fatty acid profile were analyzed. It was found that the yields obtained from SE, SC-CO 2 and CPE extractions were 17.35-20.19%, 14.76-18.16% and 3.22-6.22%, respectively. The RBO from the bran of red and black rice samples exhibited high antioxidant activities. They also contained higher amount of γ-oryzanol and α-tocopherol than those of white rice sample. In terms of extraction methods, SC-CO 2 provided better qualities of RBO as evidenced by their physicochemical and antioxidant properties. This study found that RBO produced from the bran of black rice samples using SC-CO 2 extraction method showed the best physicochemical and antioxidant properties.

  13. Isotopic tracer aided studies of fenvalerate residues in stored rice

    International Nuclear Information System (INIS)

    Varca, L.M.; Sanchez, T.E.; Magallona, E.D.

    1990-01-01

    Following application of 14 C-fenvalerate to milled rice and paddy rice at a concentration of 0.33 mg/kg, only insignificant losses were measured after 9 months. Distribution patterns in surface, methanol extractable and bound residues were studied. Paddy rice contained less extractable residues than milled rice, with the major part being found in the husk. Bound residues in both milled and paddy rice decreased also with length of storage; as much as 30% was found as bound residues after nine months. Cooking reduced the insecticide residues in milled rice by 33-40% and residues in paddy rice by 58%. (author). 8 refs, 1 fig., 4 tabs

  14. New insights into virulence mechanisms of rice pathogen Acidovorax avenae subsp. avenae strain RS-1 following exposure to ?-lactam antibiotics

    OpenAIRE

    Li, Bin; Ge, Mengyu; Zhang, Yang; Wang, Li; Ibrahim, Muhammad; Wang, Yanli; Sun, Guochang; Chen, Gongyou

    2016-01-01

    Recent research has shown that pathogen virulence can be altered by exposure to antibiotics, even when the growth rate is unaffected. Investigating this phenomenon provides new insights into understanding the virulence mechanisms of bacterial pathogens. This study investigates the phenotypic and transcriptomic responses of the rice pathogenic bacterium Acidovorax avenae subsp. avenae (Aaa) strain RS-1 to ?-lactam antibiotics especially Ampicillin (Amp). Our results indicate that exposure to A...

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

    OpenAIRE

    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 ...

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

    Directory of Open Access Journals (Sweden)

    Keyan Zhao

    2010-05-01

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

  17. Genotypic Variability of the Components and their Effects on the Rice Yield: Correlation and Path Analysis Study

    Directory of Open Access Journals (Sweden)

    Sharkhawat Hossain

    2008-06-01

    Full Text Available Twenty modern Boro rice varieties were evaluated with a view to find variability and genetic association for grain yield and yield components characters. Genotypic and Phenotypic correlation among these characters were computed. Both genotypic and phenotypic correlation coefficients were significant between plant height and number of effective tillers per plant followed by panicle length. There was a positive significant correlation between yield and number of effective tillers per plant followed by percent filled grain per panicle. Path coefficient showed that number of effective tiller per plant and plant height are the characters that contribute largely to grain yield.

  18. LHD1, an allele of DTH8/Ghd8, controls late heading date in common wild rice (Oryza rufipogon).

    Science.gov (United States)

    Dai, Xiaodong; Ding, Younian; Tan, Lubin; Fu, Yongcai; Liu, Fengxia; Zhu, Zuofeng; Sun, Xianyou; Sun, Xuewen; Gu, Ping; Cai, Hongwei; Sun, Chuanqing

    2012-10-01

    Flowering at suitable time is very important for plants to adapt to complicated environments and produce their seeds successfully for reproduction. In rice (Oryza rufipogon Griff.) photoperiod regulation is one of the important factors for controlling heading date. Common wild rice, the ancestor of cultivated rice, exhibits a late heading date and a more sensitive photoperiodic response than cultivated rice. Here, through map-based cloning, we identified a major quantitative trait loci (QTL) LHD1 (Late Heading Date 1), an allele of DTH8/Ghd8, which controls the late heading date of wild rice and encodes a putative HAP3/NF-YB/CBF-A subunit of the CCAAT-box-binding transcription factor. Sequence analysis revealed that several variants in the coding region of LHD1 were correlated with a late heading date, and a further complementary study successfully rescued the phenotype. These results suggest that a functional site for LHD1 could be among those variants present in the coding region. We also found that LHD1 could down-regulate the expression of several floral transition activators such as Ehd1, Hd3a and RFT1 under long-day conditions, but not under short-day conditions. This indicates that LHD1 may delay flowering by repressing the expression of Ehd1, Hd3a and RFT1 under long-day conditions. © 2012 Institute of Botany, Chinese Academy of Sciences.

  19. Development and evaluation of a high-throughput, low-cost genotyping platform based on oligonucleotide microarrays in rice

    Directory of Open Access Journals (Sweden)

    Liu Bin

    2008-05-01

    Full Text Available Abstract Background We report the development of a microarray platform for rapid and cost-effective genetic mapping, and its evaluation using rice as a model. In contrast to methods employing whole-genome tiling microarrays for genotyping, our method is based on low-cost spotted microarray production, focusing only on known polymorphic features. Results We have produced a genotyping microarray for rice, comprising 880 single feature polymorphism (SFP elements derived from insertions/deletions identified by aligning genomic sequences of the japonica cultivar Nipponbare and the indica cultivar 93-11. The SFPs were experimentally verified by hybridization with labeled genomic DNA prepared from the two cultivars. Using the genotyping microarrays, we found high levels of polymorphism across diverse rice accessions, and were able to classify all five subpopulations of rice with high bootstrap support. The microarrays were used for mapping of a gene conferring resistance to Magnaporthe grisea, the causative organism of rice blast disease, by quantitative genotyping of samples from a recombinant inbred line population pooled by phenotype. Conclusion We anticipate this microarray-based genotyping platform, based on its low cost-per-sample, to be particularly useful in applications requiring whole-genome molecular marker coverage across large numbers of individuals.

  20. Identification of Rice Accessions Associated with K+/Na+ Ratio and Salt Tolerance Based on Physiological and Molecular Responses

    Directory of Open Access Journals (Sweden)

    Inja Naga Bheema Lingeswara Reddy

    2017-11-01

    Full Text Available The key for rice plant survival under NaCl salt stress is maintaining a high K+/Na+ ratio in its cells. Selection for salt tolerance rice genotypes based on phenotypic performance alone will delay in progress in breeding. Use of molecular markers in tandem with physiological studies will help in better identification of salt tolerant rice accessions. Eight rice accessions along with the check Dongjin were screened using 1/2 Yoshida solution with 50 mmol/L NaCl at the seedling stage. The accessions IT001158, IT246674, IT260533 and IT291341 were classified as salt tolerant based on their K+/Na+ ratios. Seventeen SSR markers reported to be associated with K+/Na+ ratio were used to screen the accessions. Five SSR markers (RM8053, RM345, RM318, RM253 and RM7075 could differentiate accessions classified based on their K+/Na+ ratios. Banding pattern of the accessions was scored compared to the banding pattern of Dongjin. The study differentiated accessions based on their association of K+/Na+ ratio with molecular markers which are very reliable. These markers can play a significant role in screening large set of rice germplasms for salt tolerance and also help in identification of high-yielding varieties with better salt tolerance. The salt tolerant accessions can be taken forward into developing better varieties by conventional breeding and exploring genes for salt tolerance.

  1. Consumer Preferences and Buying Criteria in Rice: A Study to Identify Market Strategy for Thailand Jasmine Rice Export

    NARCIS (Netherlands)

    Suwannaporn, P.; Linnemann, A.R.

    2008-01-01

    Rice consumption per capita in many Asian countries decreased, but it is consumed more in non-rice-eating countries. This study aimed to investigate consumer preferences and attitudes toward Jasmine rice among consumers in target rice export countries to identify opportunities and strategic

  2. Mutant-inducing effect of γ-ray irradiation for hybrid rice F1 derived from cross of black glutinous rice x wild rice

    International Nuclear Information System (INIS)

    Mao Dezhi; Tang Yilan

    1998-01-01

    The hybrid rice F 1 plant derived from the back crossing of glutinous rice x wild rice was irradiated with γ-ray. The result of investigation to the induced mutant showed that through the selection and backcross, a black glutinous rice strain with the short stem, cold tolerance and high yield was developed. The analysis of the ability of heredity variance showed that the selection was effective for the husk colour, black glutinous and black Indica rice, but ineffective for the white Indica rice and seed setting

  3. MORPHO-MOLECULAR SCREENING OF RICE (ORYZA SATIVA L. GENOTYPES AT SEEDLING STAGE FOR SALT TOLERANCE

    Directory of Open Access Journals (Sweden)

    Ali Julfiker Md. Masud

    2014-10-01

    Full Text Available Providing adequate food to meet an escalating population is one of the gravest problems the humankind is now facing. To resolve this crisis identification of salt tolerant rice variety is very vital. So, in this research, ten rice genotypes were used to screen salinity tolerance at the seedling stage in hydroponic system using SSR markers. Salinity screening was done at glasshouse following IRRI standard protocol using two setups of salinized and non-salinized conditions. Genotypes under controlled condition had longer root and shoot length then salt stress genotypes. Parental polymorphism survey was done with ten SSR markers viz., RM336, RM510, RM7075, RM407, RM3201b, RM10748, AP3206f, RM3412, RM585, RM11504 and all were selected to evaluate salt tolerance in rice genotypes. The number of alleles per locus ranged from 3 (AP3206f to 9 (RM336, with an average of 6.1 alleles across 10 loci obtained in the study. The polymorphic information content values ranged from of 0.54 (AP3206f to a high of 0.86 (RM336 with an average of 0.74. The pair-wise comparisons of Nei’s (1973 genetic distance (D between varieties were computed from combined data for the 10 primers, ranged from 0.30 to 0.90 with an average of 0.86, while the similarity index based analysis ranged from 0.00 to 0.70. Finally, the FL-478, FL-378, Binadhan-8 and Binadhan-10 were selected as salt tolerant because they showed tolerance in phenotypic analysis. These phenotypically selected tolerant genotypes could be used for the selection of suitable parents and development of salt tolerant rice varieties.

  4. Evaluation of Heavy Metals Contamination from Environment to Food Matrix by TXRF: The Case of Rice and Rice Husk

    Directory of Open Access Journals (Sweden)

    Fabjola Bilo

    2015-01-01

    Full Text Available This paper is devoted to the chemical analysis of contaminated soils of India and the rice grown in the same area. Total reflection X-ray fluorescence spectroscopy is a well-established technique for elemental chemical analysis of environmental samples, and it can be a useful tool to assess food safety. Metals uptake in rice crop grown in soils from different areas was studied. In this work soil, rice husk and rice samples were analyzed after complete solubilization of samples by microwave acid digestion. Heavy metals concentration detected in rice samples decreases in the following order: Mn > Zn > Cu > Ni > Pb > Cr. The metal content in rice husk was higher than in rice. This study suggests, for the first time, a possible role of heavy metals filter played by rice husk. The knowledge of metals sequestration capability of rice husk may promote some new management practices for rice cultivation to preserve it from pollution.

  5. Phenotypic plasticity, costs of phenotypes, and costs of plasticity

    DEFF Research Database (Denmark)

    Callahan, Hilary S; Maughan, Heather; Steiner, Uli

    2008-01-01

    Why are some traits constitutive and others inducible? The term costs often appears in work addressing this issue but may be ambiguously defined. This review distinguishes two conceptually distinct types of costs: phenotypic costs and plasticity costs. Phenotypic costs are assessed from patterns...... of covariation, typically between a focal trait and a separate trait relevant to fitness. Plasticity costs, separable from phenotypic costs, are gauged by comparing the fitness of genotypes with equivalent phenotypes within two environments but differing in plasticity and fitness. Subtleties associated with both...... types of costs are illustrated by a body of work addressing predator-induced plasticity. Such subtleties, and potential interplay between the two types of costs, have also been addressed, often in studies involving genetic model organisms. In some instances, investigators have pinpointed the mechanistic...

  6. Melatonin is involved in skotomorphogenesis by regulating brassinosteroids biosynthesis in rice plants.

    Science.gov (United States)

    Hwang, Ok Jin; Back, Kyoungwhan

    2018-04-01

    Serotonin N-acetyltransferase (SNAT) is the penultimate enzyme in melatonin biosynthesis catalyzing the conversion of serotonin into N-acetylserotonin. In plants, SNAT is encoded by two isogenes of which SNAT1 is constitutively expressed and its overexpression confers increased yield in rice. However, the role of SNAT2 remains to be clarified. In contrast to SNAT1, the diurnal rhythm of SNAT2 mRNA expression peaks at night. In this study, transgenic rice plants in which SNAT2 expression was suppressed by RNAi technology showed a decrease in melatonin and a dwarf phenotype with erect leaves, reminiscent of brassinosteroids (BRs)-deficient mutants. Of note, the dwarf phenotype was dependent on the presence of dark, suggesting that melatonin is involved in dark growth (skotomorphogenesis). In support of this suggestion, SNAT2 RNAi lines exhibited photomorphogenic phenotypes such as inhibition of internodes and increased expression of light-inducible CAB genes in the dark. The causative gene for the melatonin-mediated BRs biosynthetic gene was DWARF4, a rate limiting BRs biosynthetic gene. Exogenous melatonin treatment induced several BRs biosynthetic genes, including DWARF4, D11, and RAVL1. As expected from the erect leaves, the SNAT2 RNAi lines produced less BRs than the wild type. Our results show for the first time that melatonin is a positive regulator of dark growth or shade outgrowth by regulating BR biosynthesis in plants. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

  7. [Quality of pastas supplemented with rice bran].

    Science.gov (United States)

    Sangronis, E; Rebolledo, M A

    1997-06-01

    The objective of this research was to investigate the potential of using rice bran as an ingredient in pastas spaghetti type. Two of the pastas were made with semolina from durum as raw material, supplemented with 10 and 20% rice bran. The other two were made with granular flour and the same percentage of rice bran. Proximate composition of raw material was analyzed. Pastas were elaborated in a local industry. Composition, proximal, color, texture, and sensorial quality of pastas were determined. Protein content (13.9-15.0%), ash (1.47-3.09%) and dietary fiber (6.71-8.45%) of pastas increased according to the percentage of rice bran added. The hardest pastas were those elaborated with semolina from durum wheat and with a 10% of substitution. Also, they were the most yellow. The sensory panel found differences in quality among the pastas evaluated. Pastas with 10% rice bran had the best quality. The results demonstrated that is possible to elaborate pastas with 20% as maximum of rice bran resulting products with high protein, ash and dietetic fiber content, but some undesirable characteristics were given by the rice bran as white spots, wrinkles and color changes.

  8. Using rice straw to manufacture ceramic bricks

    Directory of Open Access Journals (Sweden)

    Gorbunov German Ivanovich

    2014-12-01

    Full Text Available In the article, the co-authors offer their advanced and efficient methodologies for the recycling of the rice straw, as well as the novel approaches to the ceramic brick quality improvement through the application of the rice straw as the combustible additive and through the formation of amorphous silica in the course of the rice straw combustion. The co-authors provide characteristics of the raw materials, production techniques used to manufacture ceramic bricks, and their basic properties in the article. The co-authors describe the simulated process of formation of amorphous silica. The process in question has two independent steps (or options: 1 rice straw combustion and ash formation outside the oven (in the oxidizing medium, and further application of ash as the additive in the process of burning clay mixtures; 2 adding pre-treated rice straw as the combustible additive into the clay mixture, and its further burning in compliance with the pre-set temperature mode. The findings have proven that the most rational pre-requisite of the rice straw application in the manufacturing of ceramic bricks consists in feeding milled straw into the clay mixture to be followed by molding, drying and burning. Brick samples are highly porous, and they also demonstrate sufficient compressive strength. The co-authors have also identified optimal values of rice straw and ash content in the mixtures under research.

  9. Deep Phenotyping: Deep Learning For Temporal Phenotype/Genotype Classification

    OpenAIRE

    Najafi, Mohammad; Namin, Sarah; Esmaeilzadeh, Mohammad; Brown, Tim; Borevitz, Justin

    2017-01-01

    High resolution and high throughput, genotype to phenotype studies in plants are underway to accelerate breeding of climate ready crops. Complex developmental phenotypes are observed by imaging a variety of accessions in different environment conditions, however extracting the genetically heritable traits is challenging. In the recent years, deep learning techniques and in particular Convolutional Neural Networks (CNNs), Recurrent Neural Networks (RNNs) and Long-Short Term Memories (LSTMs), h...

  10. A rice husk gasifier for paddy drying

    International Nuclear Information System (INIS)

    Mirani, A.A.; Kalwar, S.A.; Ahmad, M.

    2013-01-01

    Due to energy crisis and constant increase in the price of fossil fuels, the world's trend changes to renewable sources of energy like solar, wind and biomass gasification. Substantial biomass potential is available in Pakistan in the form of agriculture or forest residue (rice straw, rice husk, cotton stalks, corn cobs, wood chips, wood saw, etc.). These can be best utilised for the production of producer gas or synthetic gas that can be used for drying of agricultural crops. The drying process is an important activity of post harvest processing for long-term storage. Rice husk is nowadays commonly used for biomass gasification and its heat content value is about 15MJ/kg. It constitutes about 30 percent of rice production. A rice husk gasifier was developed and evaluated on paddy drying at Japan International Cooperation Agency (JICA), Tsukuba International Center (TBIC), Japan. Rice husk gasifier has following major components; husk feeding system, ash chamber, burner, centrifugal fan, drying chamber, gasifier reactor, air duct and an electric motor of 0.37kW. The average drying plenum air temperature was recorded as 45 degree C during the drying process. The paddy 'IR 28' from initial moisture content of 24% was dried up to 14% moisture content for about 3.33h consuming 3kg/h of rice husk. The efficiency was found to be 58%. The rice husk gasifier can also be used for drying the fruits and vegetables, provided that heat exchanger should be attached with it. The overall performance of rice husk gasifier was satisfactory and will be beneficial for small scale farmers, food processors and millers as well. (author)

  11. Recent and ancient recharge deciphered by multi-dating tracer technique

    Science.gov (United States)

    Dogramaci, Shawan; Cook, Peter; Mccallum, Jimes; Purtchert, Roland

    2017-04-01

    Determining groundwater residence time from environmental tracer concentrations obtained from open bores or long screened intervals is fraught with difficulty because the sampled water represents variety of ages. Information on the distribution of groundwater age is commonly obtained by measuring more than one tracer. We examined the use of the multi-tracer technique representing different time frames (39Ar, 85Kr, 14C, 3H, CFC 11- CFC-12 CFC-113, SF6 and Cl,) to decipher the groundwater ages sampled from long screened bores in a regional aquifer in the Pilbara region of northwest Australia. We then applied a technique that assumes limited details of the form of the age distribution. Tracer concentrations suggest that groundwater samples are a mixture of young and old water - the former is inferred to represent localised recharge from an adjacent creek, and the latter to be diffuse recharge. Using our method, we were able to identify distinct age components in the groundwater. The results suggest the presence of four distinct age groups; zero and 20 years, 50 to 100 years, 100 to 600 years and approximately 1000 years old. These relatively high recharge events were consistent with local recharge sources (50-100 years) and confirmed by palaeo-climate record obtained from lake sediments. We found that although the ages of these components were well constrained, the relative proportions of each component was highly sensitive to errors of environmental tracer data. Our results show that the method we implemented can identify distinct age groups in groundwater samples without prior knowledge of the age distribution. The presence of distinct recharge times gives insight into groundwater flow conditions over long periods of time.

  12. Perspectives on deciphering mechanisms underlying plant heat stress response and thermotolerance

    Directory of Open Access Journals (Sweden)

    Kamila Lucia Bokszczanin

    2013-08-01

    Full Text Available Global warming is a major threat for agriculture and food safety and in many cases the negative effects are already apparent. The current challenge of basic and applied plant science is to decipher the molecular mechanisms of heat stress response and thermotolerance in detail and use this information to identify genotypes that will withstand unfavorable environmental conditions. Nowadays X-omics approaches complement the findings of previous targeted studies and highlight the complexity of heat stress response mechanisms giving information for so far unrecognized genes, proteins and metabolites as potential key players of thermotolerance. Even more, roles of epigenetic mechanisms and the involvement of small RNAs in thermotolerance are currently emerging and thus open new directions of yet unexplored areas of plant heat stress response. In parallel it is emerging that although the whole plant is vulnerable to heat, specific organs are particularly sensitive to elevated temperatures. This has redirected research from the vegetative to generative tissues. The sexual reproduction phase is considered as the most sensitive to heat and specifically pollen exhibits the highest sensitivity and frequently an elevation of the temperature just a few degrees above the optimum during pollen development can have detrimental effects for crop production. Compared to our knowledge on heat stress response of vegetative tissues, the information on pollen is still scarce. Nowadays, several techniques for high-throughput X-omics approaches provide major tools to explore the principles of pollen heat stress response and thermotolerance mechanisms in specific genotypes. The collection of such information will provide an excellent support for improvement of breeding programs to facilitate the development of tolerant cultivars. The review aims at describing the current knowledge of thermotolerance mechanisms and the technical advances which will foster new insights into

  13. Deciphering the genomic architecture of the stickleback brain with a novel multilocus gene-mapping approach.

    Science.gov (United States)

    Li, Zitong; Guo, Baocheng; Yang, Jing; Herczeg, Gábor; Gonda, Abigél; Balázs, Gergely; Shikano, Takahito; Calboli, Federico C F; Merilä, Juha

    2017-03-01

    Quantitative traits important to organismal function and fitness, such as brain size, are presumably controlled by many small-effect loci. Deciphering the genetic architecture of such traits with traditional quantitative trait locus (QTL) mapping methods is challenging. Here, we investigated the genetic architecture of brain size (and the size of five different brain parts) in nine-spined sticklebacks (Pungitius pungitius) with the aid of novel multilocus QTL-mapping approaches based on a de-biased LASSO method. Apart from having more statistical power to detect QTL and reduced rate of false positives than conventional QTL-mapping approaches, the developed methods can handle large marker panels and provide estimates of genomic heritability. Single-locus analyses of an F 2 interpopulation cross with 239 individuals and 15 198, fully informative single nucleotide polymorphisms (SNPs) uncovered 79 QTL associated with variation in stickleback brain size traits. Many of these loci were in strong linkage disequilibrium (LD) with each other, and consequently, a multilocus mapping of individual SNPs, accounting for LD structure in the data, recovered only four significant QTL. However, a multilocus mapping of SNPs grouped by linkage group (LG) identified 14 LGs (1-6 depending on the trait) that influence variation in brain traits. For instance, 17.6% of the variation in relative brain size was explainable by cumulative effects of SNPs distributed over six LGs, whereas 42% of the variation was accounted for by all 21 LGs. Hence, the results suggest that variation in stickleback brain traits is influenced by many small-effect loci. Apart from suggesting moderately heritable (h 2  ≈ 0.15-0.42) multifactorial genetic architecture of brain traits, the results highlight the challenges in identifying the loci contributing to variation in quantitative traits. Nevertheless, the results demonstrate that the novel QTL-mapping approach developed here has distinctive advantages

  14. Comprehensive proteome profiling in Aedes albopictus to decipher Wolbachia-arbovirus interference phenomenon.

    Science.gov (United States)

    Saucereau, Yoann; Valiente Moro, Claire; Dieryckx, Cindy; Dupuy, Jean-William; Tran, Florence-Hélène; Girard, Vincent; Potier, Patrick; Mavingui, Patrick

    2017-08-18

    Aedes albopictus is a vector of arboviruses that cause severe diseases in humans such as Chikungunya, Dengue and Zika fevers. The vector competence of Ae. albopictus varies depending on the mosquito population involved and the virus transmitted. Wolbachia infection status in believed to be among key elements that determine viral transmission efficiency. Little is known about the cellular functions mobilized in Ae. albopictus during co-infection by Wolbachia and a given arbovirus. To decipher this tripartite interaction at the molecular level, we performed a proteome analysis in Ae. albopictus C6/36 cells mono-infected by Wolbachia wAlbB strain or Chikungunya virus (CHIKV), and bi-infected. We first confirmed significant inhibition of CHIKV by Wolbachia. Using two-dimensional gel electrophoresis followed by nano liquid chromatography coupled with tandem mass spectrometry, we identified 600 unique differentially expressed proteins mostly related to glycolysis, translation and protein metabolism. Wolbachia infection had greater impact on cellular functions than CHIKV infection, inducing either up or down-regulation of proteins associated with metabolic processes such as glycolysis and ATP metabolism, or structural glycoproteins and capsid proteins in the case of bi-infection with CHIKV. CHIKV infection inhibited expression of proteins linked with the processes of transcription, translation, lipid storage and miRNA pathways. The results of our proteome profiling have provided new insights into the molecular pathways involved in tripartite Ae. albopictus-Wolbachia-CHIKV interaction and may help defining targets for the better implementation of Wolbachia-based strategies for disease transmission control.

  15. Invoking adaptation to decipher the genetic legacy of past climate change.

    Science.gov (United States)

    de Lafontaine, Guillaume; Napier, Joseph D; Petit, Rémy J; Hu, Feng Sheng

    2018-05-05

    Persistence of natural populations during periods of climate change is likely to depend on migration (range shifts) or adaptation. These responses were traditionally considered discrete processes and conceptually divided into the realms of ecology and evolution. In a milestone paper, Davis and Shaw (2001) argued that the interplay of adaptation and migration was central to biotic responses to Quaternary climate, but since then there has been no synthesis of efforts made to set up this research program. Here we review some of the salient findings from molecular genetic studies assessing ecological and evolutionary responses to Quaternary climate change. These studies have revolutionized our understanding of population processes associated with past species migration. However, knowledge remains limited about the role of natural selection for local adaptation of populations to Quaternary environmental fluctuations and associated range shifts, and for the footprints this might have left on extant populations. Next-generation sequencing technologies, high-resolution paleoclimate analyses, and advances in population genetic theory offer an unprecedented opportunity to test hypotheses about adaptation through time. Recent population genomics studies have greatly improved our understanding of the role of contemporary adaptation to local environments in shaping spatial patterns of genetic diversity across modern-day landscapes. Advances in this burgeoning field provide important conceptual and methodological bases to decipher the historical role of natural selection and assess adaptation to past environmental variation. We suggest that a process called "temporal conditional neutrality" has taken place: some alleles favored in glacial environments become selectively neutral in modern-day conditions, whereas some alleles that had been neutral during glacial periods become under selection in modern environments. Building on this view, we present a new integrative framework for

  16. Penguin Proxies: Deciphering Millennial-Scale Antarctic Ecosystem Change using Amino Acid Stable Isotope Analysis.

    Science.gov (United States)

    Michelson, C.; McMahon, K.; Emslie, S. D.; Patterson, W. P.; McCarthy, M. D.; Polito, M. J.

    2017-12-01

    The Southern Ocean ecosystem is undergoing rapid environmental change due to ongoing and historic anthropogenic impacts such as climate change and marine mammal harvesting. These disturbances may have cascading effects through the Antarctic food webs, resulting in profound shifts in the sources and cycling of organic matter supporting higher-trophic organisms, such as penguins. For example, bulk stable isotope analyses of modern and ancient preserved penguin tissues suggest variations in penguin feeding ecology throughout the Holocene with dramatic isotopic shifts in the last 200 years. However, it is not clear whether these isotopic shifts resulted from changes at the base of the food web, dietary shifts in penguins, or some combination of both factors. Newly developed compound-specific stable nitrogen isotope analysis of individual amino acids (CSIA-AA) may provide a powerful new tool to tease apart these confounding variables. Stable nitrogen isotope values of trophic amino acids (e.g., glutamic acid) increase substantially with each trophic transfer in the food web, while source amino acid (e.g., phenylalanine) stable nitrogen isotope values remain relatively unchanged and reflect ecosystem baselines. As such, we can use this CSIA-AA approach to decipher between baseline and dietary shifts in penguins over time from modern and ancient eggshells of Pygoscelis penguins in the Antarctic Peninsula and the Ross Sea regions of Antarctica. In order to accurately apply this CSIA-AA approach, we first characterized the trophic fractionation factors of individual amino acids between diet and penguin consumers in a long-term controlled penguin feeding experiment. We then applied these values to modern and ancient eggshells from the Antarctic Peninsula and Ross Sea to evaluate shifts in penguin trophic dynamics as a function of climate and anthropogenic interaction throughout much of the Holocene. This work develops a cutting edge new molecular geochemistry approach

  17. Genome-wide association study of salt tolerance at the seed germination stage in rice.

    Science.gov (United States)

    Shi, Yingyao; Gao, Lingling; Wu, Zhichao; Zhang, Xiaojing; Wang, Mingming; Zhang, Congshun; Zhang, Fan; Zhou, Yongli; Li, Zhikang

    2017-05-30

    Improving the salt tolerance of direct-seeding rice at the seed germination stage is a major breeding goal in many Asian rice-growing countries, where seedlings must often establish in soils with a high salt content. Thus, it is important to understand the genetic mechanisms of salt tolerance in rice and to screen for germplasm with salt tolerance at the seed germination stage. Here, we investigated seven seed germination-related traits under control and salt-stress conditions and conducted a genome-wide association study based on the re-sequencing of 478 diverse rice accessions. The analysis used a mixed linear model and was based on 6,361,920 single nucleotide polymorphisms in 478 rice accessions grouped into whole, indica, and non-indica panels. Eleven loci containing 22 significant salt tolerance-associated single nucleotide polymorphisms were identified based on the stress-susceptibility indices (SSIs) of vigor index (VI) and mean germination time (MGT). From the SSI of VI, six major loci were identified, explaining 20.2% of the phenotypic variation. From the SSI of MGT, five major loci were detected, explaining 26.4% of the phenotypic variation. Of these, seven loci on chromosomes 1, 5, 6, 11, and 12 were close to six previously identified quantitative gene loci/genes related to tolerance to salinity or other abiotic stresses. The strongest association region for the SSI of MGT was identified in a ~ 13.3 kb interval (15450039-15,463,330) on chromosome 1, near salt-tolerance quantitative trait loci controlling the Na + : K + ratio, total Na + uptake, and total K + concentration. The strongest association region for the SSI of VI was detected in a ~ 164.2 kb interval (526662-690,854) on chromosome 2 harboring two nitrate transporter family genes (OsNRT2.1 and OsNRT2.2), which affect gene expression under salt stress. The haplotype analysis indicated that OsNRT2.2 was associated with subpopulation differentiation and its minor/rare tolerant haplotype was

  18. Analysis of rice purchase decision on rice consumer in Bandung city

    Science.gov (United States)

    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.

  19. Alanine aminotransferase variants conferring diverse NUE phenotypes in Arabidopsis thaliana.

    Science.gov (United States)

    McAllister, Chandra H; Good, Allen G

    2015-01-01

    Alanine aminotransferase (AlaAT, E.C. 2.6.1.2), is a pyridoxal-5'-phosphate-dependent (PLP) enzyme that catalyzes the reversible transfer of an amino group from alanine to 2-oxoglutarate to produce glutamate and pyruvate, or vice versa. It has been well documented in both greenhouse and field studies that tissue-specific over-expression of AlaAT from barley (Hordeum vulgare, HvAlaAT) results in a significant increase in plant NUE in both canola and rice. While the physical phenotypes associated with over-expression of HvAlaAT have been well characterized, the role this enzyme plays in vivo to create a more N efficient plant remains unknown. Furthermore, the importance of HvAlaAT, in contrast to other AlaAT enzyme homologues in creating this phenotype has not yet been explored. To address the role of AlaAT in NUE, AlaAT variants from diverse sources and different subcellular locations, were expressed in the wild-type Arabidopsis thaliana Col-0 background and alaat1;2 (alaat1-1;alaat2-1) knockout background in various N environments. The analysis and comparison of both the physical and physiological properties of AlaAT over-expressing transgenic plants demonstrated significant differences between plants expressing the different AlaAT enzymes under different external conditions. This analysis indicates that the over-expression of AlaAT variants other than HvAlaAT in crop plants could further increase the NUE phenotype(s) previously observed.

  20. Ehd4 encodes a novel and Oryza-genus-specific regulator of photoperiodic flowering in rice.

    Directory of Open Access Journals (Sweden)

    He Gao

    Full Text Available Land plants have evolved increasingly complex regulatory modes of their flowering time (or heading date in crops. Rice (Oryza sativa L. is a short-day plant that flowers more rapidly in short-day but delays under long-day conditions. Previous studies have shown that the CO-FT module initially identified in long-day plants (Arabidopsis is evolutionary conserved in short-day plants (Hd1-Hd3a in rice. However, in rice, there is a unique Ehd1-dependent flowering pathway that is Hd1-independent. Here, we report isolation and characterization of a positive regulator of Ehd1, Early heading date 4 (Ehd4. ehd4 mutants showed a never flowering phenotype under natural long-day conditions. Map-based cloning revealed that Ehd4 encodes a novel CCCH-type zinc finger protein, which is localized to the nucleus and is able to bind to nucleic acids in vitro and transactivate transcription in yeast, suggesting that it likely functions as a transcriptional regulator. Ehd4 expression is most active in young leaves with a diurnal expression pattern similar to that of Ehd1 under both short-day and long-day conditions. We show that Ehd4 up-regulates the expression of the "florigen" genes Hd3a and RFT1 through Ehd1, but it acts independently of other known Ehd1 regulators. Strikingly, Ehd4 is highly conserved in the Oryza genus including wild and cultivated rice, but has no homologs in other species, suggesting that Ehd4 is originated along with the diversification of the Oryza genus from the grass family during evolution. We conclude that Ehd4 is a novel Oryza-genus-specific regulator of Ehd1, and it plays an essential role in photoperiodic control of flowering time in rice.

  1. Allelic diversity in an NLR gene BPH9 enables rice to combat planthopper variation.

    Science.gov (United States)

    Zhao, Yan; Huang, Jin; Wang, Zhizheng; Jing, Shengli; Wang, Yang; Ouyang, Yidan; Cai, Baodong; Xin, Xiu-Fang; Liu, Xin; Zhang, Chunxiao; Pan, Yufang; Ma, Rui; Li, Qiaofeng; Jiang, Weihua; Zeng, Ya; Shangguan, Xinxin; Wang, Huiying; Du, Bo; Zhu, Lili; Xu, Xun; Feng, Yu-Qi; He, Sheng Yang; Chen, Rongzhi; Zhang, Qifa; He, Guangcun

    2016-10-24

    Brown planthopper (BPH), Nilaparvata lugens Stål, is one of the most devastating insect pests of rice (Oryza sativa L.). Currently, 30 BPH-resistance genes have been genetically defined, most of which are clustered on specific chromosome regions. Here, we describe molecular cloning and characterization of a BPH-resistance gene, BPH9, mapped on the long arm of rice chromosome 12 (12L). BPH9 encodes a rare type of nucleotide-binding and leucine-rich repeat (NLR)-containing protein that localizes to the endomembrane system and causes a cell death phenotype. BPH9 activates salicylic acid- and jasmonic acid-signaling pathways in rice plants and confers both antixenosis and antibiosis to BPH. We further demonstrated that the eight BPH-resistance genes that are clustered on chromosome 12L, including the widely used BPH1, are allelic with each other. To honor the priority in the literature, we thus designated this locus as BPH1/9 These eight genes can be classified into four allelotypes, BPH1/9-1, -2, -7, and -9 These allelotypes confer varying levels of resistance to different biotypes of BPH. The coding region of BPH1/9 shows a high level of diversity in rice germplasm. Homologous fragments of the nucleotide-binding (NB) and leucine-rich repeat (LRR) domains exist, which might have served as a repository for generating allele diversity. Our findings reveal a rice plant strategy for modifying the genetic information to gain the upper hand in the struggle against insect herbivores. Further exploration of natural allelic variation and artificial shuffling within this gene may allow breeding to be tailored to control emerging biotypes of BPH.

  2. Cloning, characterization and expression of OsFMO(t) in rice encoding a flavin monooxygenase.

    Science.gov (United States)

    Yi, Jicai; Liu, Lanna; Cao, Youpei; Li, Jiazuo; Mei, Mantong

    2013-12-01

    Flavin monooxygenases (FMO) play a key role in tryptophan (Trp)-dependent indole-acetic acid (IAA) biosynthesis in plants and regulate plant growth and development. In this study, the full-length genomic DNA and cDNA of OsFMO(t), a FMO gene that was originally identified from a rolled-leaf mutant in rice, was isolated and cloned from wild type of the rolled-leaf mutant. OsFMO(t) was found to have four exons and three introns, and encode a protein with 422 amino acid residues that contains two basic conserved motifs, with a 'GxGxxG' characteristic structure. OsFMO(t) showed high amino acid sequence identity with FMO proteins from other plants, in particular with YUCCA from Arabidopsis, FLOOZY from Petunia, and OsYUCCA1 from rice. Our phylogenetic analysis showed that OsFMO(t) and the homologous FMO proteins belong to the same clade in the evolutionary tree. Overexpression of OsFMO(t) in transformed rice calli produced IAA-excessive phenotypes that showed browning and lethal effects when exogenous auxins such as naphthylacetic acid (NAA) were added to the medium. These results suggested that the OsFMO(t) protein is involved in IAA biosynthesis in rice and its overexpression could lead to the malformation of calli. Spatio-temporal expression analysis using RT-PCR and histochemical analysis for GUS activity revealed that expression of OsFMO(t) was totally absent in the rolled-leaf mutant. However, in the wild type variety, this gene was expressed at different levels temporally and spatially, with the highest expression observed in tissues with fast growth and cell division such as shoot apexes, tender leaves and root tips. Our results demonstrated that IAA biosynthesis regulated by OsFMO(t) is likely localized and might play an essential role in shaping local IAA concentrations which, in turn, is critical for regulating normal growth and development in rice.

  3. Estimation of loci involved in non-shattering of seeds in early rice domestication.

    Science.gov (United States)

    Ishikawa, Ryo; Nishimura, Akinori; Htun, Than Myint; Nishioka, Ryo; Oka, Yumi; Tsujimura, Yuki; Inoue, Chizuru; Ishii, Takashige

    2017-04-01

    Rice (Oryza sativa L.) is widely cultivated around the world and is known to be domesticated from its wild form, O. rufipogon. A loss of seed shattering is one of the most obvious phenotypic changes selected for during rice domestication. Previously, three seed-shattering loci, qSH1, sh4, and qSH3 were reported to be involved in non-shattering of seeds of Japonica-type cultivated rice, O. sativa cv. Nipponbare. In this study, we focused on non-shattering characteristics of O. sativa Indica cv. IR36 having functional allele at qSH1. We produced backcross recombinant inbred lines having chromosomal segments from IR36 in the genetic background of wild rice, O. rufipogon W630. Histological and quantitative trait loci analyses of abscission layer formation were conducted. In the analysis of quantitative trait loci, a strong peak was observed close to sh4. We, nevertheless, found that some lines showed complete abscission layer formation despite carrying the IR36 allele at sh4, implying that non-shattering of seeds of IR36 could be regulated by the combination of mutations at sh4 and other seed-shattering loci. We also genotyped qSH3, a recently identified seed-shattering locus. Lines that have the IR36 alleles at sh4 and qSH3 showed inhibition of abscission layer formation but the degree of seed shattering was different from that of IR36. On the basis of these results, we estimated that non-shattering of seeds in early rice domestication involved mutations in at least three loci, and these genetic materials produced in this study may help to identify novel seed-shattering loci.

  4. Laboratory Screening for Resistance in Rice to Rice Stem Borer Chilo Suppressalis Walker

    International Nuclear Information System (INIS)

    Singgih Sutrisno

    2004-01-01

    Rice stem borer Chilo suppressalis Walker is one of the major insect pests in rice in Indonesia. The use of insect pest resistant variety of rice is one of the effective techniques against pests. Breeding of resistance to insect pests rice crops often faced difficulties in obtaining a lot of insect amounts due to the unavailability of enough number insects pests in the field so that a laboratory bioassay is needed. In this experiments five rice varieties were used: a Pelita I/1, Atomita I, Cisadane, Cisanggarung, and IR 36. Rice seedling 7 days of age were put in 1 liter plastic vials for rice resistance test against the attack of insect pest C. suppressalis. The parameters observed were larval and pupal viability, pupal weight, and eggs production. The larval and pupal viability which were reared on of Pelita I/1 and Atomita I rice seedlings were 68.5 % - 55.5 % and 57.3 % - 46.7 % respectively. The respective lowest percentages were found in IR 36 which was about 41.3 % - 29.8 % .The experiment results on the parameters of pupal weight and egg production showed similar results to that on the parameters of larval and pupal viability. Rice variety of IR 36 showed more resistance to the other varieties, while Pelita I/1 and Atomita I showed the most susceptible to the attack of insect pest C. suppressalis. (author)

  5. Understanding the evolution of rice technology in China - from traditional agriculture to GM rice today.

    Science.gov (United States)

    Shen, Xiaobai

    2010-01-01

    This paper provides an historical survey of the evolution of rice technology in China, from the traditional farming system to genetically modified rice today. Using sociotechnological analytical framework, it analyses rice technology as a socio-technical ensemble - a complex interaction of material and social elements, and discusses the specificity of technology development and its socio-technical outcomes. It points to two imperatives in rice variety development: wholesale transporting agricultural technology and social mechanism to developing countries are likely lead to negative consequences; indigenous innovation including deploying GM technology for seed varietal development and capturing/cultivating local knowledge will provide better solutions.

  6. PhosphoRice: a meta-predictor of rice-specific phosphorylation sites

    Directory of Open Access Journals (Sweden)

    Que Shufu

    2012-02-01

    Full Text Available Abstract Background As a result of the growing body of protein phosphorylation sites data, the number of phosphoprotein databases is constantly increasing, and dozens of tools are available for predicting protein phosphorylation sites to achieve fast automatic results. However, none of the existing tools has been developed to predict protein phosphorylation sites in rice. Results In this paper, the phosphorylation site predictors, NetPhos 2.0, NetPhosK, Kinasephos, Scansite, Disphos and Predphosphos, were integrated to construct meta-predictors of rice-specific phosphorylation sites using several methods, including unweighted voting, unreduced weighted voting, reduced unweighted voting and weighted voting strategies. PhosphoRice, the meta-predictor produced by using weighted voting strategy with parameters selected by restricted grid search and conditional random search, performed the best at predicting phosphorylation sites in rice. Its Matthew's Correlation Coefficient (MCC and Accuracy (ACC reached to 0.474 and 73.8%, respectively. Compared to the best individual element predictor (Disphos_default, PhosphoRice archieved a significant increase in MCC of 0.071 (P Conclusions PhosphoRice is a powerful tool for predicting unidentified phosphorylation sites in rice. Compared to the existing methods, we found that our tool showed greater robustness in ACC and MCC. PhosphoRice is available to the public at http://bioinformatics.fafu.edu.cn/PhosphoRice.

  7. International tourist preference of Lodok Rice Field natural elements, the cultural rice field from Manggarai - Indonesia

    Science.gov (United States)

    March Syahadat, Ray; Trie Putra, Priambudi; Nuraini; Nailufar, Balqis; Fatmala Makhmud, Desy

    2017-10-01

    Lodok Rice Field or usually known as spiderweb rice field is a system of land division. It cultural rice field only found on Manggarai, Province of East Nusa Tenggara, Indonesia. The landscape of Lodok Rice Field was aesthetic and it has big potential for tourism development. The aim of this study was to know the perception of natural elements of Lodok Rice Field landscape that could influence international tourist to visited Lodok Rice Field. If we know the elements that could influenced the international tourist, we could used the landscape image for tourism media promotion. The methods of this study used scenic beauty estimation (SBE) by 85 respondents from 34 countries and Kruskal Wallis H test. The countries grouped by five continents (Asia, America, Europe, Africa, and Oceania). The result showed that the Asian respondents liked the elements of sky, mountain, and the rice field. Then, the other respondent from another continent liked the elements of sunshine, mountain, and the rice field. Although the Asian had different perception about landscape elements of rice field’s good view, it’s not differ significantly by Kruskal Wallis H test.

  8. Creation of transgenic rice plants producing small interfering RNA of Rice tungro spherical virus.

    Science.gov (United States)

    Le, Dung Tien; Chu, Ha Duc; Sasaya, Takahide

    2015-01-01

    Rice tungro spherical virus (RTSV), also known as Rice waika virus, does not cause visible symptoms in infected rice plants. However, the virus plays a critical role in spreading Rice tungro bacilliform virus (RTBV), which is the major cause of severe symptoms of rice tungro disease. Recent studies showed that RNA interference (RNAi) can be used to develop virus-resistance transgenic rice plants. In this report, we presented simple procedures and protocols needed for the creation of transgenic rice plants capable of producing small interfering RNA specific against RTSV sequences. Notably, our study showed that 60 out of 64 individual hygromycin-resistant lines (putative transgenic lines) obtained through transformation carried transgenes designed for producing hairpin double-stranded RNA. Northern blot analyses revealed the presence of small interfering RNA of 21- to 24-mer in 46 out of 56 confirmed transgenic lines. Taken together, our study indicated that transgenic rice plants carrying an inverted repeat of 500-bp fragments encoding various proteins of RTSV can produce small interfering RNA from the hairpin RNA transcribed from that transgene. In light of recent studies with other viruses, it is possible that some of these transgenic rice lines might be resistant to RTSV.

  9. Lead in rice: analysis of baseline lead levels in market and field collected rice grains.

    Science.gov (United States)

    Norton, Gareth J; Williams, Paul N; Adomako, Eureka E; Price, Adam H; Zhu, Yongguan; Zhao, Fang-Jie; McGrath, Steve; Deacon, Claire M; Villada, Antia; Sommella, Alessia; Lu, Ying; Ming, Lei; De Silva, P Mangala C S; Brammer, Hugh; Dasgupta, Tapash; Islam, M Rafiqul; Meharg, Andrew A

    2014-07-01

    In a large scale survey of rice grains from markets (13 countries) and fields (6 countries), a total of 1578 rice grain samples were analysed for lead. From the market collected samples, only 0.6% of the samples exceeded the Chinese and EU limit of 0.2 μg g(-1) lead in rice (when excluding samples collected from known contaminated/mine impacted regions). When evaluating the rice grain samples against the Food and Drug Administration's (FDA) provisional total tolerable intake (PTTI) values for children and pregnant women, it was found that only people consuming large quantities of rice were at risk of exceeding the PTTI from rice alone. Furthermore, 6 field experiments were conducted to evaluate the proportion of the variation in lead concentration in rice grains due to genetics. A total of 4 of the 6 field experiments had significant differences between genotypes, but when the genotypes common across all six field sites were assessed, only 4% of the variation was explained by genotype, with 9.5% and 11% of the variation explained by the environment and genotype by environment interaction respectively. Further work is needed to identify the sources of lead contamination in rice, with detailed information obtained on the locations and environments where the rice is sampled, so that specific risk assessments can be performed. Copyright © 2014 Elsevier B.V. All rights reserved.

  10. Characterization of Volatile Flavor Compounds in Chinese Rice Wine Fermented from Enzymatic Extruded Rice.

    Science.gov (United States)

    Xu, Enbo; Long, Jie; Wu, Zhengzong; Li, Hongyan; Wang, Fang; Xu, Xueming; Jin, Zhengyu; Jiao, Aiquan

    2015-07-01

    Enzymatic extrusion, instead of traditional steam cooking, to treat rice is an efficient and alternative pretreatment for Chinese rice wine fermentation. In order to determine the formation of volatiles in enzymatic extrusion-processed rice wine (EE), and to confirm its characteristic flavor compounds, headspace solid-phase micro-extraction followed by GC-MS was used. A total of 66 volatile compounds were identified in EE. During fermentation, most volatiles generated from enzymatic extruded rice had the similar trends with those from steam-cooked rice, but the differences in the concentration of volatiles indicated a changed balance of flavors release caused by enzymatic extrusion. Besides, the concentrations and sorts of volatiles in EEs fermented from different rice particle sizes, were not dramatically different. By principal component analysis, EE could be distinctly separated from other traditional Chinese rice wines according to its characteristic volatiles, namely, 2-heptanol, 1-octen-3-ol, ethyl 4-hydroxybenzoate, methylpentyl 2-propenoate, γ-hexalactone, and 4-vinylguaiacol. Enzymatic extrusion liquefaction has been a popular thermal treatment for cereals, and gradually being applied in fermentation and liquor-making industry all over the world. The characterization of volatile flavor compounds in Chinese rice wine processed by enzymatic extrusion liquefaction pretreatment, might be made use not only for a better understanding of this new-type rice wine, but for the further utilization of enzymatic extrusion in other wine or alcohol production as well. © 2015 Institute of Food Technologists®

  11. An update on the use of co-products from the milling of rice in value added food products

    Science.gov (United States)

    Because of the huge quantity of rice produced annually, milled-rice co-products; such as, rice bran, rice oil, rice wax, rice flour, and rice hull are plentiful and readily available. These co-products could be valuable sources of food ingredients, but they have been vastly under-utilized. Rice bra...

  12. PHENOTYPIC CORRELATIONS AND BODY WEIGHTS ...

    African Journals Online (AJOL)

    Dr Osondu

    Ethiopian Journal of Environmental Studies and Management Vol. 4 No.3 2011. PHENOTYPIC ... because of its high meat quality and acceptance by her populace. The meat is ... commands high price in the restaurants and markets than other ...

  13. Elucidation of complex nature of PEG induced drought-stress response in rice root using comparative proteomics approach

    Directory of Open Access Journals (Sweden)

    Lalit Agrawal

    2016-09-01

    Full Text Available Along with many adaptive strategies, dynamic changes in protein abundance seem to be the common strategy to cope up with abiotic stresses which can be best explored through proteomics. Understanding of drought response is the key to decipher regulatory mechanism of better adaptation. Rice (Oryza sativa L. proteome represents a phenomenal source of proteins that govern traits of agronomic importance, such as drought tolerance. In this study, a comparison of root cytoplasmic proteome was done for a drought tolerant rice (Heena cultivar in PEG induced drought conditions. A total of 510 protein spots were observed by PDQuest analysis and 125 differentially regulated spots were subjected for MALDI-TOF MS-MS analysis out of which 102 protein spots identified which further led to identification of 78 proteins with a significant score. These 78 differentially expressed proteins appeared to be involved in different biological pathways. The largest percentage of identified proteins was involved in bioenergy and metabolism (29% and mainly consists of malate dehydrogenase, succinyl-CoA, putative acetyl-CoA synthetase and pyruvate dehydrogenase etc. This was followed by proteins related to cell defense and rescue (22% such as monodehydroascorbate reductase and stress-induced protein sti1, then by protein biogenesis and storage class (21% e.g. putative thiamine biosynthesis protein, putative beta-alanine synthase and cysteine synthase. Further, cell signaling (9% proteins like actin and prolyl endopeptidase and proteins with miscellaneous function (19% like Sgt1 and some hypothetical protein were also represented a large contribution towards drought regulatory mechanism in rice. We propose that protein biogenesis, cell defense and superior homeostasis may render better drought-adaptation. These findings might expedite the functional determination of the drought-responsive proteins and their prioritisation as potential molecular targets for perfect adaptation.

  14. Automated local bright feature image analysis of nuclear protein distribution identifies changes in tissue phenotype

    International Nuclear Information System (INIS)

    Knowles, David; Sudar, Damir; Bator, Carol; Bissell, Mina

    2006-01-01

    The organization of nuclear proteins is linked to cell and tissue phenotypes. When cells arrest proliferation, undergo apoptosis, or differentiate, the distribution of nuclear proteins changes. Conversely, forced alteration of the distribution of nuclear proteins modifies cell phenotype. Immunostaining and fluorescence microscopy have been critical for such findings. However, there is an increasing need for quantitative analysis of nuclear protein distribution to decipher epigenetic relationships between nuclear structure and cell phenotype, and to unravel the mechanisms linking nuclear structure and function. We have developed imaging methods to quantify the distribution of fluorescently-stained nuclear protein NuMA in different mammary phenotypes obtained using three-dimensional cell culture. Automated image segmentation of DAPI-stained nuclei was generated to isolate thousands of nuclei from three-dimensional confocal images. Prominent features of fluorescently-stained NuMA were detected using a novel local bright feature analysis technique, and their normalized spatial density calculated as a function of the distance from the nuclear perimeter to its center. The results revealed marked changes in the distribution of the density of NuMA bright features as non-neoplastic cells underwent phenotypically normal acinar morphogenesis. In contrast, we did not detect any reorganization of NuMA during the formation of tumor nodules by malignant cells. Importantly, the analysis also discriminated proliferating non-neoplastic cells from proliferating malignant cells, suggesting that these imaging methods are capable of identifying alterations linked not only to the proliferation status but also to the malignant character of cells. We believe that this quantitative analysis will have additional applications for classifying normal and pathological tissues

  15. Automated local bright feature image analysis of nuclear proteindistribution identifies changes in tissue phenotype

    Energy Technology Data Exchange (ETDEWEB)

    Knowles, David; Sudar, Damir; Bator, Carol; Bissell, Mina

    2006-02-01

    The organization of nuclear proteins is linked to cell and tissue phenotypes. When cells arrest proliferation, undergo apoptosis, or differentiate, the distribution of nuclear proteins changes. Conversely, forced alteration of the distribution of nuclear proteins modifies cell phenotype. Immunostaining and fluorescence microscopy have been critical for such findings. However, there is an increasing need for quantitative analysis of nuclear protein distribution to decipher epigenetic relationships between nuclear structure and cell phenotype, and to unravel the mechanisms linking nuclear structure and function. We have developed imaging methods to quantify the distribution of fluorescently-stained nuclear protein NuMA in different mammary phenotypes obtained using three-dimensional cell culture. Automated image segmentation of DAPI-stained nuclei was generated to isolate thousands of nuclei from three-dimensional confocal images. Prominent features of fluorescently-stained NuMA were detected using a novel local bright feature analysis technique, and their normalized spatial density calculated as a function of the distance from the nuclear perimeter to its center. The results revealed marked changes in the distribution of the density of NuMA bright features as non-neoplastic cells underwent phenotypically normal acinar morphogenesis. In contrast, we did not detect any reorganization of NuMA during the formation of tumor nodules by malignant cells. Importantly, the analysis also discriminated proliferating non-neoplastic cells from proliferating malignant cells, suggesting that these imaging methods are capable of identifying alterations linked not only to the proliferation status but also to the malignant character of cells. We believe that this quantitative analysis will have additional applications for classifying normal and pathological tissues.

  16. P-TRAP: a Panicle TRAit Phenotyping tool.

    Science.gov (United States)

    A L-Tam, Faroq; Adam, Helene; Anjos, António dos; Lorieux, Mathias; Larmande, Pierre; Ghesquière, Alain; Jouannic, Stefan; Shahbazkia, Hamid Reza

    2013-08-29

    In crops, inflorescence complexity and the shape and size of the seed are among the most important characters that influence yield. For example, rice panicles vary considerably in the number and order of branches, elongation of the axis, and the shape and size of the seed. Manual low-throughput phenotyping methods are time consuming, and the results are unreliable. However, high-throughput image analysis of the qualitative and quantitative traits of rice panicles is essential for understanding the diversity of the panicle as well as for breeding programs. This paper presents P-TRAP software (Panicle TRAit Phenotyping), a free open source application for high-throughput measurements of panicle architecture and seed-related traits. The software is written in Java and can be used with different platforms (the user-friendly Graphical User Interface (GUI) uses Netbeans Platform 7.3). The application offers three main tools: a tool for the analysis of panicle structure, a spikelet/grain counting tool, and a tool for the analysis of seed shape. The three tools can be used independently or simultaneously for analysis of the same image. Results are then reported in the Extensible Markup Language (XML) and Comma Separated Values (CSV) file formats. Images of rice panicles were used to evaluate the efficiency and robustness of the software. Compared to data obtained by manual processing, P-TRAP produced reliable results in a much shorter time. In addition, manual processing is not repeatable because dry panicles are vulnerable to damage. The software is very useful, practical and collects much more data than human operators. P-TRAP is a new open source software that automatically recognizes the structure of a panicle and the seeds on the panicle in numeric images. The software processes and quantifies several traits related to panicle structure, detects and counts the grains, and measures their shape parameters. In short, P-TRAP offers both efficient results and a user

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

    Science.gov (United States)

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

    2013-07-01

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

  18. Mapping paddy rice planting area in rice-wetland coexistent areas through analysis of Landsat 8 OLI and MODIS images.

    Science.gov (United States)

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

    2016-04-01

    Accurate and up-to-date information on the spatial distribution of paddy rice fields is necessary for the studies of trace gas emissions, water source management, and food security. The phenology-based paddy rice mapping algorithm, which identifies the unique flooding stage of paddy rice, has been widely used. However, identification and mapping of paddy rice in rice-wetland coexistent areas is still a challenging task. In this study, we found that the flooding/transplanting periods of paddy rice and natural wetlands were different. The natural wetlands flood earlier and have a shorter duration than paddy rice in the Panjin Plain, a temperate region in China. We used this asynchronous flooding stage to extract the paddy rice planting area from the rice-wetland coexistent area. MODIS Land Surface Temperature (LST) data was used to derive the temperature-defined plant growing season. Landsat 8 OLI imagery was used to detect the flooding signal and then paddy rice was extracted using the difference in flooding stages between paddy rice and natural wetlands. The resultant paddy rice map was evaluated with in-situ ground-truth data and Google Earth images. The estimated overall accuracy and Kappa coefficient were 95% and 0.90, respectively. The spatial pattern of OLI-derived paddy rice map agrees well with the paddy rice layer from the National Land Cover Dataset from 2010 (NLCD-2010). The differences between Rice Landsat and Rice NLCD are in the range of ±20% for most 1-km grid cell. The results of this study demonstrate the potential of the phenology-based paddy rice mapping algorithm, via integrating MODIS and Landsat 8 OLI images, to map paddy rice fields in complex landscapes of paddy rice and natural wetland in the temperate region.

  19. Seedling vigor and genetic variability for rice seed, seedling emergence and seedling traits

    International Nuclear Information System (INIS)

    Ali, S.S.; Jafri, S.J.H.; Jamil, M.; Ijaz, M.

    1994-01-01

    Eleven local rice cultivars including Basmati 370 were evaluated for seedling vigor. Three groups of traits were evaluated viz; seed traits (Seed density, seed volume see weight, paddy length and grain length), seed emergence traits (emergence %, emergence index and emergence rate index), and seedling traits (fresh root length, dry root weight, emergence percentage, root length, dry root weight, seed weight and relative root weight were observed significant, respectively. Seed density, relative root weight, emergence rate index and root to shoot ratio were relatively more amenable to improvement. Relative expected genetic advance was the function of heritability and coefficient of phenotypic variability, latter being more important. (author)

  20. Rice saabus Euroopat taltsutama / Tõnu Prei

    Index Scriptorium Estoniae

    Prei, Tõnu, 1950-

    2005-01-01

    USA välisminister Condolezza Rice alustas ringreisi Euroopas, eesmärgiks anda vastulöök USA-d tabanud kriitikale sõjavangide kohtlemise ja teistes riikides oma luuretalituse salavanglate pidamise pärast

  1. USING RICE BRAN IN LAYING HEN DIETS

    Directory of Open Access Journals (Sweden)

    H ERSIN SAMLI

    2006-10-01

    Full Text Available Rice bran is an energy and protein rich ingredient used in poultry feeding. To balance energy and protein requirements. The purpose of this study is to examine the effects of rice bran on performance and egg quality during peak production of a commercial White laying strain of 22 week of age. Dietary treatments were consisted by inclusion of rice bran at 0, 5, 10 and 15% levels. Each treatment had 6 reps in which 12 birds were randomly assigned in wired fl oor battery cages equipped with nipple drinkers and through feeders. Layers accessed to feed and water freely. Lighting regimen was adjusted to 16h light/8h dark. The experiment lasted for 10 weeks. Overall results of the present experiment indicated that rice bran could be included up to 10% without any adverse affect on laying performance, egg quality and digestive organs.

  2. Genetic Diversity of Wild Rice Species in Yunnan Province of China

    OpenAIRE

    Zai-quan CHENG; Fu-you YING; Ding-qing LI; Teng-qiong YU; Jian FU; Hui-jun YAN; Qiao-fang ZHONG; Dun-yu ZHANG; Wei-jiao LI; Xing-qi HUANG

    2012-01-01

    Yunnan Province of China is one of the important centers for origin and evolution of cultivated rice worldwide. Wild rice is the ancestor of the cultivated rice. Many elite traits of wild rice have widened the genetic basis in cultivated rice. However, many populations of wild rice species have disappeared in the past few years. Therefore, the current status of wild rice resources should be updated and the genetic diversity of wild rice species should be examined for further germplasm preserv...

  3. Characterization of paralogous protein families in rice

    Directory of Open Access Journals (Sweden)

    Zhu Wei

    2008-02-01

    Full Text Available Abstract Background High gene numbers in plant genomes reflect polyploidy and major gene duplication events. Oryza sativa, cultivated rice, is a diploid monocotyledonous species with a ~390 Mb genome that has undergone segmental duplication of a substantial portion of its genome. This, coupled with other genetic events such as tandem duplications, has resulted in a substantial number of its genes, and resulting proteins, occurring in paralogous families. Results Using a computational pipeline that utilizes Pfam and novel protein domains, we characterized paralogous families in rice and compared these with paralogous families in the model dicotyledonous diploid species, Arabidopsis thaliana. Arabidopsis, which has undergone genome duplication as well, has a substantially smaller genome (~120 Mb and gene complement compared to rice. Overall, 53% and 68% of the non-transposable element-related rice and Arabidopsis proteins could be classified into paralogous protein families, respectively. Singleton and paralogous family genes differed substantially in their likelihood of encoding a protein of known or putative function; 26% and 66% of singleton genes compared to 73% and 96% of the paralogous family genes encode a known or putative protein in rice and Arabidopsis, respectively. Furthermore, a major skew in the distribution of specific gene function was observed; a total of 17 Gene Ontology categories in both rice and Arabidopsis were statistically significant in their differential distribution between paralogous family and singleton proteins. In contrast to mammalian organisms, we found that duplicated genes in rice and Arabidopsis tend to have more alternative splice forms. Using data from Massively Parallel Signature Sequencing, we show that a significant portion of the duplicated genes in rice show divergent expression although a correlation between sequence divergence and correlation of expression could be seen in very young genes. Conclusion

  4. The Potency of White Rice (Oryza sativa), Black Rice (Oryza sativa L. indica), and Red Rice (Oryza nivara) as Antioxidant and Tyrosinase Inhibitor

    Science.gov (United States)

    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.

  5. Diverse Rice Landraces of North-East India Enables the Identification of Novel Genetic Resources for Magnaporthe Resistance.

    Science.gov (United States)

    Umakanth, Bangale; Vishalakshi, Balija; Sathish Kumar, P; Rama Devi, S J S; Bhadana, Vijay Pal; Senguttuvel, P; Kumar, Sudhir; Sharma, Susheel Kumar; Sharma, Pawan Kumar; Prasad, M S; Madhav, Maganti S

    2017-01-01

    North-East (NE) India, the probable origin of rice has diverse genetic resources. Many rice landraces of NE India were not yet characterized for blast resistance. A set of 232 landraces of NE India, were screened for field resistance at two different hotspots of rice blast, viz., IIRR-UBN, Hyderabad and ICAR-NEH, Manipur in two consecutive seasons. The phenotypic evaluation as well as gene profiling for 12 major blast resistance genes ( Pitp , Pi33 , Pi54 , Pib , Pi20 , Pi38 , Pita2 , Pi1 , Piz , Pi9 , Pizt , and Pi40 ) with linked as well as gene-specific markers, identified 84 resistant landraces possessing different gene(s) either in singly or in combinations and also identified seven resistant landraces which do not have the tested genes, indicating the valuable genetic resources for blast resistance. To understand the molecular diversity existing in the population, distance and model based analysis were performed using 120 SSR markers. Results of both analyses are highly correlated by forming two distinct subgroups and the existence of high diversity (24.9% among the subgroups; 75.1% among individuals of each subgroup) was observed. To practically utilize the diversity in the breeding program, a robust core set having an efficiency index of 0.82 which consists of 33 landraces were identified through data of molecular, blast phenotyping, and important agro-morphological traits. The association of eight novel SSR markers for important agronomic traits which includes leaf and neck blast resistance was determined using genome-wide association analysis. The current study focuses on identifying novel resources having field resistance to blast as well as markers which can be explored in rice improvement programs. It also entails the development of a core set which can aid in representing the entire diversity for efficiently harnessing its properties to broaden the gene pool of rice.

  6. Deciphering long-term records of natural variability and human impact as recorded in lake sediments: a palaeolimnological puzzle

    DEFF Research Database (Denmark)

    Mills, Keely; Schillereff, Daniel; Saulnier-Talbot, Émilie

    2017-01-01

    that is particularly acute when considering management options for aquatic ecosystems. The duration and timing of human impacts on lake systems varies geographically, with some regions of the world (such as Africa and South America) having a longer legacy of human impact than others (e.g., New Zealand). A wide array...... of techniques (biological, chemical, physical and statistical) is available to palaeolimnologists to allow the deciphering of complex sedimentary records. Lake sediments are an important archive of how drivers have changed through time, and how these impacts manifest in lake systems. With a paucity of ‘real...

  7. [Effects of rice cleaning and cooking process on the residues of flutolanil, fenobucarb, silafluofen and buprofezin in rice].

    Science.gov (United States)

    Satoh, Motoaki; Sakaguchi, Masayuki; Kobata, Masakazu; Sakaguchi, Yoko; Tanizawa, Haruna; Miura, Yuri; Sasano, Ryoichi; Nakanishi, Yutaka

    2003-02-01

    We studied the effect of cleaning and cooking on the residues of flutolanil, fenobucarb, silafluofen and buprofezin in rice. The rice had been sprayed in a paddy field in Wakayama city, with 3 kinds of pesticide application protocols: spraying once at the usual concentration of pesticides, repeated spraying (3 times) with the usual concentration of pesticides and spraying once with 3 times the usual concentration of pesticides. The residue levels of pesticide decreased during the rice cleaning process. Silafluofen, which has a higher log Pow value, remained in the hull of the rice. Fenobucarb, which has a lower log Pow value, penetrated inside the rice. The residue concentration of pesticide in polished rice was higher than that in pre-washed rice processed ready for cooking. During the cooking procedure, the reduction of pesticides in polished rice was higher than that in brown rice.

  8. Biophysical and Mechanical properties of rice varieties: attributes to ...

    African Journals Online (AJOL)

    It requires about 25N for the rice grain (IITA306) to fail at 0.7mm at horizontal and 150N to crack the rice grain in vertical position at 21.0mm, it takes 60N for the rice grain (MAS) to fail at 1.4mm and 150N to crack the rice grain at 22.5mm as well as 58N for the rice grain (R18) to fail at 1.2mm and 125N to crack the rice grain ...

  9. Effect of gamma irradiation on rice and its food products

    International Nuclear Information System (INIS)

    Sung, W.-C.

    2005-01-01

    Two milled indica rice varieties were exposed to gamma radiation with doses ranging from 0 to 1.0 kGy. The effects of gamma irradiation on rice flour pasting properties and the qualities of its food product, rice curd, were compared to the effects of storage. A dose of 1 kGy can decrease the flour paste viscosity and tenderize the texture of the rice curd to similar levels as those obtained after 12 months of storage. It was thus shown that gamma irradiation could shorten the indica rice aging time and improve the processing stability and quality of rice products

  10. Effect of gamma irradiation on rice and its food products

    Energy Technology Data Exchange (ETDEWEB)

    Sung, W.-C. [Department of Hotel and Restaurant Management, Chia Nan University of Pharmacy and Science, 60 Erh-Jen Road, Sec. 1, Pao-An, Jen-Te Hsiang, Tainan 717, Taiwan (China)]. E-mail: sungwilliam2001@yahoo.com.tw

    2005-07-01

    Two milled indica rice varieties were exposed to gamma radiation with doses ranging from 0 to 1.0 kGy. The effects of gamma irradiation on rice flour pasting properties and the qualities of its food product, rice curd, were compared to the effects of storage. A dose of 1 kGy can decrease the flour paste viscosity and tenderize the texture of the rice curd to similar levels as those obtained after 12 months of storage. It was thus shown that gamma irradiation could shorten the indica rice aging time and improve the processing stability and quality of rice products.

  11. Deciphering the transcriptional circuitry of microRNA genes expressed during human monocytic differentiation

    KAUST Repository

    Schmeier, Sebastian; MacPherson, Cameron R; Essack, Magbubah; Kaur, Mandeep; Schaefer, Ulf; Suzuki, Harukazu; Hayashizaki, Yoshihide; Bajic, Vladimir B.

    2009-01-01

    Background: Macrophages are immune cells involved in various biological processes including host defence, homeostasis, differentiation, and organogenesis. Disruption of macrophage biology has been linked to increased pathogen infection, inflammation and malignant diseases. Differential gene expression observed in monocytic differentiation is primarily regulated by interacting transcription factors (TFs). Current research suggests that microRNAs (miRNAs) degrade and repress translation of mRNA, but also may target genes involved in differentiation. We focus on getting insights into the transcriptional circuitry regulating miRNA genes expressed during monocytic differentiation. Results: We computationally analysed the transcriptional circuitry of miRNA genes during monocytic differentiation using in vitro time-course expression data for TFs and miRNAs. A set of TF?miRNA associations was derived from predicted TF binding sites in promoter regions of miRNA genes. Time-lagged expression correlation analysis was utilised to evaluate the TF?miRNA associations. Our analysis identified 12 TFs that potentially play a central role in regulating miRNAs throughout the differentiation process. Six of these 12 TFs (ATF2, E2F3, HOXA4, NFE2L1, SP3, and YY1) have not previously been described to be important for monocytic differentiation. The remaining six TFs are CEBPB, CREB1, ELK1, NFE2L2, RUNX1, and USF2. For several miRNAs (miR-21, miR-155, miR-424, and miR-17-92), we show how their inferred transcriptional regulation impacts monocytic differentiation. Conclusions: The study demonstrates that miRNAs and their transcriptional regulatory control are integral molecular mechanisms during differentiation. Furthermore, it is the first study to decipher on a large-scale, how miRNAs are controlled by TFs during human monocytic differentiation. Subsequently, we have identified 12 candidate key controllers of miRNAs during this differentiation process. 2009 Schmeier et al; licensee Bio

  12. Deciphering the transcriptional circuitry of microRNA genes expressed during human monocytic differentiation

    KAUST Repository

    Schmeier, Sebastian

    2009-12-10

    Background: Macrophages are immune cells involved in various biological processes including host defence, homeostasis, differentiation, and organogenesis. Disruption of macrophage biology has been linked to increased pathogen infection, inflammation and malignant diseases. Differential gene expression observed in monocytic differentiation is primarily regulated by interacting transcription factors (TFs). Current research suggests that microRNAs (miRNAs) degrade and repress translation of mRNA, but also may target genes involved in differentiation. We focus on getting insights into the transcriptional circuitry regulating miRNA genes expressed during monocytic differentiation. Results: We computationally analysed the transcriptional circuitry of miRNA genes during monocytic differentiation using in vitro time-course expression data for TFs and miRNAs. A set of TF?miRNA associations was derived from predicted TF binding sites in promoter regions of miRNA genes. Time-lagged expression correlation analysis was utilised to evaluate the TF?miRNA associations. Our analysis identified 12 TFs that potentially play a central role in regulating miRNAs throughout the differentiation process. Six of these 12 TFs (ATF2, E2F3, HOXA4, NFE2L1, SP3, and YY1) have not previously been described to be important for monocytic differentiation. The remaining six TFs are CEBPB, CREB1, ELK1, NFE2L2, RUNX1, and USF2. For several miRNAs (miR-21, miR-155, miR-424, and miR-17-92), we show how their inferred transcriptional regulation impacts monocytic differentiation. Conclusions: The study demonstrates that miRNAs and their transcriptional regulatory control are integral molecular mechanisms during differentiation. Furthermore, it is the first study to decipher on a large-scale, how miRNAs are controlled by TFs during human monocytic differentiation. Subsequently, we have identified 12 candidate key controllers of miRNAs during this differentiation process. 2009 Schmeier et al; licensee Bio

  13. Gene-Specific-Candidate-Driven Study to decipher Genetic Predisposition to Rotavirus Infection

    Directory of Open Access Journals (Sweden)

    Kshitija Rane-Yadav

    2017-10-01

    predisposition to Rotavirus diarrhea. Knowledge of molecular biology of the Rotavirus pathogenesis may open up new paths for vaccines and therapy. Data presented here is first of its kind which deciphers Host-Rotavirus interaction by parallel experiments of epidemiological study and In Silico study.

  14. Deciphering mechanisms of drug sensitivity and resistance to Selective Inhibitor of Nuclear Export (SINE) compounds

    International Nuclear Information System (INIS)

    Crochiere, Marsha; Kashyap, Trinayan; Kalid, Ori; Shechter, Sharon; Klebanov, Boris; Senapedis, William; Saint-Martin, Jean-Richard; Landesman, Yosef

    2015-01-01

    Exportin 1 (XPO1) is a well-characterized nuclear export protein whose expression is up-regulated in many types of cancers and functions to transport key tumor suppressor proteins (TSPs) from the nucleus. Karyopharm Therapeutics has developed a series of small-molecule Selective Inhibitor of Nuclear Export (SINE) compounds, which have been shown to block XPO1 function both in vitro and in vivo. The drug candidate, selinexor (KPT-330), is currently in Phase-II/IIb clinical trials for treatment of both hematologic and solid tumors. The present study sought to decipher the mechanisms that render cells either sensitive or resistant to treatment with SINE compounds, represented by KPT-185, an early analogue of KPT-330. Using the human fibrosarcoma HT1080 cell line, resistance to SINE was acquired over a period of 10 months of constant incubation with increasing concentration of KPT-185. Cell viability was assayed by MTT. Immunofluorescence was used to compare nuclear export of TSPs. Fluorescence activated cell sorting (FACS), quantitative polymerase chain reaction (qPCR), and immunoblots were used to measure effects on cell cycle, gene expression, and cell death. RNA from naïve and drug treated parental and resistant cells was analyzed by Affymetrix microarrays. Treatment of HT1080 cells with gradually increasing concentrations of SINE resulted in > 100 fold decrease in sensitivity to SINE cytotoxicity. Resistant cells displayed prolonged cell cycle, reduced nuclear accumulation of TSPs, and similar changes in protein expression compared to parental cells, however the magnitude of the protein expression changes were more significant in parental cells. Microarray analyses comparing parental to resistant cells indicate that a number of key signaling pathways were altered in resistant cells including expression changes in genes involved in adhesion, apoptosis, and inflammation. While the patterns of changes in transcription following drug treatment are similar in parental

  15. An update on the use of rice in value-added food products.

    Science.gov (United States)

    Because of the huge quantity of rice produced annually, milled-rice co-products; such as, rice flour, rice bran, rice wax, and rice hull are plentiful and readily available. These co-products could be valuable sources of food ingredients, but they have been vastly under-utilized. This is a report ...

  16. Gibberellin 20-oxidase gene OsGA20ox3 regulates plant stature and disease development in rice.

    Science.gov (United States)

    Qin, Xue; Liu, Jun Hua; Zhao, Wen Sheng; Chen, Xu Jun; Guo, Ze Jian; Peng, You Liang

    2013-02-01

    Gibberellin (GA) 20-oxidase (GA20ox) catalyses consecutive steps of oxidation in the late part of the GA biosynthetic pathway. A T-DNA insertion mutant (17S-14) in rice, with an elongated phenotype, was isolated. Analysis of the flanking sequences of the T-DNA insertion site revealed that an incomplete T-DNA integration resulted in enhanced constitutively expression of downstream OsGA20ox3 in the mutant. The accumulation of bioactive GA(1) and GA(4) were increased in the mutant in comparison with the wild-type plant. Transgenic plants overexpressing OsGA20ox3 showed phenotypes similar to those of the 17S-14 mutant, and the RNA interference (RNAi) lines that had decreased OsGA20ox3 expression exhibited a semidwarf phenotype. Expression of OsGA20ox3 was detected in the leaves and roots of young seedlings, immature panicles, anthers, and pollens, based on β-glucuronidase (GUS) activity staining in transgenic plants expressing the OsGA20ox3 promoter fused to the GUS gene. The OsGA20ox3 RNAi lines showed enhanced resistance against rice pathogens Magnaporthe oryzae (causing rice blast) and Xanthomonas oryzae pv. oryzae (causing bacterial blight) and increased expression of defense-related genes. Conversely, OsGA20ox3-overexpressing plants were more susceptible to these pathogens comparing with the wild-type plants. The susceptibility of wild-type plants to X. oryzae pv. oryzae was increased by exogenous application of GA(3) and decreased by S-3307 treatment. Together, the results provide direct evidence for a critical role of OsGA20ox3 in regulating not only plant stature but also disease resistance in rice.

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

    Science.gov (United States)

    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.

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

    African Journals Online (AJOL)

    BIOTECH

    2013-10-16

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

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

    Science.gov (United States)

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

    2012-11-01

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

  20. Ethanol production from rice on radioactively contaminated field toward sustainable rice farming

    International Nuclear Information System (INIS)

    Yokoyama, Shinya; Izumi, Bintaro; Oki, Kazuo

    2011-01-01

    Radioactive species such as 137 Cs were discharged from Fukushima Daiichi Nuclear Power Plant which was severely damaged by the enormous earthquake and tsunami. Cropland has been radioactively contaminated by 137 Cs etc. and it seems impossible to plant rice due to the non-suitability for food. According to the reports, 137 Cs transferred into the rice from soil is less than 1% on the average. Therefore, it is expected that the concentration of 137 Cs in bioethanol will be well below the tentative restriction value even if bioethanol could be produced from the rice. It is proposed that the rice field should be filled with water to avoid the flow of runoff contaminated by radioactive cesium compounds because they are insoluble in aqueous phase and that bioethanol should be produced from the rice in order to maintain the multifunction of rice field and to continue the agriculture. If rice farming is halted and neglected, agricultural function of rice field as well as local community will be permanently destroyed. (author)

  1. Development and characterization of emulsions containing purple rice bran and brown rice oils

    Science.gov (United States)

    The aims of this study were to characterize purple rice bran oil (PRBO) as extracted from the bran, and to produce and characterize a nano-emulsion containing purple rice bran oil. An emulsion was prepared using PRBO (10%), sodium caseinate (5%) and water (85%). The mixture was sonicated followed ...

  2. Do rice water weevils and rice stem borers compete when sharing a host plant?

    Science.gov (United States)

    Shi, Sheng-Wei; He, Yan; Ji, Xiang-Hua; Jiang, Ming-Xing; Cheng, Jia-An

    2008-07-01

    The rice water weevil (RWW) Lissorhoptrus oryzophilus Kuschel (Coleoptera: Curculionidae) is an invasive insect pest of rice Oryza sativa L. in China. Little is known about the interactions of this weevil with indigenous herbivores. In the present study, adult feeding and population density of the weevil, injury level of striped stem borer Chilo suppressalis (Walker) (Lepidoptera: Pyralidae) and pink stem borer Sesamia inferens (Walker) (Lepidoptera: Noctuidae) to rice, as well as growth status of their host plants were surveyed in a rice field located in Southeastern Zhejiang, China, in 2004 with the objective to discover interspecific interactions on the rice. At tillering stage, both adult feeding of the weevil and injury of the stem borers tended to occur on larger tillers (bearing 5 leaves) compared with small tillers (bearing 2~4 leaves), but the insects showed no evident competition with each other. At booting stage, the stem borers caused more withering/dead hearts and the weevil reached a higher density on the plants which had more productive tillers and larger root system; the number of weevils per tiller correlated negatively with the percentage of withering/dead hearts of plants in a hill. These observations indicate that interspecific interactions exist between the rice water weevil and the rice stem borers with negative relations occurring at booting or earlier developmental stages of rice.

  3. Do rice water weevils and rice stem borers compete when sharing a host plant?*

    Science.gov (United States)

    Shi, Sheng-wei; He, Yan; Ji, Xiang-hua; Jiang, Ming-xing; Cheng, Jia-an

    2008-01-01

    The rice water weevil (RWW) Lissorhoptrus oryzophilus Kuschel (Coleoptera: Curculionidae) is an invasive insect pest of rice Oryza sativa L. in China. Little is known about the interactions of this weevil with indigenous herbivores. In the present study, adult feeding and population density of the weevil, injury level of striped stem borer Chilo suppressalis (Walker) (Lepidoptera: Pyralidae) and pink stem borer Sesamia inferens (Walker) (Lepidoptera: Noctuidae) to rice, as well as growth status of their host plants were surveyed in a rice field located in Southeastern Zhejiang, China, in 2004 with the objective to discover interspecific interactions on the rice. At tillering stage, both adult feeding of the weevil and injury of the stem borers tended to occur on larger tillers (bearing 5 leaves) compared with small tillers (bearing 2~4 leaves), but the insects showed no evident competition with each other. At booting stage, the stem borers caused more withering/dead hearts and the weevil reached a higher density on the plants which had more productive tillers and larger root system; the number of weevils per tiller correlated negatively with the percentage of withering/dead hearts of plants in a hill. These observations indicate that interspecific interactions exist between the rice water weevil and the rice stem borers with negative relations occurring at booting or earlier developmental stages of rice. PMID:18600788

  4. Simultaneous rough rice drying and rice bran stabilization using infrared radiation heating

    Science.gov (United States)

    The objective of this study was to develop a new rice drying method by using IR heating followed by tempering. Freshly harvested medium grain rice (M206) samples with different initial moisture contents (IMCs) were used in this study. The samples were dried for one- and two-passes by using a catalyt...

  5. Rice-eating quality among consumers in different rice grain preference countries

    NARCIS (Netherlands)

    Suwannaporn, P.; Linnemann, A.R.

    2008-01-01

    More rice is eaten nowadays in traditionally nonrice-eating countries. This study investigated consumer eating quality preferences among consumers in target rice export countries to identify opportunities and strategic implications. A quantitative study with 1,128 consumers of target nationalities

  6. Childhood asthma-predictive phenotype.

    Science.gov (United States)

    Guilbert, Theresa W; Mauger, David T; Lemanske, Robert F

    2014-01-01

    Wheezing is a fairly common symptom in early childhood, but only some of these toddlers will experience continued wheezing symptoms in later childhood. The definition of the asthma-predictive phenotype is in children with frequent, recurrent wheezing in early life who have risk factors associated with the continuation of asthma symptoms in later life. Several asthma-predictive phenotypes were developed retrospectively based on large, longitudinal cohort studies; however, it can be difficult to differentiate these phenotypes clinically as the expression of symptoms, and risk factors can change with time. Genetic, environmental, developmental, and host factors and their interactions may contribute to the development, severity, and persistence of the asthma phenotype over time. Key characteristics that distinguish the childhood asthma-predictive phenotype include the following: male sex; a history of wheezing, with lower respiratory tract infections; history of parental asthma; history of atopic dermatitis; eosinophilia; early sensitization to food or aeroallergens; or lower lung function in early life. Copyright © 2014 American Academy of Allergy, Asthma & Immunology. Published by Elsevier Inc. All rights reserved.

  7. Macrophage phenotypic subtypes diametrically regulate epithelial-mesenchymal plasticity in breast cancer cells

    International Nuclear Information System (INIS)

    Yang, Min; Ma, Bo; Shao, Hanshuang; Clark, Amanda M.; Wells, Alan

    2016-01-01

    Metastatic progression of breast cancer involves phenotypic plasticity of the carcinoma cells moving between epithelial and mesenchymal behaviors. During metastatic seeding and dormancy, even highly aggressive carcinoma cells take on an E-cadherin-positive epithelial phenotype that is absent from the emergent, lethal metastatic outgrowths. These phenotypes are linked to the metastatic microenvironment, though the specific cells and induction signals are still to be deciphered. Recent evidence suggests that macrophages impact tumor progression, and may alter the balance between cancer cell EMT and MErT in the metastatic microenvironment. Here we explore the role of M1/M2 macrophages in epithelial-mesenchymal plasticity of breast cancer cells by coculturing epithelial and mesenchymal cells lines with macrophages. We found that after polarizing the THP-1 human monocyte cell line, the M1 and M2-types were stable and maintained when co-cultured with breast cancer cells. Surprisingly, M2 macrophages may conferred a growth advantage to the epithelial MCF-7 cells, with these cells being driven to a partial mesenchymal phenotypic as indicated by spindle morphology. Notably, E-cadherin protein expression is significantly decreased in MCF-7 cells co-cultured with M2 macrophages. M0 and M1 macrophages had no effect on the MCF-7 epithelial phenotype. However, the M1 macrophages impacted the highly aggressive mesenchymal-like MDA-MB-231 breast cancer cells to take on a quiescent, epithelial phenotype with re-expression of E-cadherin. The M2 macrophages if anything exacerbated the mesenchymal phenotype of the MDA-MB-231 cells. Our findings demonstrate M2 macrophages might impart outgrowth and M1 macrophages may contribute to dormancy behaviors in metastatic breast cancer cells. Thus EMT and MErT are regulated by selected macrophage phenotype in the liver metastatic microenvironment. These results indicate macrophage could be a potential therapeutic target for limiting death due

  8. Highly variable penetrance of abnormal phenotypes in embryonic lethal knockout mice [version 2; referees: 1 approved, 2 approved with reservations

    Directory of Open Access Journals (Sweden)

    Robert Wilson

    2017-02-01

    Full Text Available Background: Identifying genes that are essential for mouse embryonic development and survival through term is a powerful and unbiased way to discover possible genetic determinants of human developmental disorders. Characterising the changes in mouse embryos that result from ablation of lethal genes is a necessary first step towards uncovering their role in normal embryonic development and establishing any correlates amongst human congenital abnormalities. Methods: Here we present results gathered to date in the Deciphering the Mechanisms of Developmental Disorders (DMDD programme, cataloguing the morphological defects identified from comprehensive imaging of 220 homozygous mutant and 114 wild type embryos from 42 lethal and subviable lines, analysed at E14.5. Results: Virtually all mutant embryos show multiple abnormal phenotypes and amongst the 42 lines these affect most organ systems. Within each mutant line, the phenotypes of individual embryos form distinct but overlapping sets. Subcutaneous edema, malformations of the heart or great vessels, abnormalities in forebrain morphology and the musculature of the eyes are all prevalent phenotypes, as is loss or abnormal size of the hypoglossal nerve. Conclusions: Overall, the most striking finding is that no matter how profound the malformation, each phenotype shows highly variable penetrance within a mutant line. These findings have challenging implications for efforts to identify human disease correlates.

  9. Electricity generation from rice husk in Indian rice mills: potential and financial viability

    International Nuclear Information System (INIS)

    Kapur, T.; Kandpal, T.C.; Garg, H.P.

    1998-01-01

    Rice husk generated as a by-product of rice processing is an important energy resource. The availability of this resource in India has been assessed and the technologies for exploitation of its energy potential in the rice processing industry discussed. Nomographs have been developed for estimation of the husk required to meet the energy of parboiling, drying and milling operations. The unit cost of electricity using rice husk gasifier-based power generation systems has been calculated and its financial feasibility assessed in comparison with utility-supplied and diesel-generated electricity. With the cost and efficiency data assumed here, the unit cost of electricity produced by rice husk gasifier-dual fuel engine-generator system varies between Rs 2/kWh and Rs 7/kWh. (35 Rs approximates to SUS 1.). (author)

  10. Electricity generation from rice husk in Indian rice mills: potential and financial viability

    Energy Technology Data Exchange (ETDEWEB)

    Kapur, T.; Kandpal, T.C.; Garg, H.P. [Indian Inst. of Technology, Centre for Energy Studies, New Delhi (India)

    1998-12-31

    Rice husk generated as a by-product of rice processing is an important energy resource. The availability of this resource in India has been assessed and the technologies for exploitation of its energy potential in the rice processing industry discussed. Nomographs have been developed for estimation of the husk required to meet the energy of parboiling, drying and milling operations. The unit cost of electricity using rice husk gasifier-based power generation systems has been calculated and its financial feasibility assessed in comparison with utility-supplied and diesel-generated electricity. With the cost and efficiency data assumed here, the unit cost of electricity produced by rice husk gasifier-dual fuel engine-generator system varies between Rs 2/kWh and Rs 7/kWh. (35 Rs approximates to SUS 1.). (author)

  11. Evidence for Non-Transmission of Rice Yellow Mottle Virus (RYMV through Rice Seed

    Directory of Open Access Journals (Sweden)

    Sy, AA.

    2004-01-01

    Full Text Available An indexing of the organs (radicle and plumule and components (husk, endosperm and embryo of rice seeds using Enzyme Linked Immunosorbent Assay (ELISA was carried out to detect Rice yellow mottle virus (RYMV and establish the exact location of the virus in the rice seed. RYMV was detected only in the husk (seed coat but not in the endosperm, plumule, radicle, nor embryo. None of the seedlings raised from the seeds expressed RYMV symptoms. No virus particle was detected by the ELISA test in the leaves of the screenhouse-reared plants obtained from seeds of infected plants. The results indicate that RYMV is apparently not transmitted through rice seed probably because the virus is seed-borne in the husk (seed coat of mature rice seeds.

  12. Effect of Temperature on Chinese Rice Wine Brewing with High Concentration Presteamed Whole Sticky Rice

    Directory of Open Access Journals (Sweden)

    Dengfeng Liu

    2014-01-01

    Full Text Available Production of high quality Chinese rice wine largely depends on fermentation temperature. However, there is no report on the ethanol, sugars, and acids kinetics in the fermentation mash of Chinese rice wine treated at various temperatures. The effects of fermentation temperatures on Chinese rice wine quality were investigated. The compositions and concentrations of ethanol, sugars, glycerol, and organic acids in the mash of Chinese rice wine samples were determined by HPLC method. The highest ethanol concentration and the highest glycerol concentration both were attained at the fermentation mash treated at 23°C. The highest peak value of maltose (90 g/L was obtained at 18°C. Lactic acid and acetic acid both achieved maximum values at 33°C. The experimental results indicated that temperature contributed significantly to the ethanol production, acid flavor contents, and sugar contents in the fermentation broth of the Chinese rice wines.

  13. Effect of Temperature on Chinese Rice Wine Brewing with High Concentration Presteamed Whole Sticky Rice

    Science.gov (United States)

    Zhang, Hong-Tao; Xiong, Weili; Hu, Jianhua; Xu, Baoguo; Lin, Chi-Chung; Xu, Ling; Jiang, Lihua

    2014-01-01

    Production of high quality Chinese rice wine largely depends on fermentation temperature. However, there is no report on the ethanol, sugars, and acids kinetics in the fermentation mash of Chinese rice wine treated at various temperatures. The effects of fermentation temperatures on Chinese rice wine quality were investigated. The compositions and concentrations of ethanol, sugars, glycerol, and organic acids in the mash of Chinese rice wine samples were determined by HPLC method. The highest ethanol concentration and the highest glycerol concentration both were attained at the fermentation mash treated at 23°C. The highest peak value of maltose (90 g/L) was obtained at 18°C. Lactic acid and acetic acid both achieved maximum values at 33°C. The experimental results indicated that temperature contributed significantly to the ethanol production, acid flavor contents, and sugar contents in the fermentation broth of the Chinese rice wines. PMID:24672788

  14. Overexpression of a New Zinc Finger Protein Transcription Factor OsCTZFP8 Improves Cold Tolerance in Rice

    Directory of Open Access Journals (Sweden)

    Yong-Mei Jin

    2018-01-01

    Full Text Available Cold stress is one of the most important abiotic stresses in rice. C2H2 zinc finger proteins play important roles in response to abiotic stresses in plants. In the present study, we isolated and functionally characterized a new C2H2 zinc finger protein transcription factor OsCTZFP8 in rice. OsCTZFP8 encodes a C2H2 zinc finger protein, which contains a typical zinc finger motif, as well as a potential nuclear localization signal (NLS and a leucine-rich region (L-box. Expression of OsCTZFP8 was differentially induced by several abiotic stresses and was strongly induced by cold stress. Subcellular localization assay and yeast one-hybrid analysis revealed that OsCTZFP8 was a nuclear protein and has transactivation activity. To characterize the function of OsCTZFP8 in rice, the full-length cDNA of OsCTZFP8 was isolated and transgenic rice with overexpression of OsCTZFP8 driven by the maize ubiquitin promoter was generated using Agrobacterium-mediated transformation. Among 46 independent transgenic lines, 6 single-copy homozygous overexpressing lines were selected by Southern blot analysis and Basta resistance segregation assay in both T1 and T2 generations. Transgenic rice overexpressing OsCTZFP8 exhibited cold tolerant phenotypes with significantly higher pollen fertilities and seed setting rates than nontransgenic control plants. In addition, yield per plant of OsCTZFP8-expressing lines was significantly (p<0.01 higher than that of nontransgenic control plants under cold treatments. These results demonstrate that OsCTZFP8 was a C2H2 zinc finger transcription factor that plays an important role in cold tolerance in rice.

  15. Development of Ozone Technology Rice Storage Systems (OTRISS) for Quality Improvement of Rice Production

    International Nuclear Information System (INIS)

    Nur, M; Kusdiyantini, E; Wuryanti, W; Winarni, T A; Widyanto, S A; Muharam, H

    2015-01-01

    This research has been carried out by using ozone to address the rapidly declining quality of rice in storage. In the first year, research has focused on the rice storage with ozone technology for small capacity (e.g., household) and the medium capacity (e.g., dormitories, hospitals). Ozone was produced by an ozone generator with Dielectric Barrier Discharge Plasma (DBDP). Ozone technology rice storage system (OTRISS) is using ozone charateristic which is a strong oxidizer. Ozone have a short endurance of existence and then decompose, as a result produce oxygen and radicals of oxygen. These characteristics could kill microorganisms and pests, reduce air humidity and enrich oxygen. All components used in SPBTO assembled using raw materials available in the big cities in Indonesia. Provider of high voltage (High Voltage Power Supply, 40-70 kV, 23 KH, AC) is one of components that have been assembled and tested. Ozone generator is assembled with 7 reactors of Dielectric Barrier Discharge Plasma (DBDP). Rice container that have been prepared for OTRISS have adjusted so can be integrated with generator, power supply and blower to blow air. OTRISS with a capacity of 75 kg and 100 kg have been made and tested. The ability of ozone to eliminate bacteria and fungi have been tested and resulted in a decrease of microorganisms at 3 log CFU/g. Testing in food chemistry showed that ozone treatment of rice had not changed the chemical content that still meet the standard of chemical content and nutritional applicable to ISO standard milled rice. The results of this study are very likely to be used as an alternative to rice storage systems in warehouse. Test and scale-up is being carried out in a mini warehouse whose condition is mimicked to rice in National Rice Storage of Indonesia (Bulog) to ensure quality. Next adaptations would be installed in the rice storage system in the Bulog. (paper)

  16. Integrated rice-duck farming mitigates the global warming potential in rice season.

    Science.gov (United States)

    Xu, Guochun; Liu, Xin; Wang, Qiangsheng; Yu, Xichen; Hang, Yuhao

    2017-01-01

    Integrated rice-duck farming (IRDF), as a mode of ecological agriculture, is an important way to realize sustainable development of agriculture. A 2-year split-plot field experiment was performed to evaluate the effects of IRDF on methane (CH 4 ) and nitrous oxide (N 2 O) emissions and its ecological mechanism in rice season. This experiment was conducted with two rice farming systems (FS) of IRDF and conventional farming (CF) under four paddy-upland rotation systems (PUR): rice-fallow (RF), annual straw incorporating in rice-wheat rotation system (RWS), annual straw-based biogas residues incorporating in rice-wheat rotation system (RWB), and rice-green manure (RGM). During the rice growing seasons, IRDF decreased the CH 4 emission by 8.80-16.68%, while increased the N 2 O emission by 4.23-15.20%, when compared to CF. Given that CH 4 emission contributed to 85.83-96.22% of global warming potential (GWP), the strong reduction in CH 4 emission led to a significantly lower GWP of IRDF as compared to CF. The reason for this trend was because IRDF has significant effect on dissolved oxygen (DO) and soil redox potential (Eh), which were two pivotal factors for CH 4 and N 2 O emissions in this study. The IRDF not only mitigates the GWP, but also increases the rice yield by 0.76-2.43% compared to CF. Moreover, compared to RWS system, RF, RWB and RGM systems significantly reduced CH 4 emission by 50.17%, 44.89% and 39.51%, respectively, while increased N 2 O emission by 10.58%, 14.60% and 23.90%, respectively. And RWS system had the highest GWP. These findings suggest that mitigating GWP and improving rice yield could be simultaneously achieved by the IRDF, and employing suitable PUR would benefit for relieving greenhouse effect. Copyright © 2016 Elsevier B.V. All rights reserved.

  17. A novel class of gibberellin 2-oxidases control semidwarfism, tillering, and root development in rice.

    Science.gov (United States)

    Lo, Shuen-Fang; Yang, Show-Ya; Chen, Ku-Ting; Hsing, Yue-Ie; Zeevaart, Jan A D; Chen, Liang-Jwu; Yu, Su-May

    2008-10-01

    Gibberellin 2-oxidases (GA2oxs) regulate plant growth by inactivating endogenous bioactive gibberellins (GAs). Two classes of GA2oxs inactivate GAs through 2beta-hydroxylation: a larger class of C(19) GA2oxs and a smaller class of C(20) GA2oxs. In this study, we show that members of the rice (Oryza sativa) GA2ox family are differentially regulated and act in concert or individually to control GA levels during flowering, tillering, and seed germination. Using mutant and transgenic analysis, C(20) GA2oxs were shown to play pleiotropic roles regulating rice growth and architecture. In particular, rice overexpressing these GA2oxs exhibited early and increased tillering and adventitious root growth. GA negatively regulated expression of two transcription factors, O. sativa homeobox 1 and TEOSINTE BRANCHED1, which control meristem initiation and axillary bud outgrowth, respectively, and that in turn inhibited tillering. One of three conserved motifs unique to the C(20) GA2oxs (motif III) was found to be important for activity of these GA2oxs. Moreover, C(20) GA2oxs were found to cause less severe GA-defective phenotypes than C(19) GA2oxs. Our studies demonstrate that improvements in plant architecture, such as semidwarfism, increased root systems and higher tiller numbers, could be induced by overexpression of wild-type or modified C(20) GA2oxs.

  18. Genomic DNA sequence and cytosine methylation changes of adult rice leaves after seeds space flight

    Science.gov (United States)

    Shi, Jinming

    In this study, cytosine methylation on CCGG site and genomic DNA sequence changes of adult leaves of rice after seeds space flight were detected by methylation-sensitive amplification polymorphism (MSAP) and Amplified fragment length polymorphism (AFLP) technique respectively. Rice seeds were planted in the trial field after 4 days space flight on the shenzhou-6 Spaceship of China. Adult leaves of space-treated rice including 8 plants chosen randomly and 2 plants with phenotypic mutation were used for AFLP and MSAP analysis. Polymorphism of both DNA sequence and cytosine methylation were detected. For MSAP analysis, the average polymorphic frequency of the on-ground controls, space-treated plants and mutants are 1.3%, 3.1% and 11% respectively. For AFLP analysis, the average polymorphic frequencies are 1.4%, 2.9%and 8%respectively. Total 27 and 22 polymorphic fragments were cloned sequenced from MSAP and AFLP analysis respectively. Nine of the 27 fragments from MSAP analysis show homology to coding sequence. For the 22 polymorphic fragments from AFLP analysis, no one shows homology to mRNA sequence and eight fragments show homology to repeat region or retrotransposon sequence. These results suggest that although both genomic DNA sequence and cytosine methylation status can be effected by space flight, the genomic region homology to the fragments from genome DNA and cytosine methylation analysis were different.

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

    Science.gov (United States)

    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.

  20. Genetic Analysis and Mapping of TWH Gene in Rice Twisted Hull Mutant

    Directory of Open Access Journals (Sweden)

    Jin-bo LI

    2009-03-01

    Full Text Available A mutant with twisted hulls was found in a breeding population of rice (Oryza sativa L.. The mutant shows less grain weight and inferior grain quality in addition to twisted hulls. Genetic analysis indicated that the phenotype of mutant was controlled by a single recessive gene (temporarily designated as TWH. To map the TWH gene, an F2 population was generated by crossing the twh mutant to R725, an indica rice variety with normal hulls. For bulked segregant analysis, the bulk of mutant plants was prepared by mixing equal amount of plant tissue from 10 twisted-hull plants and the bulk of normal plants was obtained by pooling equal amount tissue of 10 normal-hull plants. Two hundred and seven pairs of simple sequence repeat (SSR primers, which are distributed on 12 rice chromosomes, were used for polymorphism analysis of the parents and the two bulks. The TWH locus was initially mapped close to the SSR marker RM526 on chromosome 2. Therefore, further mapping was performed using 50 pairs of SSR primers around the marker RM526. The TWH was delimited between the SSR markers RM14128 and RM208 on the long arm of chromosome 2 at the genetic distances of 1.4 cM and 2.7 cM, respectively. These results provide the foundation for further fine mapping, cloning and functional analysis of the TWH gene.

  1. Association between QTLs and morphological traits toward sheath blight resistance in rice (Oryza sativa L.)

    Science.gov (United States)

    Hossain, Md Kamal; Jena, Kshirod Kumar; Bhuiyan, Md Atiqur Rahman; Wickneswari, Ratnam

    2016-01-01

    Sheath blight is considered the most significant disease of rice and causes enormous yield losses over the world. Breeding for resistant varieties is the only viable option to combat the disease efficiently. Seventeen diverged rice genotypes along with 17 QTL-linked SSR markers were evaluated under greenhouse conditions. Pearson’s correlation showed only the flag leaf angle had a significant correlation with sheath blight resistance under greenhouse screening. Multivariate analysis based on UPGMA clustering and principal component analysis (PCA) indicated that the flag leaf angle, flag leaf length, and plant compactness were significantly associated with the following SSR marker alleles: RM209 (116,130), RM202 (176), RM224 (126), RM257 (156), RM426 (175), and RM6971 (196), which are linked to the SB QTLs: QRlh11, qSBR11-3, qSBR11-1, qSBR9-1, qShB3-2, and qSB-9. A Mantel test suggested a weak relationship between the observed phenotypes and allelic variation patterns, implying the independent nature of morphological and molecular variations. Teqing and Tetep were found to be the most resistant cultivars. IR65482-4-136-2-2, MR219-4, and MR264 showed improved resistance potentials. These results suggest that the morphological traits and QTLs which have been found to associate with sheath blight resistance are a good choice to enhance resistance through pyramiding either 2 QTLs or QTLs and traits in susceptible rice cultivars. PMID:27795687

  2. Salt tolerant SUV3 overexpressing transgenic rice plants conserve physicochemical properties and microbial communities of rhizosphere.

    Science.gov (United States)

    Sahoo, Ranjan K; Ansari, Mohammad W; Tuteja, Renu; Tuteja, Narendra

    2015-01-01

    Key concerns in the ecological evaluation of GM crops are undesirably spread, gene flow, other environmental impacts, and consequences on soil microorganism's biodiversity. Numerous reports have highlighted the effects of transgenic plants on the physiology of non-targeted rhizospheric microbes and the food chain via causing adverse effects. Therefore, there is an urgent need to develop transgenics with insignificant toxic on environmental health. In the present study, SUV3 overexpressing salt tolerant transgenic rice evaluated in New Delhi and Cuttack soil conditions for their effects on physicochemical and biological properties of rhizosphere. Its cultivation does not affect soil properties viz., pH, Eh, organic C, P, K, N, Ca, Mg, S, Na and Fe(2+). Additionally, SUV3 rice plants do not cause any change in the phenotype, species characteristics and antibiotic sensitivity of rhizospheric bacteria. The population and/or number of soil organisms such as bacteria, fungi and nematodes were unchanged in the soil. Also, the activity of bacterial enzymes viz., dehydrogenase, invertase, phenol oxidases, acid phosphatases, ureases and proteases was not significantly affected. Further, plant growth promotion (PGP) functions of bacteria such as siderophore, HCN, salicylic acid, IAA, GA, zeatin, ABA, NH3, phosphorus metabolism, ACC deaminase and iron tolerance were, considerably, not influenced. The present findings suggest ecologically pertinent of salt tolerant SUV3 rice to sustain the health and usual functions of the rhizospheric organisms. Copyright © 2014 Elsevier Ltd. All rights reserved.

  3. NAL1 allele from a rice landrace greatly increases yield in modern indica cultivars.

    Science.gov (United States)

    Fujita, Daisuke; Trijatmiko, Kurniawan Rudi; Tagle, Analiza Grubanzo; Sapasap, Maria Veronica; Koide, Yohei; Sasaki, Kazuhiro; Tsakirpaloglou, Nikolaos; Gannaban, Ritchel Bueno; Nishimura, Takeshi; Yanagihara, Seiji; Fukuta, Yoshimichi; Koshiba, Tomokazu; Slamet-Loedin, Inez Hortense; Ishimaru, Tsutomu; Kobayashi, Nobuya

    2013-12-17

    Increasing crop production is essential for securing the future food supply in developing countries in Asia and Africa as economies and populations grow. However, although the Green Revolution led to increased grain production in the 1960s, no major advances have been made in increasing yield potential in rice since then. In this study, we identified a gene, SPIKELET NUMBER (SPIKE), from a tropical japonica rice landrace that enhances the grain productivity of indica cultivars through pleiotropic effects on plant architecture. Map-based cloning revealed that SPIKE was identical to NARROW LEAF1 (NAL1), which has been reported to control vein pattern in leaf. Phenotypic analyses of a near-isogenic line of a popular indica cultivar, IR64, and overexpressor lines revealed increases in spikelet number, leaf size, root system, and the number of vascular bundles, indicating the enhancement of source size and translocation capacity as well as sink size. The near-isogenic line achieved 13-36% yield increase without any negative effect on grain appearance. Expression analysis revealed that the gene was expressed in all cell types: panicles, leaves, roots, and culms supporting the pleiotropic effects on plant architecture. Furthermore, SPIKE increased grain yield by 18% in the recently released indica cultivar IRRI146, and increased spikelet number in the genetic background of other popular indica cultivars. The use of SPIKE in rice breeding could contribute to food security in indica-growing regions such as South and Southeast Asia.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2010-09-15

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

  5. Hybrid male sterility in rice is due to epistatic interactions with a pollen killer locus.

    Science.gov (United States)

    Kubo, Takahiko; Yoshimura, Atsushi; Kurata, Nori

    2011-11-01

    In intraspecific crosses between cultivated rice (Oryza sativa) subspecies indica and japonica, the hybrid male sterility gene S24 causes the selective abortion of male gametes carrying the japonica allele (S24-j) via an allelic interaction in the heterozygous hybrids. In this study, we first examined whether male sterility is due solely to the single locus S24. An analysis of near-isogenic lines (NIL-F(1)) showed different phenotypes for S24 in different genetic backgrounds. The S24 heterozygote with the japonica genetic background showed male semisterility, but no sterility was found in heterozygotes with the indica background. This result indicates that S24 is regulated epistatically. A QTL analysis of a BC(2)F(1) population revealed a novel sterility locus that interacts with S24 and is found on rice chromosome 2. The locus was named Epistatic Factor for S24 (EFS). Further genetic analyses revealed that S24 causes male sterility when in combination with the homozygous japonica EFS allele (efs-j). The results suggest that efs-j is a recessive sporophytic allele, while the indica allele (EFS-i) can dominantly counteract the pollen sterility caused by S24 heterozygosity. In summary, our results demonstrate that an additional epistatic locus is an essential element in the hybrid sterility caused by allelic interaction at a single locus in rice. This finding provides a significant contribution to our understanding of the complex molecular mechanisms underlying hybrid sterility and microsporogenesis.

  6. OsPRX2 contributes to stomatal closure and improves potassium deficiency tolerance in rice.

    Science.gov (United States)

    Mao, Xiaohui; Zheng, Yanmei; Xiao, Kaizhuan; Wei, Yidong; Zhu, Yongsheng; Cai, Qiuhua; Chen, Liping; Xie, Huaan; Zhang, Jianfu

    2018-01-01

    Peroxiredoxins (Prxs) which are thiol-based peroxidases have been implicated in the toxic reduction and intracellular concentration regulation of hydrogen peroxide. In Arabidopsis thaliana At2-CysPrxB (At5g06290) has been demonstrated to be essential in maintaining the water-water cycle for proper H 2 O 2 scavenging. Although the mechanisms of 2-Cys Prxs have been extensively studied in Arabidopsis thaliana, the function of 2-Cys Prxs in rice is unclear. In this study, a rice homologue gene of At2-CysPrxB, OsPRX2 was investigated aiming to characterize the effect of 2-Cys Prxs on the K + -deficiency tolerance in rice. We found that OsPRX2 was localized in the chloroplast. Overexpressed OsPRX2 causes the stomatal closing and K + -deficiency tolerance increasing, while knockout of OsPRX2 lead to serious defects in leaves phenotype and the stomatal opening under the K + -deficiency tolerance. Detection of K + accumulation, antioxidant activity of transgenic plants under the starvation of potassium, further confirmed that OsPRX2 is a potential target for engineering plants with improved potassium deficiency tolerance. Copyright © 2017 Elsevier Inc. All rights reserved.

  7. Cytoplasmic-genetic male sterility gene provides direct evidence for some hybrid rice recently evolving into weedy rice

    Science.gov (United States)

    Zhang, Jingxu; Lu, Zuomei; Dai, Weimin; Song, Xiaoling; Peng, Yufa; Valverde, Bernal E.; Qiang, Sheng

    2015-01-01

    Weedy rice infests paddy fields worldwide at an alarmingly increasing rate. There is substantial evidence indicating that many weedy rice forms originated from or are closely related to cultivated rice. There is suspicion that the outbreak of weedy rice in China may be related to widely grown hybrid rice due to its heterosis and the diversity of its progeny, but this notion remains unsupported by direct evidence. We screened weedy rice accessions by both genetic and molecular marker tests for the cytoplasmic male sterility (CMS) genes (Wild abortive, WA, and Boro type, BT) most widely used in the production of indica and japonica three-line hybrid rice as a diagnostic trait of direct parenthood. Sixteen weedy rice accessions of the 358 tested (4.5%) contained the CMS-WA gene; none contained the CMS-BT gene. These 16 accessions represent weedy rices recently evolved from maternal hybrid rice derivatives, given the primarily maternal inheritance of this trait. Our results provide key direct evidence that hybrid rice can be involved in the evolution of some weedy rice accessions, but is not a primary factor in the recent outbreak of weedy rice in China. PMID:26012494

  8. Cytoplasmic-genetic male sterility gene provides direct evidence for some hybrid rice recently evolving into weedy rice.

    Science.gov (United States)

    Zhang, Jingxu; Lu, Zuomei; Dai, Weimin; Song, Xiaoling; Peng, Yufa; Valverde, Bernal E; Qiang, Sheng

    2015-05-27

    Weedy rice infests paddy fields worldwide at an alarmingly increasing rate. There is substantial evidence indicating that many weedy rice forms originated from or are closely related to cultivated rice. There is suspicion that the outbreak of weedy rice in China may be related to widely grown hybrid rice due to its heterosis and the diversity of its progeny, but this notion remains unsupported by direct evidence. We screened weedy rice accessions by both genetic and molecular marker tests for the cytoplasmic male sterility (CMS) genes (Wild abortive, WA, and Boro type, BT) most widely used in the production of indica and japonica three-line hybrid rice as a diagnostic trait of direct parenthood. Sixteen weedy rice accessions of the 358 tested (4.5%) contained the CMS-WA gene; none contained the CMS-BT gene. These 16 accessions represent weedy rices recently evolved from maternal hybrid rice derivatives, given the primarily maternal inheritance of this trait. Our results provide key direct evidence that hybrid rice can be involved in the evolution of some weedy rice accessions, but is not a primary factor in the recent outbreak of weedy rice in China.

  9. Oxidative stress at high altitude: genotype–phenotype correlations

    Directory of Open Access Journals (Sweden)

    Pandey P

    2014-05-01

    Full Text Available Priyanka Pandey,1,2 MA Qadar Pasha1,2 1CSIR-Institute of Genomics and Integrative Biology, Delhi, India; 2Department of Biotechnology, University of Pune, Ganeshkhind, Pune, India Abstract: It has been well-documented that the hypobaric hypoxic environment at high altitude (HA causes stress to both the permanent residents of HA and the sojourners. This oxidative stress primarily disturbs the oxygen-sensing and vascular homeostasis pathways, thereby upsetting normal human physiology, especially in sojourners. These environmental challenges have caused dynamic evolutionary changes within natives of HA, allowing them to develop adaptive plasticity. This review focuses on the genomic and biochemical features of the molecules involved in the oxygen-sensing and vascular homeostasis pathways with respect to HA pulmonary edema (HAPE and adaptation. We review the role of genetic markers such as HIF-prolyl hydroxylase 2, endothelial PAS domain-containing protein 1, endothelial nitric oxide synthase, endothelin 1, cytochrome b-245 alpha polypeptide, and glutathione S-transferase pi 1, as well as three circulatory biomarkers (nitric oxide, endothelin 1, and 8-iso-prostaglandin F2α, by highlighting approaches such as candidate gene and genome-wide, adopted in deciphering the pathways. A disagreement between the two approaches has also been highlighted. In addition, we discuss that an overrepresentation of wild-type alleles in HA natives and mutant alleles of same polymorphisms in HAPE patients implies that the allelic variants at the same locus are involved in adaptation and HAPE, respectively. Moreover, healthy sojourners present a number of genomic features similar to HA natives, further strengthening the concept of genetic predisposition. A trend in correlation between protective and risk alleles and altered levels of circulatory markers clearly documents the phenomenon of genotype–phenotype correlations. We conclude that the genetic and biochemical

  10. Efficacy and economics of different herbicides in aerobic rice system

    African Journals Online (AJOL)

    Jane

    2011-08-03

    Aug 3, 2011 ... options for effective and economic weed control in rice under aerobic system ... constraint to aerobic rice production and therefore, ... Herbicide has become an attractive alternative to manual ... MATERIALS AND METHODS.

  11. Water culture of the rice containing Cs-137

    International Nuclear Information System (INIS)

    Choi, Yong Ho; Keum, Dong Kwon; Lim, Kwang Muk; Jun, In; Park, Doo Won

    2008-10-01

    Pot experiments were carried out in a greenhouse in order to produce Cs-137-containing rice seeds as a source material for use in manufacturing reference rice samples of a high Cs-137 activity. Two kinds of soil were used and two pots were prepared for each kind of soil. Rice plants were water-cultured in the pots and Cs-137 was applied to the surface water to induce a Cs-137 contamination of rice seeds via a plant uptake of Cs-137. Mature rice plants were harvested and Cs-137-containing rice seeds were obtained after some treatment of the harvested plants. These produced rice seeds are going to be provided for the KRISS so as to be used in manufacturing reference rice samples for Cs-137

  12. Identification of quantitative trait loci for salinity tolerance in rice ...

    Indian Academy of Sciences (India)

    2016-12-05

    Dec 5, 2016 ... most serious biophysical constraints of rice production in many rice-producing areas ..... Thus, the large gaps in the chromosomal regions without ..... an elite maize population: I. Linkage analysis and determination of QTLs for.

  13. Production Cost Efficiency and Profitability of Abakaliki Rice in ...

    African Journals Online (AJOL)

    acer

    2014-11-17

    Nov 17, 2014 ... positive and significant effect on the total cost of rice production. They were all significant ... failure is experienced due to the flooded rice field. In addition ... for random effects on production beyond the control .... Standard error.

  14. Systemic induced tolerance against root-knot nematodes in rice

    African Journals Online (AJOL)

    user

    Rice plantlets were randomly grown in laboratory, sprayed with hormones and riboflavin .... between riboflavin, SA, JA and ET pathways in rice-nematodes interaction, ..... oxidative damage caused by aging as well as biotic and abiotic stress.

  15. greenhouse gaseous emission and energy analysis in rice ...

    African Journals Online (AJOL)

    ACSS

    Agriculture in Africa is associated with low food production. The attempt ... objective of this study was to assess greenhouse gas (GHG) emissions and energy impacts of rice production in. Ghana. .... Assessment (LCA) techniques, tropical rice.

  16. 10559 A NATIONAL SURVEY OF RICE (ORYZA SATIVA L.) GRAIN ...

    African Journals Online (AJOL)

    User

    The study provided quantitative measures of the quality status of rice grains available in Sierra ... using the most convenient methods at their disposal. ... rice, moisture content of grains and percentages of foreign matter, chalky immature grains ...

  17. ?-Oryzanols of North American Wild Rice (Zizania palustris)

    OpenAIRE

    Aladedunye, Felix; Przybylski, Roman; Rudzinska, Magdalena; Klensporf-Pawlik, Dorota

    2013-01-01

    ?-Oryzanol, a natural mixture of ferulic acid esters of triterpene alcohols and sterols, are an important bioactive components present in rice bran oil. In light of the recent increase in the popularity of wild rice among consumers, and the possibility of a direct relationship between ?-oryzanol composition and its bioactivity, the oryzanol profile of major wild rice (Zizania palustris) grown in North America was studied and compared to regular brown rice (Oryza sativa L.). A total of twenty-...

  18. Rice Genome Research: Current Status and Future Perspectives

    Directory of Open Access Journals (Sweden)

    Bin Han

    2008-11-01

    Full Text Available Rice ( L. is the leading genomics system among the crop plants. The sequence of the rice genome, the first cereal plant genome, was published in 2005. This review summarizes progress made in rice genome annotations, comparative genomics, and functional genomics researches. It also maps out the status of rice genomics globally and provides a vision of future research directions and resource building.

  19. Organic rice of Bangladesh: focus on disease control

    OpenAIRE

    Hossain, Shaikh Tanveer

    2012-01-01

    Diseases play an important role in rice production. In modern agriculture, application of hazardous chemicals is a common practice allover the world. But organic rice production system does not allow synthetic agro-chemicals due to its adverse effect on environment as well as human health. Thirty six fungal, twenty one viral, six bacterial and six nematode diseases have been recorded in rice. In Bangladesh, 31 rice diseases have been so far identified of which ten are considered as major. She...

  20. Deciphering Detailed Plate Kinematics of the Indian Ocean: A Combined Indian-Australian-French Initiative

    Science.gov (United States)

    Vadakkeyakath, Y.; Müller, R.; Dyment, J.; Bhattacharya, G.; Lister, G. S.; Kattoju, K. R.; Whittaker, J.; Shuhail, M.; Gibbons, A.; Jacob, J.; White, L. T.; Bissessur, P. D.; Kiranmai, S.

    2012-12-01

    -Australian and the Antarctic-Australian plate boundaries. These new studies also revealed the existence of several complexities, which need to be resolved in order to decipher plate kinematics of the Indian Ocean as a whole. Any improved model of plate kinematics of the Indian Ocean region should be compatible with the motions that are evident at all the above-mentioned plate boundaries and also is able to explain the identified complexities. With an aim to develop such a unified model for the plate tectonic evolution of the Indian Ocean in high resolution, a project was initiated for the synthesis of available data and results with the above groups of Indian, Australian and French scientists. The planned work under the auspices of this project will allow examining different reconstruction models to iteratively arrive at a model that is compatible with motions across different plate circuits and also accommodates various microcontinents and continental fragments and other hitherto identified complexities.

  1. Effect of waxy rice flour and cassava starch on freeze-thaw stability of rice starch gels.

    Science.gov (United States)

    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.

  2. Effect of germination on the physicochemical and antioxidant characteristics of rice flour from three rice varieties from Nigeria.

    Science.gov (United States)

    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.

  3. Phenotypic spectrum of GABRA1

    DEFF Research Database (Denmark)

    Johannesen, Katrine; Marini, Carla; Pfeffer, Siona

    2016-01-01

    OBJECTIVE: To delineate phenotypic heterogeneity, we describe the clinical features of a cohort of patients with GABRA1 gene mutations. METHODS: Patients with GABRA1 mutations were ascertained through an international collaboration. Clinical, EEG, and genetic data were collected. Functional analy...

  4. Leaf segmentation in plant phenotyping

    NARCIS (Netherlands)

    Scharr, Hanno; Minervini, Massimo; French, Andrew P.; Klukas, Christian; Kramer, David M.; Liu, Xiaoming; Luengo, Imanol; Pape, Jean Michel; Polder, Gerrit; Vukadinovic, Danijela; Yin, Xi; Tsaftaris, Sotirios A.

    2016-01-01

    Image-based plant phenotyping is a growing application area of computer vision in agriculture. A key task is the segmentation of all individual leaves in images. Here we focus on the most common rosette model plants, Arabidopsis and young tobacco. Although leaves do share appearance and shape

  5. Delineating SPTAN1 associated phenotypes

    DEFF Research Database (Denmark)

    Syrbe, Steffen; Harms, Frederike L; Parrini, Elena

    2017-01-01

    De novo in-frame deletions and duplications in the SPTAN1 gene, encoding the non-erythrocyte αII spectrin, have been associated with severe West syndrome with hypomyelination and pontocerebellar atrophy. We aimed at comprehensively delineating the phenotypic spectrum associated with SPTAN1 mutati...

  6. Advanced Backcross QTL Analysis for the Whole Plant Growth Duration Salt Tolerance in Rice (Oryza sativa L.)

    Institute of Scientific and Technical Information of China (English)

    CHAI Lu; LI Zhi-kang; ZHANG Jian; PAN Xiao-biao; ZHANG Fan; ZHENG Tian-qing; ZHAO Xiu-qing; WANG Wen-sheng; Ali Jauhar; XU Jian-long

    2014-01-01

    Salinity is a major factor limiting rice yield in coastal areas of Asia. To facilitate breeding salt tolerant rice varieties, the whole-plant growth duration salt tolerance (ST) was genetically dissected by phenotyping two sets of BC2F5 introgression lines (ILs) for four yield traits under severe natural salt stress and non-stress ifled conditions using SSR markers and the methods of advanced backcross QTL (AB-QTL) analysis and selective introgression. Many QTLs affecting four yield traits under salt stress and non-stress conditions were identiifed, most (>90%) of which were clustered in 13 genomic regions of the rice genome and involved in complex epistasis. Most QTLs affecting yield traits were differentially expressed under salt stress and non-stress conditions. Our results suggested that genetics complementarily provides an adequate explanation for the hidden genetic diversity for ST observed in both IL populations. Some promising Huanghuazhan (HHZ) ILs with favorable donor alleles at multiple QTLs and signiifcantly improved yield traits under salt stress and non-stress conditions were identiifed, providing excellent materials and relevant genetic information for improving rice ST by marker-assisted selection (MAS) or genome selection.

  7. Radiation disinfection of rice-straw products

    International Nuclear Information System (INIS)

    Ito, Hitoshi; Ishigaki, Isao; Ohki, Yumi.

    1991-01-01

    For the quarantine treatment of rice-straw products from foreign countries, irradiation effects of gamma-rays and electron beams on plant pathogenic microorganisms especially on fungi were investigated. The total aerobic bacteria in rice-straw was determined to be 3x10 7 - 3x10 8 per gram which consisted mainly of Pseudomonas, Flavobacterium, Arthrobacter and Erwinia. The principal bacteria in rice-straw could be eliminated with 5 kGy of gamma irradiation. Deinococcus proteolyticus and Pseudomonas radiora were the main survivors at 5 to 12 kGy of irradiation. Saprophytic fungus which belongs to Dimorphospora also survived up to 8 kGy of irradiation. The D 10 values of 26 strains of fungi isolated from rice-straw were 1.1 to 2.5 times higher in the dry condition compared to the values when irradiated in 0.067 M phosphate buffer solution. The induction dose in the dry condition also increased from 1.5 to 10 times than that in the wet condition. In the case of electron beam irradiation of fungi under dry conditions, D 10 values were about 1.3 times higher than that of gamma irradiation. From this study, the dose necessary to reduce the plant pathogenic fungi in rice-straw at a level below 10 -4 per gram was estimated to be as 7-8 kGy for gamma-irradiation and 10 kGy for electron beam irradiation. (author)

  8. Nuclear analytical methods on ancient Thai rice

    International Nuclear Information System (INIS)

    Won-in, K.; Thongleurm, C.; Dararutana, P.

    2013-01-01

    For more than half of humanity, rice is life. Rice is a grain which has shaped the history, culture, diet and economy of billions of people in Asia. In Thailand, it is the essence of life. Archaeological evidence revealed that rice had been planted in northeastern area of Thailand more than 5,500 years ago which is earlier than in China and India. The ancient rice grains were found in various archaeological sites in Thailand such as Nakhon Nayok, Suphan Buri and Prachin Buri Provinces. In this work, the ancient black rice from Nakhon Nayok Province was elementally analyzed using scanning electron microscope coupled with energy dispersive X-ray fluorescence spectroscopy, proton induced X-ray emission spectroscopy and micro-beam energy dispersive X-ray fluorescence spectroscopy. Infrared (IR) spectroscopy was also used to study the chemical composition and bio-molecular structure. The grains were oblique in shape with a rough surface. Three major elements (Si, Ca and Al) and other trace elements were detected. The IR spectra provided some information about the presence of molecular bonds. (author)

  9. Making Rice Production More Environmentally-Friendly

    Directory of Open Access Journals (Sweden)

    Norman Uphoff

    2016-05-01

    Full Text Available Irrigated rice production is one of the most essential agricultural activities for sustaining our global population, and at the same time, one of the agricultural sectors considered most eco-unfriendly. This is because it consumes a larger share of available freshwater resources, competing with varied ecosystems as well as other economic sectors; its paddy fields are responsible for significant emission of greenhouse gases; and the reliance on chemical fertilizers and various agrochemicals contributes to pollution of soils and water systems. These stresses on soils, hydrology and atmosphere are actually not necessary for rice production, which can be increased by modifying agronomic practices though more agroecologically-sound management practices. These, combined under the rubric of the System of Rice Intensification (SRI, can reduce requirements of irrigation water, chemical fertilizer and agrochemicals while increasing paddy yields and farmer’s net incomes. Here we discuss how irrigated rice production can be made more eco-friendly for the benefit of farmers, consumers and the environment. This is achieved by introducing practices that improve the growth and functioning of rice plants’ root systems and enhance the abundance, diversity and activity of beneficial soil organisms that live around plant roots and within the plants themselves as symbiotic endophytes.

  10. Arsenic biotransformation and volatilization in transgenic rice

    Science.gov (United States)

    Meng, Xiang-Yan; Qin, Jie; Wang, Li-Hong; Duan, Gui-Lan; Sun, Guo-Xin; Wu, Hui-Lan; Chu, Cheng-Cai; Ling, Hong-Qing; Rosen, Barry P.; Zhu, Yong-Guan

    2011-01-01

    Summary Biotransformation of arsenic includes oxidation, reduction, methylation and conversion to more complex organic arsenicals. Members of the class of arsenite [As(III)] S-adenosylmethyltransferase enzymes catalyze As(III) methylation to a variety of mono-, di- and trimethylated species, some of which are less toxic than As(III) itself. However, no methyltransferase gene has been identified in plants. Here, an arsM gene from the soil bacterium Rhodopseudomonas palustris was expressed in Japonica rice (Oryza sativa L.) cultivar Nipponbare, and the transgenic rice produced methylated arsenic species, which were measured by inductively coupled plasma mass spectrometry (ICP-MS) and high performance liquid chromatography-inductively coupled plasma-mass spectrometry (HPLC-ICP-MS). Both monomethylarsenate [MAs(V)] and dimethylarsenate [DMAs(V)] were detected in the root and shoot of transgenic rice. After 12-d exposure to As(III), the transgenic rice gave off 10-fold more volatile arsenicals. The present study demonstrates that expression of an arsM gene in rice induces arsenic methylation and volatilization, providing a potential stratagem for phytoremediation theoretically. PMID:21517874

  11. OsGSR1 is involved in crosstalk between gibberellins and brassinosteroids in rice.

    Science.gov (United States)

    Wang, Li; Wang, Zhen; Xu, Yunyuan; Joo, Se-Hwan; Kim, Seong-Ki; Xue, Zhen; Xu, Zhihong; Wang, Zhiyong; Chong, Kang

    2009-02-01

    Gibberellins (GAs) and brassinosteroids (BRs), two growth-promoting phytohormones, regulate many common physiological processes. Their interactions at the molecular level remain unclear. Here, we demonstrate that OsGSR1, a member of the GAST (GA-stimulated transcript) gene family, is induced by GA and repressed by BR. RNA interference (RNAi) transgenic rice plants with reduced OsGSR1 expression show phenotypes similar to plants deficient in BR, including short primary roots, erect leaves and reduced fertility. The OsGSR1 RNAi transgenic rice shows a reduced level of endogenous BR, and the dwarf phenotype could be rescued by the application of brassinolide. The yeast two-hybrid assay revealed that OsGSR1 interacts with DIM/DWF1, an enzyme that catalyzes the conversion from 24-methylenecholesterol to campesterol in BR biosynthesis. These results suggest that OsGSR1 activates BR synthesis by directly regulating a BR biosynthetic enzyme at the post-translational level. Furthermore, OsGSR1 RNAi plants show a reduced sensitivity to GA treatment, an increased expression of the GA biosynthetic gene OsGA20ox2, which is feedback inhibited by GA signaling, and an elevated level of endogenous GA: together, these suggest that OsGSR1 is a positive regulator of GA signaling. These results demonstrate that OsGSR1 plays important roles in both BR and GA pathways, and also mediates an interaction between the two signaling pathways.

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

    Science.gov (United States)

    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.

  13. Comparative Demand Analysis for Rice in Three States of South ...

    African Journals Online (AJOL)

    Dauda Omoba

    2013-01-01

    Jan 1, 2013 ... The contribution of the effect of the price of rice on the budget share of rice in the study ...... it is a luxury in rural areas of Delta state. This may imply that ... between brands of rice in rural Lagos and urban. Edo was the highest ...

  14. Determinants of rice output among ADP contact farmers in mining ...

    African Journals Online (AJOL)

    The study analyzed factors affecting rice output among Agricultural Development Programme (ADP) contact farmers in the mining and non mining locations of IVO LGA of Ebonyi State, Nigeria. Multistage random sampling technique was used to select agricultural circles and rice farmers. The sample size was 120 rice ...

  15. Rice methylmercury exposure and mitigation: a comprehensive review.

    Science.gov (United States)

    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.

  16. Developing selection protocols for weed competitiveness in aerobic rice

    NARCIS (Netherlands)

    Zhao, D.L.; Atlin, G.N.; Bastiaans, L.; Spiertz, J.H.J.

    2006-01-01

    Aerobic rice production systems, wherein rice is dry-sown in non-puddled soil and grown as an upland crop, offer large water savings but are subject to severe weed infestation. Weed-competitive cultivars will be critical to the adoption of aerobic rice production by farmers. Breeding

  17. Physical and Chemical Properties of Some Selected Rice Varieties

    African Journals Online (AJOL)

    User

    Physical and chemical properties of nine rice varieties grown and processed in Ebonyi .... Therefore, one tonne of a slender variety of rice will need more storage space than the ..... during washing and boiling of milled rice Starch 36:386-390.

  18. A mechanistic model on methane oxidation in the rice rhizosphere

    NARCIS (Netherlands)

    Bodegom, van P.M.; Leffelaar, P.A.; Goudriaan, J.

    2001-01-01

    A mechanistic model is presented on the processes leading to methane oxidation in rice rhizosphere. The model is driven by oxygen release from a rice root into anaerobic rice soil. Oxygen is consumed by heterotrophic and methanotrophic respiration, described by double Monod kinetics, and by iron

  19. Overwintering physiology of the rice stem borer larvae, Chilo ...

    African Journals Online (AJOL)

    The rice stem borer, Chilo suppressalis (Walker), is a major rice pest around the world. A strong ability of the rice stem borer to adapt/resist cold temperature (cold hardiness) contributes to its survival through winter. However, the physiological mechanism of its cold hardiness is poorly understood. In this study, we ...

  20. simulating rice yields under climate change scenarios using

    African Journals Online (AJOL)

    Prof. Adipala Ekwamu

    The effects of climate change on rice production and yield cannot be overlooked in finding measures to increase production and yield. The CERES-Rice (Ver. 4.0) model was calibrated and evaluated for use in simulating rice yields under different climate change scenarios in Ghana using data from the Anum Valley ...

  1. Physiology and productivity of rice crop influenced by drought stress ...

    African Journals Online (AJOL)

    Rice is sensitive to moisture stress and in view of the water scarcity in the coming years, it is imperative to evaluate the performance of rice cultivar under moisture deficit. The present study aimed to evaluate the physiological responses of two rice cultivars under drought stress induced at panicle initiation and soft dough ...

  2. Upland rice yield as affected by Brachiaria coverage management

    Directory of Open Access Journals (Sweden)

    Adriano S. Nascente

    2015-01-01

    Full Text Available An important point in no-tillage system is the time between cover crop glyphosate desiccation and rice sowing. This study aimed to verify the effect of Brachiaria ruziziensis management time before rice sowing on rice yield and its components. The experiment was conducted under greenhouse conditions and consisted of four types of B. ruziziensis management: with Brachiaria and with herbicide (WBWH, without Brachiaria shoots and with herbicide (NBWH, without Brachiaria shoots and without herbicide (NBNH, and with Brachiaria and without herbicide (WBNH, at four times: 30, 20, 10, and 0 days, preceding the rice sowing. The amount of B. ruziziensis dry matter increased as the management was done closer to the rice sowing date. The WBWH and WBNH managements (this one causes the lowest rice grain yield must be done 30 days before rice sowing; while NBWH management must be done ten or more days before rice sowing. On the other hand, NBNH management (this one favors the best rice grain yield can be done until rice sowing day. Despite some reduction in rice yield caused by the B. ruziziensis management, when it was done at the proper time the rice grain yield was similar to the control (without Brachiaria sowing and without herbicide application.

  3. Extracting silica from rice husk treated with potassium permanganate

    International Nuclear Information System (INIS)

    Javed, S.H.; Naveed, S.

    2008-01-01

    As an agro-waste material the rice husk is abundantly available is rice growing areas. In many areas rice husk after burning involves disposal problems because of higher quantities of silica present in it. Rice husk contains about 20 per cent silica, which is present in hydrated amorphous form. On thermal treatment the silica converts into crystobalite, which is a crystalline form of silica. However amorphous silica can be produced under controlled conditions ensuring high reactivity and large surface area. Leaching the rice husk with organic acids and alkalies removes the metallic impurities from its surface. How a dilute solution of potassium permanganate affects the rice husk is the subject of this research paper. The rice husk was treated with the dilute solution of potassium permanganate at room temperature and then analyzed by SEM, TGA and the ash by analytical treatment after burning under controlled temperature. The SEM results revealed that the protuberances of the rice husk were eaten away by the solution of potassium permanganate. Pyrolysis of rice husks showed that the thermal degradation of the treated rice husk was faster than the untreated rice husk where as analytical results confirmed the presence of more amorphous silica than untreated rice husk. (author)

  4. An overview of global rice production, supply, trade, and consumption.

    Science.gov (United States)

    Muthayya, Sumithra; Sugimoto, Jonathan D; Montgomery, Scott; Maberly, Glen F

    2014-09-01

    Rice is the staple food for over half the world's population. Approximately 480 million metric tons of milled rice is produced annually. China and India alone account for ∼50% of the rice grown and consumed. Rice provides up to 50% of the dietary caloric supply for millions living in poverty in Asia and is, therefore, critical for food security. It is becoming an important food staple in both Latin America and Africa. Record increases in rice production have been observed since the start of the Green Revolution. However, rice remains one of the most protected food commodities in world trade. Rice is a poor source of vitamins and minerals, and losses occur during the milling process. Populations that subsist on rice are at high risk of vitamin and mineral deficiency. Improved technologies to fortify rice have the potential to address these deficiencies and their associated adverse health effects. With the rice industry consolidating in many countries, there are opportunities to fortify a significant share of rice for distribution or for use in government safety net programs that target those most in need, especially women and children. Multisectoral approaches are needed for the promotion and implementation of rice fortification in countries. © 2014 New York Academy of Sciences.

  5. Economic survey of rice marketing in Anambra state, Nigeria ...

    African Journals Online (AJOL)

    This study exploratorily surveyed the process of marketing of rice in Anambra State with particular reference to rice processing, storage and pricing. The results of the analysis show that old people who are mostly illiterate but highly experienced engaged in rice marketing business. Furthermore, there is a significant ...

  6. Rice value chain analysis in Tanzania: identification of constraints ...

    African Journals Online (AJOL)

    The importance of rice (Oryza sativa L.) as a food and cash crop in Eastern Africa, is increasing, but its value chain is becoming complex. In 2012/13, rice value chain analysis was conducted in rice farming systems of Lake, Eastern and Southern-Highlands zones of Tanzania. A sample of 240 producers, 60 traders and 30 ...

  7. Upland and lowland rice in the Netherlands Indies

    NARCIS (Netherlands)

    Maat, H.

    2016-01-01

    The global trade in rice is historically recent and its total quantity relatively small. Colonial explorations were the main incentive for its development, but only beginning in the 19th century did rice-producing countries in Asia export rice outside the continent in bulk. In previous centuries

  8. Global Rice Atlas: Disaggregated seasonal crop calendar and production

    NARCIS (Netherlands)

    Balanza, Jane Girly; Gutierrez, Mary Anne; Villano, Lorena; Nelson, A.D.; Zwart, S.J.; Boschetti, Mirco; Koo, Jawoo; Reinke, Russell; Murty, M. V.R.; Laborte, Alice G.

    2014-01-01

    Purpose: Rice is an important staple crop cultivated in more than 163 million ha globally. Although information on the distribution of global rice production is available by country and, at times, at subnational level, information on its distribution within a year is often lacking in different rice

  9. RICD: A rice indica cDNA database resource for rice functional genomics

    Directory of Open Access Journals (Sweden)

    Zhang Qifa

    2008-11-01

    Full Text Available Abstract Background The Oryza sativa L. indica subspecies is the most widely cultivated rice. During the last few years, we have collected over 20,000 putative full-length cDNAs and over 40,000 ESTs isolated from various cDNA libraries of two indica varieties Guangluai 4 and Minghui 63. A database of the rice indica cDNAs was therefore built to provide a comprehensive web data source for searching and retrieving the indica cDNA clones. Results Rice Indica cDNA Database (RICD is an online MySQL-PHP driven database with a user-friendly web interface. It allows investigators to query the cDNA clones by keyword, genome position, nucleotide or protein sequence, and putative function. It also provides a series of information, including sequences, protein domain annotations, similarity search results, SNPs and InDels information, and hyperlinks to gene annotation in both The Rice Annotation Project Database (RAP-DB and The TIGR Rice Genome Annotation Resource, expression atlas in RiceGE and variation report in Gramene of each cDNA. Conclusion The online rice indica cDNA database provides cDNA resource with comprehensive information to researchers for functional analysis of indica subspecies and for comparative genomics. The RICD database is available through our website http://www.ncgr.ac.cn/ricd.

  10. Puffing of okara/rice blends using a rice cake machine.

    Science.gov (United States)

    Xie, M; Huff, H; Hsieh, F; Mustapha, A

    2008-10-01

    Okara is the insoluble byproduct of soymilk and tofu manufactures. It is cheap, high in nutrients, and possesses great potential to be applied to functional human foods. In this study, a puffed okara/rice cake product was developed with blends of okara pellets and parboiled rice. Consumer preference and acceptance tests were conducted for the product. Okara pellets were prepared by grinding the strands obtained from extruding a mixture of dried okara and rice flour (3:2, w/w) with a twin-screw extruder. Okara pellets and parboiled rice were blended in 4 ratios, 90:10, 70:30, 40:60, and 0:100 (w/w), and tempered to 14% and 17% moisture. The blends were puffed at 221, 232, and 243 degrees C for 4, 5, or 6 s. The okara/rice cakes were evaluated for specific volume (SPV), texture, color, and percent weight loss after tumbling. Overall, the decrease in okara content and increase in moisture, heating temperature and time led to greater specific volume (SPV) and hardness, lighter color, and lower percent weight loss after tumbling. The consumer tests indicated that the okara/rice cake containing 70% okara pellets was preferred and the 90% one was liked the least. The possible drivers of liking for the puffed okara/rice cakes could be the okara content, hardness, SPV, bright color, and percent weight loss after tumbling.

  11. Contribution of rice straw carbon to CH4 emission from rice paddies using 13C-enriched rice straw

    Science.gov (United States)

    Watanabe, Akira; Yoshida, Mariko; Kimura, Makoto

    1998-04-01

    It is generally recognized that the application of rice straw (RS) increases CH4 emission from rice paddies. To estimate the contribution of RS carbon to CH4 emission, a pot experiment was conducted using 13C-enriched RS. The percentage contributions of RS carbon to CH4 emission throughout the rice growth period were 10±1, 32±3, and 43±3% for the treatments with RS applied at the rates of 2, 4, and 6 g kg-1 soil, respectively. The increase in the rate of application of RS increased CH4 emission derived from both RS carbon and other carbon sources. The percentage contribution of RS carbon to CH4 emission was larger in the earlier period (maximum 96%) when the decomposition rate of RS was larger. After RS decomposition had slowed, CH4 emission derived from RS carbon decreased. However, the δ13C values of CH4 emitted from the pots with 13C-enriched RS applied at rates of 4 and 6 g kg-1 soil were significantly higher than those from the pots with natural RS until the harvesting stage. An increased atom-13C% of roots of rice plants growing in the pots with 6 g kg-1 of 13C-enriched RS at around the maximum tiller number stage and a decrease during the following 2 months suggested that rice plants assimilated RS carbon once and then released a portion of it. This supply of RS carbon from roots may be one of the sources of CH4 in the late period of rice growth.

  12. Interoperability between phenotype and anatomy ontologies.

    Science.gov (United States)

    Hoehndorf, Robert; Oellrich, Anika; Rebholz-Schuhmann, Dietrich

    2010-12-15

    Phenotypic information is important for the analysis of the molecular mechanisms underlying disease. A formal ontological representation of phenotypic information can help to identify, interpret and infer phenotypic traits based on experimental findings. The methods that are currently used to represent data and information about phenotypes fail to make the semantics of the phenotypic trait explicit and do not interoperate with ontologies of anatomy and other domains. Therefore, valuable resources for the analysis of phenotype studies remain unconnected and inaccessible to automated analysis and reasoning. We provide a framework to formalize phenotypic descriptions and make their semantics explicit. Based on this formalization, we provide the means to integrate phenotypic descriptions with ontologies of other domains, in particular anatomy and physiology. We demonstrate how our framework leads to the capability to represent disease phenotypes, perform powerful queries that were not possible before and infer additional knowledge. http://bioonto.de/pmwiki.php/Main/PheneOntology.

  13. Effects of Position of Rainfed Rice Field in a Toposequence on Water Availability and Rice Yield in Central Java, Indonesia

    OpenAIRE

    SUGANDA, HUSEIN; PANINGBATAN, E.P; GUERRA, L.C; TUONG, T.P

    2003-01-01

    The productivity of rainfed rice needs to be increased in order to support the Indonesian Food Security programs, especially rice. Rainfall is one of the main sources of the water availability on the rainfed rice field. This research was conducted from October 2000 to February 2001 at four sites in Central Java Province. The objectives of this research were to study thevariability of water availability that influenced by toposequen's position and to analyze the rice yields due to treatments o...

  14. Effects of fish and prawn culture on physico-chemical parameters of water and rice yield in rice fields

    OpenAIRE

    Razzak, M.A.; Nahar, A.; Mirhaj, M.; Becker, K.; Dewan, S.

    2009-01-01

    An experiment was conducted with five treatments i.e. rice combined with fish having regular urea fertilization (T1), rice combined with prawn having regular urea fertilization (T2), rice combined with fish with supplementary feeding (T3), rice combined with prawn with supplementary feeding (T4) and without fish and prawn (T5) was kept as control. The dissolved oxygen values obtained in treatments with fish both in morning and afternoon were lower than the values of prawn containing treatment...

  15. Characterization and evaluation of rice blast resistance of Chinese indica hybrid rice parental lines

    Directory of Open Access Journals (Sweden)

    Yunyu Wu

    2017-12-01

    Full Text Available The development of resistant varieties and hybrid combinations has been the most effective and economical strategy to control blast disease caused by Magnaporthe oryzae. However, the distribution of major R genes and blast resistance characterization in hybrid rice parents has not been well investigated, resulting in their limited use in hybrid rice blast-resistance breeding. In the present study, 88 elite indica hybrid rice parental lines were evaluated with 30 isolates of M. oryzae collected from the main planting area of indica hybrid rice in China and were characterized for the presence of 11 major resistance genes using molecular markers. The pathogenicity assays showed that four types of hybrid rice parent line showed some resistance to M. oryzae. However, the proportions of highly resistant lines and the mean resistance frequency (RF varied among the four types, with resistance in decreasing order shown by three-line restorer lines, three-line maintainer lines, two-line sterile lines, and two-line restorer lines. All 88 hybrid rice parental lines carried more than one R gene, but none carried the R genes Pi1 and Pi2. Although Pid3 and Pi9 were present only in three-line restorer lines and Pigm only in three-line maintainer lines, the remaining six R genes (Pib, Pid2, Pi5, Pia, Pi54, and Pita were present in the four types of hybrid rice parent with significantly different distribution frequencies. The correlation between R genes and resistance reactions was investigated. The results are expected to provide useful information for rational utilization of major R genes in hybrid rice breeding programs. Keywords: Hybrid rice parental lines, Magnaporthe oryzae, Pi genes, Resistance evaluation, Molecular markers

  16. Evaluation of rice germplasm under salt stress at the seedling stage through SSR markers

    Directory of Open Access Journals (Sweden)

    M. Al-Amin

    2013-06-01

    Full Text Available Twenty eight rice germplasms were used for identification of salt tolerant rice genotypes at the seedling stage at the experimental farm and Biotechnology laboratory of the Bangladesh Institute of Nuclear Agriculture (BINA, Mymensingh during February 2009 to October 2009. Phenotyping for salinity screening of the rice genotypes was done using salinized (EC level 12 dS m-1 nutrient solution in hydroponic system. Genotypes were evaluated for salinity tolerance on 1-9 scale based on seedling growth parameters following modified Standard Evaluation Scoring (SES of IRRI. Phenotypically, on the basis of SES and % total dry matter (TDM reduction of the genotypes viz. PBSAL-614, PBSAL-613, PBSAL-730, Horkuch, S-478/3 Pokkali and PBSAL (STL-15 were found to be salt tolerant; on the other hand Iratom-24, S-653/32, S-612/32, S-604/32, S-633/32, Charnock (DA6, BINA Dhan-6 and S-608/32 were identified as salt susceptible. For genotyping, ten SSR markers were used for polymorphism, where 3 primers (RM127, RM443 and RM140 were selected for evaluation of salt tolerance. In respect of Primer RM127, 7 lines were found salt tolerant and 11 lines were moderately tolerant and 10 lines were susceptible. Nine tolerant, 9 moderately tolerant and 10 susceptible lines were found when the primer RM140 was used and primer RM443 identified 8 lines as tolerant, 9 lines as moderately tolerant and 11 lines as susceptible. Thus, the salt tolerant lines can be used in further evaluation for salinity tolerance and the SSR markers used in this study are proving valuable for identifying salt tolerant genes in marker assisted breeding.

  17. Analysis of cytoplasmic effects and fine-mapping of a genic male sterile line in rice.

    Directory of Open Access Journals (Sweden)

    Peng Qin

    Full Text Available Cytoplasm has substantial genetic effects on progeny and is important for yield improvement in rice breeding. Studies on the cytoplasmic effects of cytoplasmic male sterility (CMS show that most types of CMS have negative effects on yield-related traits and that these negative effects vary among CMS. Some types of genic male sterility (GMS, including photo-thermo sensitive male sterility (PTMS, have been widely used in rice breeding, but the cytoplasmic effects of GMS remain unknown. Here, we identified a GMS mutant line, h2s, which exhibited small, white anthers and failed to produce mature pollen. Unlike CMS, the h2s had significant positive cytoplasmic effects on the seed set rate, weight per panicle, yield, and general combining ability (GCA for plant height, seed set rate, weight per panicle, and yield. These effects indicated that h2s cytoplasm may show promise for the improvement of rice yield. Genetic analysis suggested that the phenotype of h2s was controlled by a single recessive locus. We mapped h2s to a 152 kb region on chromosome 6, where 22 candidate genes were predicted. None of the 22 genes had previously been reported to be responsible for the phenotypes of h2s. Sequencing analysis showed a 12 bp deletion in the sixth exon of Loc_Os06g40550 in h2s in comparison to wild type, suggesting that Loc_Os06g40550 is the best candidate gene. These results lay a strong foundation for cloning of the H2S gene to elucidate the molecular mechanism of male reproduction.

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

    Directory of Open Access Journals (Sweden)

    Kouki eYoshida

    2013-10-01

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

  19. The Conserved and Unique Genetic Architecture of Kernel Size and Weight in Maize and Rice.

    Science.gov (United States)

    Liu, Jie; Huang, Juan; Guo, Huan; Lan, Liu; Wang, Hongze; Xu, Yuancheng; Yang, Xiaohong; Li, Wenqiang; Tong, Hao; Xiao, Yingjie; Pan, Qingchun; Qiao, Feng; Raihan, Mohammad Sharif; Liu, Haijun; Zhang, Xuehai; Yang, Ning; Wang, Xiaqing; Deng, Min; Jin, Minliang; Zhao, Lijun; Luo, Xin; Zhou, Yang; Li, Xiang; Zhan, Wei; Liu, Nannan; Wang, Hong; Chen, Gengshen; Li, Qing; Yan, Jianbing

    2017-10-01

    Maize ( Zea mays ) is a major staple crop. Maize kernel size and weight are important contributors to its yield. Here, we measured kernel length, kernel width, kernel thickness, hundred kernel weight, and kernel test weight in 10 recombinant inbred line populations and dissected their genetic architecture using three statistical models. In total, 729 quantitative trait loci (QTLs) were identified, many of which were identified in all three models, including 22 major QTLs that each can explain more than 10% of phenotypic variation. To provide candidate genes for these QTLs, we identified 30 maize genes that are orthologs of 18 rice ( Oryza sativa ) genes reported to affect rice seed size or weight. Interestingly, 24 of these 30 genes are located in the identified QTLs or within 1 Mb of the significant single-nucleotide polymorphisms. We further confirmed the effects of five genes on maize kernel size/weight in an independent association mapping panel with 540 lines by candidate gene association analysis. Lastly, the function of ZmINCW1 , a homolog of rice GRAIN INCOMPLETE FILLING1 that affects seed size and weight, was characterized in detail. ZmINCW1 is close to QTL peaks for kernel size/weight (less than 1 Mb) and contains significant single-nucleotide polymorphisms affecting kernel size/weight in the association panel. Overexpression of this gene can rescue the reduced weight of the Arabidopsis ( Arabidopsis thaliana ) homozygous mutant line in the AtcwINV2 gene (Arabidopsis ortholog of ZmINCW1 ). These results indicate that the molecular mechanisms affecting seed development are conserved in maize, rice, and possibly Arabidopsis. © 2017 American Society of Plant Biologists. All Rights Reserved.

  20. Deciphering the genomic structure, function and evolution of carotenogenesis related phytoene synthases in grasses

    Directory of Open Access Journals (Sweden)

    Dibari Bianca

    2012-06-01

    Full Text Available Abstract Background Carotenoids are isoprenoid pigments, essential for photosynthesis and photoprotection in plants. The enzyme phytoene synthase (PSY plays an essential role in mediating condensation of two geranylgeranyl diphosphate molecules, the first committed step in carotenogenesis. PSY are nuclear enzymes encoded by a small gene family consisting of three paralogous genes (PSY1-3 that have been widely characterized in rice, maize and sorghum. Results In wheat, for which yellow pigment content is extremely important for flour colour, only PSY1 has been extensively studied because of its association with QTLs reported for yellow pigment whereas PSY2 has been partially characterized. Here, we report the isolation of bread wheat PSY3 genes from a Renan BAC library using Brachypodium as a model genome for the Triticeae to develop Conserved Orthologous Set markers prior to gene cloning and sequencing. Wheat PSY3 homoeologous genes were sequenced and annotated, unravelling their novel structure associated with intron-loss events and consequent exonic fusions. A wheat PSY3 promoter region was also investigated for the presence of cis-acting elements involved in the response to abscisic acid (ABA, since carotenoids also play an important role as precursors of signalling molecules devoted to plant development and biotic/abiotic stress responses. Expression of wheat PSYs in leaves and roots was investigated during ABA treatment to confirm the up-regulation of PSY3 during abiotic stress. Conclusions We investigated the structural and functional determinisms of PSY genes in wheat. More generally, among eudicots and monocots, the PSY gene family was found to be associated with differences in gene copy numbers, allowing us to propose an evolutionary model for the entire PSY gene family in Grasses.

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

    OpenAIRE

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

    2015-01-01

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

  2. Deciphering signature of selection affecting beef quality traits in Angus cattle.

    Science.gov (United States)

    Taye, Mengistie; Yoon, Joon; Dessie, Tadelle; Cho, Seoae; Oh, Sung Jong; Lee, Hak-Kyo; Kim, Heebal

    2018-01-01

    Artificial selection towards a desired phenotype/trait has modified the genomes of livestock dramatically that generated breeds that greatly differ in morphology, production and environmental adaptation traits. Angus cattle are among the famous cattle breeds developed for superior beef quality. This paper aimed at exploring genomic regions under selection in Angus cattle that are associated with meat quality traits and other associated phenotypes. The whole genome of 10 Angus cattle was compared with 11 Hanwoo (A-H) and 9 Jersey (A-J) cattle breeds using a cross-population composite likelihood ratio (XP-CLR) statistical method. The top 1% of the empirical distribution was taken as significant and annotated using UMD3.1. As a result, 255 and 210 genes were revealed under selection from A-H and A-J comparisons, respectively. The WebGestalt gene ontology analysis resulted in sixteen (A-H) and five (A-J) significantly enriched KEGG pathways. Several pathways associated with meat quality traits (insulin signaling, type II diabetes mellitus pathway, focal adhesion pathway, and ECM-receptor interaction), and feeding efficiency (olfactory transduction, tight junction, and metabolic pathways) were enriched. Genes affecting beef quality traits (e.g., FABP3, FTO, DGAT2, ACS, ACAA2, CPE, TNNI1), stature and body size (e.g., PLAG1, LYN, CHCHD7, RPS20), fertility and dystocia (e.g., ESR1, RPS20, PPP2R1A, GHRL, PLAG1), feeding efficiency (e.g., PIK3CD, DNAJC28, DNAJC3, GHRL, PLAG1), coat color (e.g., MC1-R) and genetic disorders (e.g., ITGB6, PLAG1) were found to be under positive selection in Angus cattle. The study identified genes and pathways that are related to meat quality traits and other phenotypes of Angus cattle. The findings in this study, after validation using additional or independent dataset, will provide useful information for the study of Angus cattle in particular and beef cattle in general.

  3. Review: Deciphering animal robustness. A synthesis to facilitate its use in livestock breeding and management.

    Science.gov (United States)

    Friggens, N C; Blanc, F; Berry, D P; Puillet, L

    2017-12-01

    As the environments in which livestock are reared become more variable, animal robustness becomes an increasingly valuable attribute. Consequently, there is increasing focus on managing and breeding for it. However, robustness is a difficult phenotype to properly characterise because it is a complex trait composed of multiple components, including dynamic elements such as the rates of response to, and recovery from, environmental perturbations. In this review, the following definition of robustness is used: the ability, in the face of environmental constraints, to carry on doing the various things that the animal needs to do to favour its future ability to reproduce. The different elements of this definition are discussed to provide a clearer understanding of the components of robustness. The implications for quantifying robustness are that there is no single measure of robustness but rather that it is the combination of multiple and interacting component mechanisms whose relative value is context dependent. This context encompasses both the prevailing environment and the prevailing selection pressure. One key issue for measuring robustness is to be clear on the use to which the robustness measurements will employed. If the purpose is to identify biomarkers that may be useful for molecular phenotyping or genotyping, the measurements should focus on the physiological mechanisms underlying robustness. However, if the purpose of measuring robustness is to quantify the extent to which animals can adapt to limiting conditions then the measurements should focus on the life functions, the trade-offs between them and the animal's capacity to increase resource acquisition. The time-related aspect of robustness also has important implications. Single time-point measurements are of limited value because they do not permit measurement of responses to (and recovery from) environmental perturbations. The exception being single measurements of the accumulated consequence of a

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

    Directory of Open Access Journals (Sweden)

    Mawsheng Chern

    2016-05-01

    Full Text Available 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.

  5. Genetic analysis of rice blast disease resistance genes using USDA rice mini-core and a mapping population

    Science.gov (United States)

    Rice blast disease caused by the fungal pathogen Magnaporthe oryzae (M. oryzae) is one of the most destructive diseases of cultivated rice, resulting in significant yield loss each year all over the world. Developing and utilizing blast resistant rice varieties is the most economical and effective m...

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

    OpenAIRE

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

    2016-01-01

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

  7. Effects of Variety and Hydration of Rice Flour on Cake Making Properties

    OpenAIRE

    長沼, 誠子; NAGANUMA, Seiko

    1993-01-01

    The pysicochemical characteristics and sensory attributes of rice layer cake were investigated to study the effects of rice variety and rice flour treatment on cake making properties. The rice layer cake were made from rice flour ground from 4 rice varieties (Sasanishiki, Akitakomachi, Kiyonishiki and Akihikari), water, sugar, oil, and baking powder. The treatment of rice frour with water before adding other ingredients improved appearance, texture and palatability of the baking products. The...

  8. Physicochemical Characteristics of Artificial Rice from Composite Flour: Modified Cassava Starch, Canavalia ensiformis and Dioscorea esculenta

    OpenAIRE

    Sumardiono Siswo; Pudjihastuti Isti; Abyor Handayani Noer; Kusumayanti Heny

    2018-01-01

    Indonesia is the third largest country on the global paddy rice production and also considered as a rice importer. Even, Indonesia has the biggest per capita consumption of paddy rice (140 kg of paddy rice per person per year). Product diversification using local commodities. Artificial rice is potential to be developed as a new value product using different types of grains. It is one of appropriate solutions for reducing imported rice rate. Artificial rice was produced using high nutrition c...

  9. Analysis of QTL for resistance to radiation in rice

    International Nuclear Information System (INIS)

    Zhao Fei; Zhou Yifeng; Ren Sanjuan; Fu Junjie; Zhuang Jieyun; Shen Shengquan

    2010-01-01

    The recombinant inbred line (RIL) population derived from rice variates Zhenshan 97B/Miyang 46 and their genetic linkage maps were used to map QTLs controlling resistant to radiation. The trait was measured by the relative germination rate (RGR) and the relative surviving plant rate (RSPR) after the seeds of each line treated with γ-rays irradiation at two 350 and 550 Gy. The results indicated that the lines treated with γ-irradiation showed different performance in resistance to radiation. Under the treatment of 350 Gy, two QTLs with additive effects were detected, of which qRR (g) 81 was only significant for relative germination rate, and it had the positive additive effects from the male parent, explaining 6.53% of the total phenotypic variations. The qRR(s)2-2 was another significant one for relative surviving plant rate, whose positive effects came from the female parent,explaining 12.81% of the total phenotypic variations. Similarly, 4 QTLs were detected under irradiation dose of 550 Gy, and qRR(g)1-2 and qRR(g)8-2 were detected for relative germination rate, with positive effects coming from female and male parent,respectively,explaining 14.38% of the total variations. qRR(s)5-2 and qRR(s)10 were detected for relative surviving plant rate, with positive effects coming from the male parent, explaining 19.65% of total variations. Under different irradiation dose, 9 pairs of double QTL epistasis effects could be identified in this population. The results suggested that the expression of QTL with resistance to radiation might have relation with the irradiation dose. (authors)

  10. Obtaining high purity silica from rice hulls

    Directory of Open Access Journals (Sweden)

    José da Silva Júnior

    2010-01-01

    Full Text Available Many routes for extracting silica from rice hulls are based on direct calcining. These methods, though, often produce silica contaminated with inorganic impurities. This work presents the study of a strategy for obtaining silica from rice hulls with a purity level adequate for applications in electronics. The technique is based on two leaching steps, using respectively aqua regia and Piranha solutions, which extract the organic matrix and inorganic impurities. The material was characterized by Fourier-transform infrared spectroscopy (FTIR, powder x-ray diffraction (XRD, x-ray fluorescence (XRF, scanning electron microscopy (SEM, particle size analysis by laser diffraction (LPSA and thermal analysis.

  11. Thermoplastic starch materials prepared from rice starch

    International Nuclear Information System (INIS)

    Pontes, Barbara R.B.; Curvelo, Antonio A.S.

    2009-01-01

    Rice starch is a source still little studied for the preparation of thermoplastic materials. However, its characteristics, such as the presence of proteins, fats and fibers may turn into thermoplastics with a better performance. The present study intends the evaluation of the viability of making starch thermoplastic from rice starch and glycerol as plasticizer. The results of X-ray diffraction and scanning electronic microscopy demonstrate the thermoplastic acquisition. The increase of plasticizer content brings on more hydrophilic thermoplastics with less resistance to tension and elongation at break. (author)

  12. Gene conversion in the rice genome

    DEFF Research Database (Denmark)

    Xu, Shuqing; Clark, Terry; Zheng, Hongkun

    2008-01-01

    -chromosomal conversions distributed between chromosome 1 and 5, 2 and 6, and 3 and 5 are more frequent than genome average (Z-test, P ... is not tightly linked to natural selection in the rice genome. To assess the contribution of segmental duplication on gene conversion statistics, we determined locations of conversion partners with respect to inter-chromosomal segment duplication. The number of conversions associated with segmentation is less...... involved in conversion events. CONCLUSION: The evolution of gene families in the rice genome may have been accelerated by conversion with pseudogenes. Our analysis suggests a possible role for gene conversion in the evolution of pathogen-response genes....

  13. The LANSCE RICE control system upgrade.

    Energy Technology Data Exchange (ETDEWEB)

    Oothoudt, Michael; Schaller, S. (Stuart); Bjorklund, E. A. (Eric A.); Burns, M. J. (Mary J.); Carr, G. (Gary); Carr, G. (Gary); Faucett, John Allen,; Hayden, D. J. (David J.); Lusk, M. D. (Matthew D.); Merl, R. B. (Robert B.); Potter, J. M. (Jerry M.); Reynolds, J. A. (Jerome A.); Romero, D. B. (Dolores B.); Shelley, F. E. (Fred E.)

    2003-01-01

    The LANSCE (Los Alamos Neutron Science Center) control system upgrade program continues with the impending replacement of the RICE (Remote Instrumentation and Control Equipment) subsystem. The RICE subsystem upgrade is a challenge because of its technology (late 1960s), number of channels (>10,000), and unique characteristics (all-modules data takes, timed/flavored data takes). The plan is to replace at least the non-timed data and the command portions of the subsystem with Programmable Logic Controllers (PLCs). We discuss motivations, technological challenges, proof-of-principle, and planning. The boundary condition, as usual, is that we must implement these major changes on a running accelerator.

  14. Radiation induced chlorophyll mutations in rice

    International Nuclear Information System (INIS)

    Bari, G.; Mustafa, G.; Soomro, A.M.; Baloch, A.W.

    1985-01-01

    Air dried grains of four local varieties of rice were treated with gamma-rays and fast neutrons for determining their mutagenic effectiveness through the occurence of chlorophyll mutations. Fast neutrons were more effective in inducing chlorophyll mutations and the rice variety Basmati 370 produced maximum number of mutations followed by varieties Sonahri Sugdasi, Jajai 77 and Sada Gulab. The highest frequency of chlorophyll mutations was that of albina types followed by striata types. The xantha, viridis and tigrina types of mutations were less frequent. (authors)

  15. The LANSCE RICE control system upgrade

    International Nuclear Information System (INIS)

    Oothoudt, Michael; Schaller, S.; Bjorklund, E.A.; Burns, M.J.; Carr, G.; Faucett, John Allen; Hayden, D.J.; Lusk, M.D.; Merl, R.B.; Potter, J.M.; Reynolds, J.A.; Romero, D.B.; Shelley, F.E.

    2003-01-01

    The LANSCE (Los Alamos Neutron Science Center) control system upgrade program continues with the impending replacement of the RICE (Remote Instrumentation and Control Equipment) subsystem. The RICE subsystem upgrade is a challenge because of its technology (late 1960s), number of channels (>10,000), and unique characteristics (all-modules data takes, timed/flavored data takes). The plan is to replace at least the non-timed data and the command portions of the subsystem with Programmable Logic Controllers (PLCs). We discuss motivations, technological challenges, proof-of-principle, and planning. The boundary condition, as usual, is that we must implement these major changes on a running accelerator.

  16. A comparison of rice chloroplast genomes

    DEFF Research Database (Denmark)

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

    2004-01-01

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

  17. Managing flood prone ecosystem for rice production in Bihar plains

    International Nuclear Information System (INIS)

    Khan, A.R.; Singh, S.S.

    2002-06-01

    A large area of the eastern region especially Bihar (0.5 million hectare) faces flood submergence and/or drought every year which creates an unfavorable environment for crop production. In this ecosystem only flood prone rice is grown whose cultivation is entirely different than normal rice crop. Managing the flood prone ecosystem for rice production needs to evaluate the reasons and a comprehensive appropriate technology through research efforts for better rice production under such harsh ecology. An attempt was made to develop a suitable agronomic package for rice cultivation during and after flooding in flood prone plains of Bihar. (author)

  18. Cell fusion as a tool for rice improvement

    Energy Technology Data Exchange (ETDEWEB)

    Hayashi, Y; Kyozuka, J; Terada, R; Nishibayashi, S; Shimamoto, K [Plantech Research Institute, Kamoshida, Midori-ku, Yokohama (Japan)

    1990-01-01

    Full text: Cell fusion offers a unique opportunity to hybridize sexually incompatible species and to mix cytoplasmic genomes in higher plants. Recent progress in plant regeneration from rice protoplasts facilitates an evaluation of the cell fusion method for rice improvement. By using electrofusion of protoplasts, we obtained hybrid/cybrid plants of the following combinations: Hybrids of rice x barnyard grass (E. oryzicola); Hybrids of rice x wild Oryza species; Cybrids of rice with transferred cms cytoplasm. For the latter, protoplasts irradiated with 70 krad x-rays were used. (author)

  19. Defined fungal starter granules for purple glutinous rice wine

    OpenAIRE

    Ngo Thi Phuong Dung, N.T.P.

    2004-01-01

    The Mekong Delta region ofSouth Vietnamis particularly known as a production area of purple glutinous rice wine ( RuouNepThan ). The latter differs from regular rice wine for its sherry-like taste and flavour and its attractive brown-red colour. Wine is made from purple glutinous rice at home or by small cottage industries, by washing, soaking, steam-cooking, cooling and inoculation of the cooled rice with powdered rice-wine starter ( Men ). The fermentation takes place in two stages, i.e. an...

  20. Sensory acceptability evaluation of irradiated rice, oryza sativa indica

    International Nuclear Information System (INIS)

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

    1971-01-01

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