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Sample records for local rice varieties

  1. Field evaluation of rice varieties for resistance to major diseases

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The development and use of improved disease resistant rice varieties remains of foremost importance to rice producers, with field evaluation under local environments essential. In this study, we evaluated new and existing varieties, potential releases, and Texas elite breeding lines for resistance t...

  2. Effect of rice variety and nutrient management on rice productivity in organic rice system

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Demand for organic rice has been increasing for decades. However, the information on sustainable organic rice production systems is still lacking. The objective of this study was to investigate the effects of soil amendment products, nitrogen rate, and variety on rice grain yield, yield components, ...

  3. Effect of germination on the physicochemical and antioxidant characteristics of rice flour from three rice varieties from Nigeria.

    PubMed

    Chinma, Chiemela Enyinnaya; Anuonye, Julian Chukwuemeka; Simon, Omotade Comfort; Ohiare, Raliat Ozavize; Danbaba, Nahemiah

    2015-10-15

    This study determined the effect of germination (48 h) on the physicochemical and antioxidant characteristics of rice flour from three rice varieties from Nigeria. Local rice varieties (Jamila, Jeep and Kwandala) were evaluated and compared to an improved variety (MR 219). Physicochemical and antioxidant properties of flours were determined using standard methods. Protein, magnesium, phosphorus, potassium and antioxidant properties of rice flours increased after germination while phytic acid and total starch contents decreased. Foaming capacity and stability of rice flours increased after germination. Germination resulted to changes in pasting and thermal characteristics of rice flours. Germinated rice flours had better physicochemical and antioxidant properties with reduced phytic acid and starch contents compared to MR 219, which can be utilized as functional ingredients in the preparation of rice-based products.

  4. Dynamic vapor sorption isotherms of medium grain rice varieties

    Technology Transfer Automated Retrieval System (TEKTRAN)

    It is known that the two popular medium rice varieties, namely M202 and M206, in California have different fissuring resistances. Therefore, the main goal of this study was to investigate the sorption behavior of these two varieties by a new approach using dynamic vapor sorption (DVS) method for elu...

  5. Production of a saccharifying rice malt for brewing using different rice varieties and malting parameters.

    PubMed

    Mayer, Heidi; Marconi, Ombretta; Regnicoli, Gian Franco; Perretti, Giuseppe; Fantozzi, Paolo

    2014-06-11

    This study was conducted to produce rice malt suitable for beer brewing. An all-rice beer would be particularly appealing to individuals with celiac disease because rice does not contain gluten proteins. Furthermore, rice malt could also contribute to new beer flavors and brands. A screening of 10 rice varieties was conducted. The varieties Balilla and Centauro were found to be suitable for the production of an all-rice malt beer without the need of exogenous enzymes. They were characterized by a low diastatic power but nevertheless they saccharified well, likely due to other endogenous amylolytic enzymes such as limit dextrinase and α-glucosidase. The addition of CaCl2 and lactic acid during mashing lowered the pH value and increased saccharification. However, the Balilla variety saccharified without the need of these additives. We also show that the soluble nitrogen and free amino nitrogen content of rice malt wort can be increased by the incorporation of the acrospires and rootlets during mashing.

  6. From QTL to variety-harnessing the benefits of QTLs for drought, flood and salt tolerance in mega rice varieties of India through a multi-institutional network.

    PubMed

    Singh, Renu; Singh, Yashi; Xalaxo, Suchit; Verulkar, S; Yadav, Neera; Singh, Shweta; Singh, Nisha; Prasad, K S N; Kondayya, K; Rao, P V Ramana; Rani, M Girija; Anuradha, T; Suraynarayana, Y; Sharma, P C; Krishnamurthy, S L; Sharma, S K; Dwivedi, J L; Singh, A K; Singh, P K; Nilanjay; Singh, N K; Kumar, Rajesh; Chetia, S K; Ahmad, T; Rai, M; Perraju, P; Pande, Anita; Singh, D N; Mandal, N P; Reddy, J N; Singh, O N; Katara, J L; Marandi, B; Swain, P; Sarkar, R K; Singh, D P; Mohapatra, T; Padmawathi, G; Ram, T; Kathiresan, R M; Paramsivam, K; Nadarajan, S; Thirumeni, S; Nagarajan, M; Singh, A K; Vikram, Prashant; Kumar, Arvind; Septiningshih, E; Singh, U S; Ismail, A M; Mackill, D; Singh, Nagendra K

    2016-01-01

    Rice is a staple cereal of India cultivated in about 43.5Mha area but with relatively low average productivity. Abiotic factors like drought, flood and salinity affect rice production adversely in more than 50% of this area. Breeding rice varieties with inbuilt tolerance to these stresses offers an economically viable and sustainable option to improve rice productivity. Availability of high quality reference genome sequence of rice, knowledge of exact position of genes/QTLs governing tolerance to abiotic stresses and availability of DNA markers linked to these traits has opened up opportunities for breeders to transfer the favorable alleles into widely grown rice varieties through marker-assisted backcross breeding (MABB). A large multi-institutional project, "From QTL to variety: marker-assisted breeding of abiotic stress tolerant rice varieties with major QTLs for drought, submergence and salt tolerance" was initiated in 2010 with funding support from Department of Biotechnology, Government of India, in collaboration with International Rice Research Institute, Philippines. The main focus of this project is to improve rice productivity in the fragile ecosystems of eastern, northeastern and southern part of the country, which bear the brunt of one or the other abiotic stresses frequently. Seven consistent QTLs for grain yield under drought, namely, qDTY1.1, qDTY2.1, qDTY2.2, qDTY3.1, qDTY3.2, qDTY9.1 and qDTY12.1 are being transferred into submergence tolerant versions of three high yielding mega rice varieties, Swarna-Sub1, Samba Mahsuri-Sub1 and IR 64-Sub1. To address the problem of complete submergence due to flash floods in the major river basins, the Sub1 gene is being transferred into ten highly popular locally adapted rice varieties namely, ADT 39, ADT 46, Bahadur, HUR 105, MTU 1075, Pooja, Pratikshya, Rajendra Mahsuri, Ranjit, and Sarjoo 52. Further, to address the problem of soil salinity, Saltol, a major QTL for salt tolerance is being transferred into

  7. Water management, rice varieties and mycorrhizal inoculation influence arsenic concentration and speciation in rice grains.

    PubMed

    Zhang, Xin; Wu, Songlin; Ren, Baihui; Chen, Baodong

    2016-05-01

    A pot experiment was carried out to investigate the effects of water management and mycorrhizal inoculation on arsenic (As) uptake by two rice varieties, the As-resistant BRRI dhan 47 (B47) and As-sensitive BRRI dhan 29 (B29). Grain As concentration of B47 plants was significantly lower than that of B29, and grain As concentration of B47 was higher under flooding conditions than that under aerobic conditions. In general, mycorrhizal inoculation (Rhizophagus irregularis) had no significant effect on grain As concentrations, but decreased the proportion of inorganic arsenic (iAs) in grains of B47. The proportion of dimethylarsinic acid (DMA) in the total grain As was dramatically higher under flooding conditions. Results demonstrate that rice variety selection and appropriate water management along with mycorrhizal inoculation could be practical countermeasures to As accumulation and toxicity in rice grains, thus reducing health risks of As exposure in rice diets.

  8. Genetic shift in local rice populations during rice breeding programs in the northern limit of rice cultivation in the world.

    PubMed

    Fujino, Kenji; Obara, Mari; Ikegaya, Tomohito; Tamura, Kenichi

    2015-09-01

    The rapid accumulation of pre-existing mutations may play major roles in the establishment and shaping of adaptability for local regions in current rice breeding programs. The cultivated rice, Oryza sativa L., which originated from tropical regions, is now grown worldwide due to the concerted efforts of breeding programs. However, the process of establishing local populations and their origins remain unclear. In the present study, we characterized DNA polymorphisms in the rice variety KITAAKE from Hokkaido, one of the northern limits of rice cultivation in the world. Indel polymorphisms were attributed to transposable element-like insertions, tandem duplications, and non-TE deletions as the original mutation events in the NIPPONBARE and KITAAKE genomes. The allele frequencies of the KITAAKE alleles markedly shifted to the current variety types among the local population from Hokkaido in the last two decades. The KITAAKE alleles widely distributed throughout wild rice and cultivated rice over the world. These have accumulated in the local population from Hokkaido via Japanese landraces as the ancestral population of Hokkaido. These results strongly suggested that combinations of pre-existing mutations played a role in the establishment of adaptability. This approach using the re-sequencing of local varieties in unique environmental conditions will be useful as a genetic resource in plant breeding programs in local regions.

  9. In vitro assessment on the impact of soil arsenic in the eight rice varieties of West Bengal, India.

    PubMed

    Bhattacharya, Piyal; Samal, Alok C; Majumdar, Jayjit; Banerjee, Satabdi; Santra, Subhas C

    2013-11-15

    Rice is an efficient accumulator of arsenic and thus irrigation with arsenic-contaminated groundwater and soil may induce human health hazard via water-soil-plant-human pathway. A greenhouse pot experiment was conducted on three high yielding, one hybrid and four local rice varieties to investigate the uptake, distribution and phytotoxicity of arsenic in rice plant. 5, 10, 20, 30 and 40 mg kg(-1) dry weights arsenic dosing was applied in pot soil and the results were compared with the control samples. All the studied high yielding and hybrid varieties (Ratna, IET 4094, IR 50 and Gangakaveri) were found to be higher accumulator of arsenic as compared to all but one local rice variety, Kerala Sundari. In these five rice varieties accumulation of arsenic in grain exceeded the WHO permissible limit (1.0 mg kg(-1)) at 20 mg kg(-1) arsenic dosing. Irrespective of variety, arsenic accumulation in different parts of rice plant was found to increase with increasing arsenic doses, but not at the same rate. A consistent negative correlation was established between soil arsenic and chlorophyll contents while carbohydrate accumulation depicted consistent positive correlation with increasing arsenic toxicity in rice plant.

  10. Effect of enzyme activity on the starch structure and processing quality of selected rice varieties

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Although most commercialized long grain rice varieties have intermediate amylose content (~22%), high amylose (>25%) varieties are important for the canning and parboiling industry. Research has shown that high amylose rice varieties that have the best processing quality have high setback and low br...

  11. Phytochemical profiles and iron chelating capability of rice varieties

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Whole-grain rice, especially the dark color bran rice, contains high phenolic content and antioxidant capacity, which have potential in disease prevention. However, little information is available regarding the differences in phytochemical profiles of rice of different bran color. Studies indicated ...

  12. Comparative Study on Vegetative and Reproductive Development between Weedy Rice Morphotypes and Commercial Rice Varieties in Perak, Malaysia

    PubMed Central

    Ahmed, Quazi Nasim; Hussain, PMD Zainudin; Othman, Ahmad Sofiman

    2012-01-01

    This study was conducted to examine the variabilities in the chronology of vegetative and reproductive development of weedy rice (Oryza spp.) in comparison with commercial varieties. Data at different growth stages of 14 weedy rice morphotypes and 4 commercial rice varieties were recorded and analysed. Plant height of all weedy rice morphotypes were observed to be significantly higher compared to the commercial varieties at every growth stages; increase in height was between 10–37 cm for weedy rice morphotype, for every 2 weeks. Initial tillering ability at 14 days after planting (DAP) was higher in weedy morphotypes, however all the commercial rice varieties produced significantly higher number of tillers throughout the rest of the vegetative phases. Correlation between plant height and tiller number detected that taller plants produce fewer tillers than shorter plants. Higher leaf area index (LAI) of all weedy morphotypes except PWR01 at early growth stages indicated the vigorous growth of the morphotypes. Weedy rice morphotypes showed a wide range of anthesis and maturity duration. Accessions from the same weedy rice morphotypes were more heterogeneous in the flowering, anthesis and maturity period than the commercial varieties. These traits enables identification of weedy rice morphotypes at their different growth stages in the field. PMID:24575230

  13. Combining Limited Multiple Environment Trials Data with Crop Modeling to Identify Widely Adaptable Rice Varieties

    PubMed Central

    Li, Tao; Ali, Jauhar; Franje, Neil Johann; Revilleza, Jastin Edrian; Redoña, Edilberto; Xu, Jianlong

    2016-01-01

    Multi-Environment Trials (MET) are conventionally used to evaluate varietal performance prior to national yield trials, but the accuracy of MET is constrained by the number of test environments. A modeling approach was innovated to evaluate varietal performance in a large number of environments using the rice model ORYZA (v3). Modeled yields representing genotype by environment interactions were used to classify the target population of environments (TPE) and analyze varietal yield and yield stability. Eight Green Super Rice (GSR) and three check varieties were evaluated across 3796 environments and 14 seasons in Southern Asia. Based on drought stress imposed on rainfed rice, environments were classified into nine TPEs. Relative to the check varieties, all GSR varieties performed well except GSR-IR1-5-S14-S2-Y2, with GSR-IR1-1-Y4-Y1, and GSR-IR1-8-S6-S3-Y2 consistently performing better in all TPEs. Varietal evaluation using ORYZA (v3) significantly corresponded to the evaluation based on actual MET data within specific sites, but not with considerably larger environments. ORYZA-based evaluation demonstrated the advantage of GSR varieties in diverse environments. This study substantiated that the modeling approach could be an effective, reliable, and advanced approach to complement MET in the assessment of varietal performance on spatial and temporal scales whenever quality soil and weather information are accessible. With available local weather and soil information, this approach can also be adopted to other rice producing domains or other crops using appropriate crop models. PMID:27723774

  14. Combining Limited Multiple Environment Trials Data with Crop Modeling to Identify Widely Adaptable Rice Varieties.

    PubMed

    Li, Tao; Ali, Jauhar; Marcaida, Manuel; Angeles, Olivyn; Franje, Neil Johann; Revilleza, Jastin Edrian; Manalo, Emmali; Redoña, Edilberto; Xu, Jianlong; Li, Zhikang

    2016-01-01

    Multi-Environment Trials (MET) are conventionally used to evaluate varietal performance prior to national yield trials, but the accuracy of MET is constrained by the number of test environments. A modeling approach was innovated to evaluate varietal performance in a large number of environments using the rice model ORYZA (v3). Modeled yields representing genotype by environment interactions were used to classify the target population of environments (TPE) and analyze varietal yield and yield stability. Eight Green Super Rice (GSR) and three check varieties were evaluated across 3796 environments and 14 seasons in Southern Asia. Based on drought stress imposed on rainfed rice, environments were classified into nine TPEs. Relative to the check varieties, all GSR varieties performed well except GSR-IR1-5-S14-S2-Y2, with GSR-IR1-1-Y4-Y1, and GSR-IR1-8-S6-S3-Y2 consistently performing better in all TPEs. Varietal evaluation using ORYZA (v3) significantly corresponded to the evaluation based on actual MET data within specific sites, but not with considerably larger environments. ORYZA-based evaluation demonstrated the advantage of GSR varieties in diverse environments. This study substantiated that the modeling approach could be an effective, reliable, and advanced approach to complement MET in the assessment of varietal performance on spatial and temporal scales whenever quality soil and weather information are accessible. With available local weather and soil information, this approach can also be adopted to other rice producing domains or other crops using appropriate crop models.

  15. Resistance of Rice Varieties to the Stored-Product Insect, Sitophilus zeamais (Coleoptera: Curculionidae).

    PubMed

    Antunes, Catarina; Mendes, Raquel; Lima, Arlindo; Barros, Graça; Fields, Paul; Da Costa, Luísa Beirão; Rodrigues, José Carlos; Silva, Maria José; Correia, Augusto Manuel; Carvalho, Maria Otilia

    2016-02-01

    Four common Portuguese rice varieties--Thaibonnet, Gladio, Albatros, and Eurosis--were tested for their relative susceptibility to Sitophilus zeamais Motschulsky, a common pest of stored rice in Portugal and in tropical countries. Physical (moisture content, hardness, length, and width) and chemical (by attenuated total reflection-Fourier transform infrared spectroscopy) properties of rice kernels were measured. Insect bioassays measured median developmental time, Dobie's index of susceptibility, percentage of damaged grains and weight loss, and progeny developed. This was done for paddy, brown rice, and polished rice for each variety. There were small, but significant, differences in insect resistance among the varieties. However, it was different for paddy and polished rice. In paddy, these differences were correlated with hull damage, and Eurosis was the most susceptible variety. In polished rice, resistance was correlated with hardness, and Thaibonnet was the most susceptible variety. In general, paddy rice was more resistant to insect attack, followed by polished rice and then brown rice. Paddy kernels selected with undamaged hull were completely resistant to attack. Implications for IPM and breeding for resistant varieties are discussed.

  16. Analysis of elite variety tag SNPs reveals an important allele in upland rice.

    PubMed

    Lyu, Jun; Zhang, Shilai; Dong, Yang; He, Weiming; Zhang, Jing; Deng, Xianneng; Zhang, Yesheng; Li, Xin; Li, Baoye; Huang, Wangqi; Wan, Wenting; Yu, Yang; Li, Qiong; Li, Jun; Liu, Xin; Wang, Bo; Tao, Dayun; Zhang, Gengyun; Wang, Jun; Xu, Xun; Hu, Fengyi; Wang, Wen

    2013-01-01

    Elite crop varieties usually fix alleles that occur at low frequencies within non-elite gene pools. Dissecting these alleles for desirable agronomic traits can be accomplished by comparing the genomes of elite varieties with those from non-elite populations. Here we deep-sequence six elite rice varieties and use two large control panels to identify elite variety tag single-nucleotide polymorphism alleles (ETASs). Guided by this preliminary analysis, we comprehensively characterize one protein-altering ETAS in the 9-cis-epoxycarotenoid dioxygenase gene of the IRAT104 upland rice variety. This allele displays a drastic frequency difference between upland and irrigated rice, and a selective sweep is observed around this allele. Functional analysis indicates that in upland rice, this allele is associated with significantly higher abscisic acid levels and denser lateral roots, suggesting its association with upland rice suitability. This report provides a potential strategy to mine rare, agronomically important alleles.

  17. Characterization of resistance genes to rice blast fungus Magnaporthe oryzae in a “Green Revolution” rice variety

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The indica rice variety Dee Geo Woo Gen (DGWG) was the source of the semi-dwarf gene (SD1) which played an important role in the Green Revolution. In the present study, resistance (R) genes to the U.S. race (isolate) IB54 of Magnaporthe oryzae, causal agent of rice blast disease, was investigated. T...

  18. Soluble starch synthase I effects differences in amylopectin structure between indica and japonica rice varieties.

    PubMed

    Takemoto-Kuno, Yoko; Suzuki, Keitaro; Nakamura, Sumiko; Satoh, Hikaru; Ohtsubo, Keníchi

    2006-11-29

    The effect of soluble starch synthase I (SSI) on differences of amylopectin structure between the indica and japonica rice varieties was investigated. Native-PAGE/active staining analysis showed that the SSI activity of an indica rice variety, "Kasalath", was significantly lower than that of a japonica rice variety, "Nipponbare", and that the low activity in "Kasalath" was maintained during seed development. The result of northern blot analyses suggests that the low expression of SSI in "Kasalath" is controlled at the transcription levels of SSI mRNA. Chain length distribution of amylopectin in F3 endosperms derived from a cross between two varieties showed that not only SSIIa but also SSI regulated the population of short chains. These results indicate that the low activity of SSI gives rise to the decrease of short chains in amylopectin of indica rice varieties, suggesting that SSI effects the differences in physicochemical properties between two varieties.

  19. Dietary rice bran supplementation prevents salmonella colonization differentially across varieties and by priming intestinal immunity

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The global burden of enteric dysfunction and diarrhoeal disease remains a formidable problem that requires novel interventions. This study investigated the immune-modulatory capacity of bran across rice varieties with phytochemical differences. 129SvEvTac mice were fed a 10% rice bran or control die...

  20. Physicochemical and sensory analysis of USA rice varieties developed for the basmati and jasmine markets

    Technology Transfer Automated Retrieval System (TEKTRAN)

    There is a steady demand for imported basmati and jasmine rice in The USA. Rice varieties that can be domestically produced and compete with these imports, have been developed from basmati, jasmine, and other aromatic germplasm sources. This study evaluated differences among eight USA aromatic varie...

  1. Phenolic acids and antioxidant activities in husk of different Thai rice varieties.

    PubMed

    Butsat, S; Siriamornpun, S

    2010-08-01

    This study was designed to investigate the free and bound phenolic acids as well as their antioxidant activities in husk of 12 Thai rice varieties consisting of pigmented rice and normal rice. The pigmented rice husk gave higher free total phenolic contents than normal rice husk. However, there was no significant difference in bound total phenolic contents between pigmented rice and normal rice husks. Ferulic and p-coumaric acids were the major phenolic acids in the free fraction of pigmented rice husks, whereas vanillic acid was the dominant phenolic acid in the free fraction of normal rice husks. On the other hand, p-coumaric acid was highly found in bound form of both pigmented and normal rice husks. The antioxidant activity of husk extracts was positively correlated with the total free phenolics content and individual of phenolic acids especially ferulic acid. On the basis of this study, it is suggested that the rice husk could be a potential phenolic acid source and may therefore offer an effective source of natural antioxidant. Our findings provide valuable information on phenolic acids composition and antioxidant activity of husk for further food application.

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

    PubMed Central

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

    2012-01-01

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

  3. Comparative transcriptome analysis of two rice varieties in response to rice stripe virus and small brown planthoppers during early interaction.

    PubMed

    Zheng, Wenjing; Ma, Li; Zhao, Jiaming; Li, Zhiqiang; Sun, Fuyu; Lu, Xiaochun

    2013-01-01

    Rice stripe, a virus disease, transmitted by a small brown planthopper (SBPH), has greatly reduced production of japonica rice in East Asia, especially in China. Although we have made great progress in mapping resistance genes, little is known about the mechanism of resistance. By de novo transcriptome assembling, we gained sufficient transcript data to analyze changes in gene expression of early interaction in response to SBPH and RSV infection in rice. Respectively 648 and 937 DEGs were detected from the disease-resistant (Liaonong 979) and the susceptible (Fengjin) varieties, most of which were up-regulated. We found 37 genes related to insect resistance, which mainly included genes for jasmonate-induced protein, TIFY protein, lipoxygenase, as well as trypsin inhibitor genes and transcription factor genes. In the interaction process between RSV and rice, 87 genes were thought to be related to RSV resistance; these primarily included 12 peroxidase biosynthesis genes, 12 LRR receptor-like protein kinase genes, 6 genes coding pathogenesis-related proteins, 4 glycine-rich cell wall structural protein genes, 2 xyloglucan hydrolase genes and a cellulose synthase. The results indicate that the rice-pathogen interaction happened both in disease-resistant and susceptible varieties, and some genes related to JA biosynthesis played key roles in the interaction between SBPHs and rice. When rice was infected by RSV a hypersensitive reaction (HR) in the disease-resistant variety was suppressed, which resulted from an increase in peroxidase expression and down-regulation of LRR receptor-like protein kinase and pathogenesis-related proteins, while, the changes of peroxidase biosynthesis, glycine-rich cell wall structural protein, cellulose synthase and xyloglucan endotransglucosylase/hydrolase could lead to the strengthening of physical barriers of rice, which may be an important resistance mechanism to RSV in rice.

  4. Relationship of Rice Grain Amylose, Gelatinization Temperature and Pasting Properties for Breeding Better Eating and Cooking Quality of Rice Varieties

    PubMed Central

    Wang, Xiaoqian; Franje, Neil Johann; Revilleza, Jastin Edrian; Xu, Jianlong; Li, Zhikang

    2016-01-01

    A total of 787 non-waxy rice lines– 116 hybrids and 671 inbreds–were used to study the apparent amylose content (AAC), gelatinization temperature (GT), and rapid visco analyzer (RVA) pasting viscosity properties of rice starch to understand their importance in breeding better rice varieties. The investigated traits showed a wide range of diversity for both hybrid (HG) and inbred (IG) groups. The combinations of the different categories of AAC and GT were random in HG but were non-random in IG. For inbred lines, the high level of AAC tended to combine with the low level of GT, the intermediate level of AAC tended to have high or intermediate GT, and the low level of AAC tended to have high or low GT. Some stable correlations of the AAC, GT, and RVA properties may be the results derived from the physicochemical relationships among these traits, which rice breeders could utilize for selection in advanced breeding generations. Through cluster analysis, IG and HG were divided into 52 and 31 sub-clusters, respectively. Identifying the cultivars having AAC, GT, and RVA properties similar to that of popular high-quality rice varieties seems to be an interesting strategy and could be directly used for adaptation trials to breed high-quality rice varieties in targeted areas in a more customized manner. PMID:27992591

  5. Status in physical properties of coloured rice varieties before and after inducing retro-gradation.

    PubMed

    Itagi, HameedaBanu N; Singh, Vasudeva

    2015-12-01

    Three varieties of paddy in brown, red (non-waxy) and black (waxy) forms were de-husked and milled before and after inducing retro-gradation and their physical properties were studied. Normalized grain weight, porosity of parboiled paddy (PP) and its de-husked rice (DR), were high compared to their respective native. True and bulk density were lowest for black variety, its DR, its raw and parboiled forms compared to other varieties of paddy. Angle of repose increased from raw paddy to PP whereas it decreased from raw DR to parboiled DR. Under similar conditions of milling of DR, raw and parboiled milled rice of black variety was the darkest. Raw husk showed higher EMC compared to husk of parboiled. Hardness followed the pattern: Raw: Paddy (~230-280 N) > DR (~120-260 N) > Milled rice (~110 N); for parboiled: DR (~270-480 N) > PP (~260-425 N) > Parboiled milled rice (~250-340 N). Cooking time was high for DR of parboiled ones and least for waxy raw milled rice. Results of this study will be helpful in understanding the quality of pigmented rice cultivars, design and fabrication of some of the equipments in rice processing industry.

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

    PubMed

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

    2013-01-01

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

  7. Morphological Study of the Relationships between Weedy Rice Accessions (Oryza sativa Complex) and Commercial Rice Varieties in Pulau Pinang Rice Granary Area

    PubMed Central

    Hussain, Zainudin PMD; Man, Azmi; Othman, Ahmad Sofiman

    2010-01-01

    Weedy rice (WR) is found in many direct-seeded rice fields. WR possesses morphological characteristics that are similar to cultivated rice varieties in the early stage of growth, making them more difficult to control than other weeds. A comparative morphological study was conducted by collecting WR accessions from four sites within the Pulau Pinang rice growing areas. The objective of the study was to characterise WR accessions of the Pulau Pinang rice granary by comparing their morphological characteristics to those of commercially grown rice in the area. Their morphometric relations were established by comparing 17 morphological characteristics of the WR accessions and the commercial varieties. A total of 36 WR morphotypes were identified from these 4 sites based on 17 characteristics, which included grain shattering habit and germination rate. The Principal Component Analysis (PCA) showed that 45.88% of the variation observed among the WR accessions and commercial varieties were within the first 3 axes. PB6, PP2 and SGA5 WR accessions had a higher number of tillers and longer panicle lengths, culm heights and leaf lengths compared to the commercial rice. The grain sizes of the commercial varieties were slightly longer, and the chlorophyll contents at 60–70 days after sowing (DAS) were higher than those of the WR accessions. Results from this study are useful for predicting potential WR accession growth, which might improve WR management and agriculture practices that control WR in the future. PMID:24575197

  8. [Glycemic index of two varieties of pasta and two varieties of rice].

    PubMed

    Ridner, Edgardo; Di Sibio, Antonio

    2015-06-01

    The IG has been extensively studied as an indicator of the physiological effects of a carbohydrate meal with applications in the management and prevention of diabetes, dyslipidemia and obesity. A standard assay was performed to measure the glycemic index (GI) of two significant sources of carbohydrates following the World Health Organization (WHO) recommended methodology, determining the incremental area under the blood glucose response curve of a 50g carbohydrate portion of the test food compared to the same amount of carbohydrate from a glucose solution by the same subject measured in capillary whole blood before and 15, 30, 45, 60, 90 and 120 minutes after ingestion in a total of 9 subjects. The following results were obtained: Parboil rice: 73, Long Grain White Rice: 59; Pasta of durum wheat (Triticum durum): 71, Pasta of regular flour (Triticum aestivium): 38. This test confirms the low glycemic index of pasta made from durum wheat, and is the first measurement for pasta of common wheat flour properly characterized. It also indicates the values of the prevailing presentations of rice in the region, adding a reference for professionals and authorities.

  9. Voltammetric Electronic Tongue for Different Varieties of Rice Classification Based on Square Wave Voltammetry

    NASA Astrophysics Data System (ADS)

    Hu, Hongsheng; Niu, Qunfeng; Pan, Yinqing; Wang, Li

    A classification method of discriminate rice from different varieties with voltammetric electronic tongue based on square wave voltammetry is investigated. The rice samples are crushed and mixed with distilled water to get the rice solution, and the solution should be stirred and filtered before the experiment. In order to obtain the electrochemical response signals of the rice samples and extract the characteristic value of the singles, the electronic tongue which works respectively with titanium (Ti) electrode and tungsten electrode (W) to test the sample solution under square wave voltammetry. The Principal Component Analysis (PCA) and Clustering Analysis (CA) are adopted to classify and recognize the rice samples. Experimental results show that good classification and recognition results are got in this paper when using Principal Component Analysis and Cluster Analysis to analyze the response signals which are obtained by voltammetric electronic tongue worked with Ti electrode and W electrode under square wave potential.

  10. Comparison of key aroma compounds in cooked brown rice varieties based on aroma extract dilution analyses.

    PubMed

    Jezussek, Magnus; Juliano, Bienvenido O; Schieberle, Peter

    2002-02-27

    The aroma compounds present in cooked brown rice of the three varieties Improved Malagkit Sungsong (IMS), Basmati 370 (B 370), and Khaskhani (KK), and of the variety Indica (German supermarket sample), were identified on the basis of aroma extract dilution analyses (AEDA). A total of 41 odor-active compounds were identified, of which eleven are reported for the first time as rice constituents. 2-Amino acetophenone (medicinal, phenolic), which was up to now unknown in rice aroma, exhibited the highest flavor dilution (FD) factor among the 30 to 39 odor-active compounds detected in all four varieties. 2-Acetyl-1-pyrroline, exhibiting an intense popcorn-like aroma-note, was confirmed as a further key aroma constituent in IMS, B 370, and KK, but was not important in Indica. Differences in the FD factors between the varieties were found for the previously unknown rice aroma compound 3-hydroxy-4,5-dimethyl-2(5H)-furanone (Sotolon; seasoning-like), which was higher in B 370 than in IMS and KK. In IMS, a yet unknown, spicy smelling component with a very high FD factor could be detected, which contributed with lower FD factors to the overall aromas of B 370 and KK, and was not present in Indica. The latter variety, which was available on the German market, differed most in its overall aroma from the three Asian brown rices.

  11. Modern elite rice varieties of the 'Green Revolution' have retained a large introgression from wild rice around the Pi33 rice blast resistance locus.

    PubMed

    Ballini, Elsa; Berruyer, Romain; Morel, Jean-Benoît; Lebrun, Marc-Henri; Nottéghem, Jean-Loup; Tharreau, Didier

    2007-01-01

    During the breeding process of cultivated crops, resistance genes to pests and diseases are commonly introgressed from wild species. The size of these introgressions is predicted by theoretical models but has rarely been measured in cultivated varieties. By combining resistance tests with isogenic strains, genotyping and sequencing of different rice accessions, it was shown that, in the elite rice variety IR64, the resistance conferring allele of the rice blast resistance gene Pi33 was introgressed from the wild rice Oryza rufipogon (accession IRGC101508). Further characterization of this introgression revealed a large introgression at this locus in IR64 and the related variety IR36. The introgressed fragment represents approximately half of the short arm of rice chromosome 8. This is the first report of a large introgression in a cultivated variety of rice. Such a large introgression is likely to have been maintained during backcrossing only if a selection pressure was exerted on this genomic region. The possible traits that were selected are discussed.

  12. Methane emission from fields with differences in nitrogen fertilizers and rice varieties in Taiwan paddy soils.

    PubMed

    Liou, Rey-May; Huang, Shan-Ney; Lin, Chin-Wei

    2003-01-01

    Flooded rice fields are one of the major biogenic methane sources. In this study, methane emission rates were measured after transplanting in paddy fields with application of two kinds of nitrogen fertilizers (ammonium sulfate, NH4+-N and potassium nitrate, NO3(-)-N) and with two kinds of rice varieties (Japonica and Indica). The experiment was conducted in fields located at Tainan District Agricultural Improvement Station in Chia-Yi county (23 degrees 25'08"N, 120 degrees 16'26"E) of southern Taiwan throughout the first and the second crop seasons in 1999. The seasonal methane flux in the first crop season with NH4+-N and NO3(-)-N ranged from 2.48 to 2.78 and from 8.65 to 9.22 g CH4 m(-2); and the values ranged 24.6-34.2 and 36.4-52.6 g CH4 m(-2) in the second crop season, respectively. In the first crop season, there were significantly increased 3.1-3.7-fold in methane emission fluxes due to plantation of Indica rice. In comparison of two rice varieties, the Indica rice variety showed a tendency for larger methane emission than the Japonica rice variety in the second crop season. Moreover, ammonium sulfate treatment significantly reduced CH4 emissions by 37-85% emissions compared to potassium nitrate plots. It was concluded that the CH4 emission was markedly dependent on the type of nitrogen fertilizer and rice variety in Taiwan paddy soils.

  13. Genetic structure and diversity of indigenous rice (Oryza sativa) varieties in the Eastern Himalayan region of Northeast India.

    PubMed

    Choudhury, Baharul; Khan, Mohamed Latif; Dayanandan, Selvadurai

    2013-12-01

    The Eastern Himalayan region of Northeast (NE) India is home to a large number of indigenous rice varieties, which may serve as a valuable genetic resource for future crop improvement to meet the ever-increasing demand for food production. However, these varieties are rapidly being lost due to changes in land-use and agricultural practices, which favor agronomically improved varieties. A detailed understanding of the genetic structure and diversity of indigenous rice varieties is crucial for efficient utilization of rice genetic resources and for developing suitable conservation strategies. To explore the genetic structure and diversity of rice varieties in NE India, we genotyped 300 individuals of 24 indigenous rice varieties representing sali, boro, jum and glutinous types, 5 agronomically improved varieties, and one wild rice species (O. rufipogon) using seven SSR markers. A total of 85 alleles and a very high level of gene diversity (0.776) were detected among the indigenous rice varieties of the region. Considerable level of genetic variation was found within indigenous varieties whereas improved varieties were monoporphic across all loci. The comparison of genetic diversity among different types of rice revealed that sali type possessed the highest gene diversity (0.747) followed by jum (0.627), glutinous (0.602) and boro (0.596) types of indigenous rice varieties, while the lowest diversity was detected in agronomically improved varieties (0.459). The AMOVA results showed that 66% of the variation was distributed among varieties indicating a very high level of genetic differentiation in rice varieties in the region. Two major genetically defined clusters corresponding to indica and japonica groups were detected in rice varieties of the region. Overall, traditionally cultivated indigenous rice varieties in NE India showed high levels of genetic diversity comparable to levels of genetic diversity reported from wild rice populations in various parts of the

  14. Hull characteristics as related to susceptibility of different varieties of rough rice to Rhyzopertha dominica (F.) (Coleoptera: Bostrichidae)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Rhyzopertha dominica (F.), an important pest of stored grains, causes economic damage to rough rice through physical damage to the kernel, resulting in reductions in grain quality. In this test, 28 varieties of commercial rough rice, 10 long-grain varieties, 11 medium-grain varieties, and 7 short-...

  15. Silicon-mediated resistance in a susceptible rice variety to the rice leaf folder, Cnaphalocrocis medinalis Guenée (Lepidoptera: Pyralidae).

    PubMed

    Han, Yongqiang; Lei, Wenbin; Wen, Lizhang; Hou, Maolin

    2015-01-01

    The rice leaf folder, Cnaphalocrocis medinalis (Guenée), is one of the most destructive rice pests in Asian countries. Rice varieties resistant to the rice leaf folder are generally characterized by high silicon content. In this study, silicon amendment, at 0.16 and 0.32 g Si/kg soil, enhanced resistance of a susceptible rice variety to the rice leaf folder. Silicon addition to rice plants at both the low and high rates significantly extended larval development and reduced larval survival rate and pupation rate in the rice leaf folder. When applied at the high rate, silicon amendment reduced third-instars' weight gain and pupal weight. Altogether, intrinsic rate of increase, finite rate of increase and net reproduction rate of the rice leaf folder population were all reduced at both the low and high silicon addition rates. Although the third instars consumed more in silicon-amended treatments, C:N ratio in rice leaves was significantly increased and food conversion efficiencies were reduced due to increased silicon concentration in rice leaves. Our results indicate that reduced food quality and food conversion efficiencies resulted from silicon addition account for the enhanced resistance in the susceptible rice variety to the rice leaf folder.

  16. Silicon-Mediated Resistance in a Susceptible Rice Variety to the Rice Leaf Folder, Cnaphalocrocis medinalis Guenée (Lepidoptera: Pyralidae)

    PubMed Central

    Han, Yongqiang; Lei, Wenbin; Wen, Lizhang; Hou, Maolin

    2015-01-01

    The rice leaf folder, Cnaphalocrocis medinalis (Guenée), is one of the most destructive rice pests in Asian countries. Rice varieties resistant to the rice leaf folder are generally characterized by high silicon content. In this study, silicon amendment, at 0.16 and 0.32 g Si/kg soil, enhanced resistance of a susceptible rice variety to the rice leaf folder. Silicon addition to rice plants at both the low and high rates significantly extended larval development and reduced larval survival rate and pupation rate in the rice leaf folder. When applied at the high rate, silicon amendment reduced third-instars’ weight gain and pupal weight. Altogether, intrinsic rate of increase, finite rate of increase and net reproduction rate of the rice leaf folder population were all reduced at both the low and high silicon addition rates. Although the third instars consumed more in silicon-amended treatments, C:N ratio in rice leaves was significantly increased and food conversion efficiencies were reduced due to increased silicon concentration in rice leaves. Our results indicate that reduced food quality and food conversion efficiencies resulted from silicon addition account for the enhanced resistance in the susceptible rice variety to the rice leaf folder. PMID:25837635

  17. Contributions of climate, varieties, and agronomic management to rice yield change in the past three decades in China

    NASA Astrophysics Data System (ADS)

    Zhang, He; Tao, Fulu; Xiao, Dengpan; Shi, Wenjiao; Liu, Fengshan; Zhang, Shuai; Liu, Yujie; Wang, Meng; Bai, Huizi

    2016-06-01

    The long-term field experiment data at four representative agro-meteorological stations, together with a crop simulation model, were used to disentangle the contributions of climate change, variety renewal, and fertilization management to rice yield change in the past three decades. We found that during 1981-2009 varieties renewal increased rice yield by 16%-52%, management improvement increased yield by 0-16%, and the contributions of climate change to rice yield varied from — 16% to 10%. Varieties renewal and management improvement offset the negative impacts of climate change on rice production. Among the major climate variables, decreases in solar radiation reduced rice yield on average by 0.1%per year. The impact of temperature change had an explicit spatial pattern. It increased yield by 0.04%-0.4% per year for single rice at Xinbin and Ganyu station and for late rice at Tongcheng station, by contrast reduced yield by 0.2%-0.4% per year for single rice at Mianyang station and early rice at Tongcheng station. During 1981-2009, rice varieties renewal was characterized by increases in thermal requirements, grain number per spike and harvest index. The new varieties were less sensitive to climate change than old ones. The development of high thermal requirements, high yield potential and heat tolerant rice varieties, together with improvement of agronomic management, should be encouraged to meet the challenges of climate change and increasing food demand in future.

  18. Effects of Seeding Rates and Rice Water Weevil (Coleoptera: Curculionidae) Density on Damage in Two Medium Grain Varieties of Rice.

    PubMed

    Aghaee, Mohammad-Amir; Espino, Luis; Goding, Kevin; Goldman, Evan; Godfrey, Larry D

    2016-04-01

    Rice water weevil (Lissorhoptrus oryzophilus Kuschel) is a common pest of rice production in the United States whose larvae cause yield loss by feeding on the roots. We conducted studies from 2011–2013 on M-202 and M-206, two commonly grown California medium grain rice varieties, to determine if M-206 demonstrated tolerance to rice water weevil damage. Observations from field studies suggested the possibility of a level of tolerance in M-206 that was more prevalent at high seeding rates. We did this study using two different experimental units, open and ring plots. In both units, we quantified grain yields across four levels, 56, 112, 168, and 224 kg/ha, of seeding rates to detect potential yield recovery by M-206. In the open plots, we used naturally occurring weevil populations compared with controls that reduced the populations with insecticides. In the ring plots, we tested three levels of weevil infestation, none, low, and high, to look at the weevil density effects on yield and scarred plants. Our studies showed that M-206 and M-202 had generally similar densities of immature weevils and yield. Compensation for yield loss did not occur at higher seeding rates. These results suggest that M-206 does not have the ability to tolerate rice water weevil damage better than M-202. There was weak evidence that the number of scarred plants increased as plant density was reduced. The results are discussed in relation to the utility of this study to grower choices of varieties for long-term rice water weevil management.

  19. Morphological and starch structural characteristics of the Japonica rice mutant variety Seolgaeng for dry-milled flour

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Producing fine, good quality rice flour is more difficult than wheat flour because the rice grain is harder. In this study, we analyzed the relationship between the morphology and starch of kernels from genetically different rice varieties that can be used to make dry-milled flour. The non-glutinous...

  20. Cover crop, soil amendments, and variety effects on organic rice production in Texas

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The major challenges in organic rice production include optimization of nutrient utilization, weed management, and variety selection. In this study, we tested the effects of two soil amendment products, two fertilizer rates, and three cover cropping systems (clover, ryegrass, and fallow) on organic ...

  1. Site Suitability Analysis for Dissemination of Salt-tolerant Rice Varieties in Southern Bangladesh

    NASA Astrophysics Data System (ADS)

    Sinha, D. D.; Singh, A. N.; Singh, U. S.

    2014-11-01

    Bangladesh is a country of 14.4 million ha geographical area and has a population density of more than 1100 persons per sq. km. Rice is the staple food crop, growing on about 72 % of the total cultivated land and continues to be the most important crop for food security of the country. A project "Sustainable Rice Seed Production and Delivery Systems for Southern Bangladesh" has been executed by the International Rice Research Institute (IRRI) in twenty southern districts of Bangladesh. These districts grow rice in about 2.9 million ha out of the country's total rice area of 11.3 million ha. The project aims at contributing to the Government of Bangladesh's efforts in improving national and household food security through enhanced and sustained productivity by using salinity-, submergence- and drought- tolerant and high yielding rice varieties. Out of the 20 project districts, 12 coastal districts are affected by the problem of soil salinity. The salt-affected area in Bangladesh has increased from about 0.83 million ha in 1973 to 1.02 million ha in 2000, and 1.05 million ha in 2009 due to the influence of cyclonic storms like "Sidr", "Laila" and others, leading to salt water intrusion in croplands. Three salinity-tolerant rice varieties have recently been bred by IRRI and field tested and released by the Bangladesh Rice Research Institute (BRRI) and Bangladesh Institute of Nuclear Agriculture (BINA). These varieties are BRRI dhan- 47 and Bina dhan-8 and - 10. However, they can tolerate soil salinity level up to EC 8-10 dSm-1, whereas the EC of soils in several areas are much higher. Therefore, a large scale dissemination of these varieties can be done only when a site suitability analysis of the area is carried out. The present study was taken up with the objective of preparing the site suitability of the salt-tolerant varieties for the salinity-affected districts of southern Bangladesh. Soil salinity map prepared by Soil Resources Development Institute of

  2. Elemental analysis of different varieties of rice samples using XRF technique

    NASA Astrophysics Data System (ADS)

    Kaur, Jaspreet; Kumar, Anil

    2016-05-01

    Rice is most consumed staple food in the world providing over 21% of the calorie intake of world's population having high yielding capacity. Elements detected in rice are Al, As, Br, Cd, Cl, Co, Cs, Cu, Fe, Hg, K, Mg, Mn, Mo, Rb, Se and Zn by using Instrumental Neutron Activation with k0 standardization (R. Jayasekera etal,2004). Some of these trace elements are C, H, O, N, S, Ca, P, K, Na, Cl, Mn, Ti, Mg, Cu, Fe, Ni, Si and Zn are essential for growth of human physique The deficiency or excess of these elements in food is known to cause a variety of malnutrition or health disorders in the world. Every year, various varieties of rice are launched by Punjab Agriculture University, Ludhiana. The main purpose of which is to increases the yield to attain the maximum profit. But this leads to changing the elemental concentration in them, which may affect the human health according to variation in the nutrition values. The main objective is to study the presence of elemental concentration in various varieties of rice using EDXRF technique.

  3. Salt Tolerant and Sensitive Rice Varieties Display Differential Methylome Flexibility under Salt Stress

    PubMed Central

    Ferreira, Liliana J.; Azevedo, Vanessa; Maroco, João; Oliveira, M. Margarida; Santos, Ana Paula

    2015-01-01

    DNA methylation has been referred as an important player in plant genomic responses to environmental stresses but correlations between the methylome plasticity and specific traits of interest are still far from being understood. In this study, we inspected global DNA methylation levels in salt tolerant and sensitive rice varieties upon salt stress imposition. Global DNA methylation was quantified using the 5-methylcytosine (5mC) antibody and an ELISA-based technique, which is an affordable and quite pioneer assay in plants, and in situ imaging of methylation sites in interphase nuclei of tissue sections. Variations of global DNA methylation levels in response to salt stress were tissue- and genotype-dependent. We show a connection between a higher ability of DNA methylation adjustment levels and salt stress tolerance. The salt-tolerant rice variety Pokkali was remarkable in its ability to quickly relax DNA methylation in response to salt stress. In spite of the same tendency for reduction of global methylation under salinity, in the salt-sensitive rice variety IR29 such reduction was not statistically supported. In ‘Pokkali’, the salt stress-induced demethylation may be linked to active demethylation due to increased expression of DNA demethylases under salt stress. In ‘IR29’, the induction of both DNA demethylases and methyltransferases may explain the lower plasticity of DNA methylation. We further show that mutations for epigenetic regulators affected specific phenotypic parameters related to salinity tolerance, such as the root length and biomass. This work emphasizes the role of differential methylome flexibility between salt tolerant and salt sensitive rice varieties as an important player in salt stress tolerance, reinforcing the need to better understand the connection between epigenetic networks and plant responses to environmental stresses. PMID:25932633

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

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

    2016-01-01

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

  6. Breeding of a target genotype variety based on identified chalkiness marker-QTL associations in rice (Oryza sativa L.).

    PubMed

    Liu, X; Du, Y R; Li, X H; Li, X L; Yang, W Q; Wang, Y

    2015-10-21

    The aim of this study was to breed a target genotype variety based on the identified chalkiness marker-QTL (quantitative trait locus) associations in rice. First, a permanent mapping population of rice that consisted of 525 recombinant inbred lines (RILs), which were derived from Zhenshan 97/Minghui 63, was used to identify QTLs with additive effects for rice quantitative traits and percentage of grain chalkiness (PGC). Subsequently, based on the identified QTLs in rice, the molecular marker 68923-PGC was selected to screen the low chalkiness rice line. Then, using the integration of molecular marker breeding and traditional breeding, we analyzed the genotype and phenotype of inbred lines from 525 RILs; we identified one rice variety with particularly high yields, good taste, and broad adaptability. The new variety was temporarily named RIL10, which was a high quality, high yield, and broadly adaptable variety, and it is predominantly a feature that has contributed to its geographical adaptability, which would be planted from 35°E to 18°E in Chinain China, where 2/3 of rice production occurs. RIL10 was a marker-assisted selection breeding achievement for producing a high quality, high yield, and broadly adaptable rice variety.

  7. Variety recognition of rice seeds using image analysis and artificial neural network

    NASA Astrophysics Data System (ADS)

    Cheng, Fang; Ying, Yibin

    2004-11-01

    The objective of this research is to develop algorithms to classify varieties of rice seeds based on external features. The rice seeds used for this study involved five varieties of Jinyou402, Shanyou10, Zhongyou207, Jiayou and IIyou3207. Images of rice seeds were acquired with a color machine vision system. Each image was processed to extract twenty-two quantitative features. The classification ability of all the features was evaluated for different varieties recognition. The shape difference between Jinyou402 and Shanyou10 is obvious. The classification of Jinyou402 and Shanyou10 achieved an accuracy of 100% when a single feature such as the length-width ratio was used. Jinyou402 and IIyou couldn't be classified very well using one or two features. Then a perceptron was created and achieved an accuracy of 100% for both of Jinyou402 and IIyou. The shape difference between Jinyou402 and Zhongyou207 is obscure with naked eyes. All features were analyzed with principal components analysis method. A two-layer back propagation network was created and trained using gradient descent with momentum and adaptive learning rate. Nr. of hidden nodes was tested and early stopping skill was used. The total error of the finally established net is 2% for the classification of Jinyou402 and Zhongyou207. At last, all the images of five varieties were recognized as five classes. Another feed-forward network was created and trained using conjugate gradient back-propagation with Polak-Ribiere updates. Samples were disordered to train the network. The network achieved an average accuracy of about 85% for the five varieties.

  8. [On-farm conservation and utilization of paddy rice, wheat and maize landrace varieties in 15 unique ethnic groups in Yunnan, China].

    PubMed

    Xu, Fu-Rong; Yang, Ya-Yun; Zhang, En-Lai; A, Xin-Xiang; Tang, Cui-Feng; Dong, Chao; Zhang, Fei-Fei; Liu, Xu; Dai, Lu-Yuan

    2012-11-01

    On-farm conservation and utilization of crop landraces have been proposed as means of conserving plant germplasm, in contrast to ex situ germplasm conservation, but little is known about the effectiveness of this approach. This paper reports the findings from a survey conducted in 15 unique ethnic groups of the Yunnan Province on the conservation and utilization of paddy rice, wheat (including wheat, barley, oats, and rye) and maize landrace varieties through participatory rural appraisal (PRA) and questionnaires. The surveyed regions covered 306 villages (the village group) from 237 administrative villages in 124 towns (township) distributed in 36 counties of 11 prefectures (city) in Yunnan Province. The survey showed that 44.8%, 77.5%, and 37.3% of the visited villages had lost their paddy rice, wheat, and maize landraces, respectively. A total of 901 landraces were collected, including 371 rice, 119 wheat, and 411 maize varieties, respectively. There were 2.9 on-farm varieties on average per village, 3.3, 8.0 and 5.2 varieties on average per 100 households, 1 000 peasants and 100 Ha farmland areas, respectively. Among the 306 villages, two villages (Laomian and Qingkou) maintained the highest crop diversity with 18 varieties (including 10 rice and 8 maize varieties) and 14 paddy rice varieties. Also, on-farm varieties in different ethnic groups varied significantly from each other, ranging from 16 to 120 varieties per group. The diversity of paddy rice varieties was the highest, ranging from 1 to 72, and the diversity was mainly distributed in southern, southwest Yunnan of tropical, subtropical ethnic regions. The wheat varieties ranged from 0 to 47 and distributed in northern, northwest Yunnan of high altitude, temperature, and cold ethnic regions. The maize varieties ranged from 4 to 40. These patterns of variation in on-farm varieties are directly associated with traditional culture and custom for the ethnic minorities and reflect the lack of improved

  9. Root Associated Bacillus sp. Improves Growth, Yield and Zinc Translocation for Basmati Rice (Oryza sativa) Varieties

    PubMed Central

    Shakeel, Muhammad; Rais, Afroz; Hassan, Muhammad Nadeem; Hafeez, Fauzia Yusuf

    2015-01-01

    Plant associated rhizobacteria prevailing in different agro-ecosystems exhibit multiple traits which could be utilized in various aspect of sustainable agriculture. Two hundred thirty four isolates were obtained from the roots of basmati-385 and basmati super rice varieties growing in clay loam and saline soil at different locations of Punjab (Pakistan). Out of 234 isolates, 27 were able to solubilize zinc (Zn) from different Zn ores like zinc phosphate [Zn3 (PO4)2], zinc carbonate (ZnCO3) and zinc oxide (ZnO). The strain SH-10 with maximum Zn solubilization zone of 24 mm on Zn3 (PO4)2ore and strain SH-17 with maximum Zn solubilization zone of 14–15 mm on ZnO and ZnCO3ores were selected for further studies. These two strains solubilized phosphorous (P) and potassium (K) in vitro with a solubilization zone of 38–46 mm and 47–55 mm respectively. The strains also suppressed economically important rice pathogens Pyricularia oryzae and Fusarium moniliforme by 22–29% and produced various biocontrol determinants in vitro. The strains enhanced Zn translocation toward grains and increased yield of basmati-385 and super basmati rice varieties by 22–49% and 18–47% respectively. The Zn solubilizing strains were identified as Bacillus sp. and Bacillus cereus by 16S rRNA gene analysis. PMID:26635754

  10. Physiological factors affecting transcription of genes involved in the flavonoid biosynthetic pathway in different rice varieties.

    PubMed

    Chen, Xiaoqiong; Itani, Tomio; Wu, Xianjun; Chikawa, Yuuki; Irifune, Kohei

    2013-01-01

    Flavonoids play an important role in the grain color and flavor of rice. Since their characterization in maize, the flavonoid biosynthetic genes have been extensively studied in grape, Arabidopsis, and Petunia. However, we are still a long way from understanding the molecular features and mechanisms underlying the flavonoid biosynthetic pathway. The present study was undertaken to understand the physiological factors affecting the transcription and regulation of these genes. We report that the expression of CHI, CHS, DFR, LAR, and ANS, the 5 flavonoid biosynthetic genes in different rice varieties, differ dramatically with respect to the stage of development, white light, and sugar concentrations. We further demonstrate that white light could induce the transcription of the entire flavonoid biosynthetic gene pathway; however, differences were observed in the degrees of sensitivity and the required illumination time. Our study provides valuable insights into understanding the regulation of the flavonoid biosynthetic pathway.

  11. Value added products with popular low grade rice varieties of Andhra Pradesh.

    PubMed

    Anitha, G; Rajyalakshmi, P

    2014-12-01

    Eight Popular Low Grade Rice Varieties (PLRVs) MTU 3626, MTU 1001, MTU 1010, MTU 4870 and NLR 145, NLR 34242, NLR 30491, NLR 34449, (developed and released by ANGR agricultural University, Andhra Pradesh) having poor cooking quality were selected for the study. ANGRAU variety BPT 5204 popularly consumed as staple rice was used as check. Eight products of traditional/commercial importance were standardized incorporating PLRVs as a major ingredient in the form of rice flour (burfi, noodles and extruded snack product and vennaundalu (butter coated balls), palathalikalu (dough rolled into strips, steamed/cooked in milk); rice semolina (instant kheer mix and instant upma mix), and flaked rice (nutritious bar). The products were evaluated for nutritional, cooking quality characteristics, consumer acceptability and shelf-life. Consumer acceptability of the PLR products was carried out with 60 farm women based on 9 point hedonic scale. Shelf-life of the products (packed in both metalized PP and PE pouches) was evaluated monthly for chemical, microbiological and sensory parameters. Energy values of control and PLR products showed no significant difference. Upon cooking, PLR Noodles showed no significant difference with water absorption and volume but more (p < 0.05) solid loss and cooked weight. Utilization of PLR flakes in nutritious bar resulted in highly crispy and crunchy texture, enhanced flavor and taste as compared to control. The percent total solids and suspended solids were more (though not significant) in PLR kheer and palathalikalu. Extruded product (control and PLR) showed no significant difference with length, diameter, weight and volume expansion ratio and water absorption index (WAI). Consumer acceptability was high for PLR products palathalikalu (95%), instant kheer mix (92%) and extruded product (88%). As per sensory scores, all the PLR products were well accepted with no observable changes in flavor or taste upon storage. PLR products showed increased

  12. Simple and rapid molecular techniques for identification of amylose levels in rice varieties.

    PubMed

    Cheng, Acga; Ismail, Ismanizan; Osman, Mohamad; Hashim, Habibuddin

    2012-01-01

    The polymorphisms of Waxy (Wx) microsatellite and G-T single-nucleotide polymorphism (SNP) in the Wx gene region were analyzed using simplified techniques in fifteen rice varieties. A rapid and reliable electrophoresis method, MetaPhor agarose gel electrophoresis (MAGE), was effectively employed as an alternative to polyacrylamide gel electrophoresis (PAGE) for separating Wx microsatellite alleles. The amplified products containing the Wx microsatellite ranged from 100 to 130 bp in length. Five Wx microsatellite alleles, namely (CT)(10), (CT)(11), (CT)(16), (CT)(17), and (CT)(18) were identified. Of these, (CT)(11) and (CT)(17) were the predominant classes among the tested varieties. All varieties with an apparent amylose content higher than 24% were associated with the shorter repeat alleles; (CT)(10) and (CT)(11), while varieties with 24% or less amylose were associated with the longer repeat alleles. All varieties with intermediate and high amylose content had the sequence AGGTATA at the 5'-leader intron splice site, while varieties with low amylose content had the sequence AGTTATA. The G-T polymorphism was further verified by the PCR-AccI cleaved amplified polymorphic sequence (CAPS) method, in which only genotypes containing the AGGTATA sequence were cleaved by AccI. Hence, varieties with desirable amylose levels can be developed rapidly using the Wx microsatellite and G-T SNP, along with MAGE.

  13. Improvement of tomato local varieties by grafting in organic farming

    NASA Astrophysics Data System (ADS)

    Moreno, Marta M.; Villena, Jaime; Moreno, Carmen; García, Arántzazu M.; Mancebo, Ignacio; Meco, Ramón

    2015-04-01

    Grafting is the union of two or more pieces of living plant tissue that grow as a single plant. The early use of grafted vegetables was associated with protected cultivation which involves successive cropping (Lee et al., 2010). For this reason, in the past, grafting was used with vegetable crops to limit the effects of soil-borne diseases. However, the reasons for grafting as well as the kinds of vegetable grafted have increased considerably over the years. In tomato (Solanum lycopersicum L.), one of the most important horticultural crops in the world, the effect of grafting has also been widely studied. These effects on commercial tomato varieties can be summarized in increasing plant vigor and crop yield or inducing tolerance to abiotic stresses, although the effects on tomato fruit quality or on the sensory properties are not so patent (David et al., 2008). However, a few studies about the effect of grafting on local tomato varieties, which are especially recommended for organic production in spite of their lower yields in many cases, have been developed. In this work we evaluated the effect of grafting on tomato local varieties under organic management using vigorous commercial rootstocks, and aspects related to vigor, yield and tomato fruit composition were analyzed. In general terms, grafting increased the plant vigor, the crop yield and the fruit antioxidant content, although no modification of morphological fruit attributes was observed. Keywords: grafting, Solanum lycopersicum L., local varieties, organic farming. References: Davis A.R., Perkins-Veazie P., Hassell R., Levi A., King S.R., Zhang X. 2008. Grafting effects on vegetable quality. HortScience 43(6): 1670-1671. Lee J.M., Kubota C., Tsao S.J., Bie Z., Hoyos-Echevarría P., Morra L., Oda M. 2010. Current status of vegetable grafting: Diffusion, grafting techniques, automation. Scientia Horticulturae 127: 93-105.

  14. Identification of novel miRNAs from drought tolerant rice variety Nagina 22.

    PubMed

    Mutum, Roseeta Devi; Kumar, Santosh; Balyan, Sonia; Kansal, Shivani; Mathur, Saloni; Raghuvanshi, Saurabh

    2016-08-08

    MicroRNAs regulate a spectrum of developmental and biochemical processes in plants and animals. Thus, knowledge of the entire miRNome is essential to understand the complete regulatory schema of any organism. The current study attempts to unravel yet undiscovered miRNA genes in rice. Analysis of small RNA libraries from various tissues of drought-tolerant 'aus' rice variety Nagina 22 (N22) identified 71 novel miRNAs. These were validated based on precursor hairpin structure, small RNA mapping pattern, 'star' sequence, conservation and identification of targets based on degradome data. While some novel miRNAs were conserved in other monocots and dicots, most appear to be lineage-specific. They were segregated into two different classes based on the closeness to the classical miRNA definition. Interestingly, evidence of a miRNA-like cleavage was found even for miRNAs that lie beyond the classical definition. Several novel miRNAs displayed tissue-enriched and/or drought responsive expression. Generation and analysis of the degradome data from N22 along with publicly available degradome identified several high confidence targets implicated in regulation of fundamental processes such as flowering and stress response. Thus, discovery of these novel miRNAs considerably expands the dimension of the miRNA-mediated regulation in rice.

  15. Identification of novel miRNAs from drought tolerant rice variety Nagina 22

    PubMed Central

    Mutum, Roseeta Devi; Kumar, Santosh; Balyan, Sonia; Kansal, Shivani; Mathur, Saloni; Raghuvanshi, Saurabh

    2016-01-01

    MicroRNAs regulate a spectrum of developmental and biochemical processes in plants and animals. Thus, knowledge of the entire miRNome is essential to understand the complete regulatory schema of any organism. The current study attempts to unravel yet undiscovered miRNA genes in rice. Analysis of small RNA libraries from various tissues of drought-tolerant ‘aus’ rice variety Nagina 22 (N22) identified 71 novel miRNAs. These were validated based on precursor hairpin structure, small RNA mapping pattern, ‘star’ sequence, conservation and identification of targets based on degradome data. While some novel miRNAs were conserved in other monocots and dicots, most appear to be lineage-specific. They were segregated into two different classes based on the closeness to the classical miRNA definition. Interestingly, evidence of a miRNA-like cleavage was found even for miRNAs that lie beyond the classical definition. Several novel miRNAs displayed tissue-enriched and/or drought responsive expression. Generation and analysis of the degradome data from N22 along with publicly available degradome identified several high confidence targets implicated in regulation of fundamental processes such as flowering and stress response. Thus, discovery of these novel miRNAs considerably expands the dimension of the miRNA-mediated regulation in rice. PMID:27499088

  16. Single spore isolation and morphological characterization of local Malaysian isolates of rice blast fungus Magnoporthe grisea

    NASA Astrophysics Data System (ADS)

    Mishra, Ankitta; Ratnam, Wickneswari; Bhuiyan, Md Atiqur Rahman; Ponaya, Ariane; Jena, Khisord K.

    2015-09-01

    Rice blast is a destructive disease, caused by the fungal pathogen Magnaporthe grisea. It causes considerable damage to rice and leads to crop loss in rice growing regions worldwide. Although fungicides can be used to control rice blast, they generate additional cost in rice production and contamination of environment and food. Therefore, the use of resistant varieties is thought to be one of the most economically and environmentally efficient ways of crop protection from the disease. Six new local Malaysian isolates of M. grisea were isolated using single spore isolation method. Five isolates were from infected leaf samples collected from Kompleks Latihan MADA, Kedah and one was from Kelantan. These isolates were identified using morphological characteristics and microscopic studies and later confirmed by ITSequences. These isolates were induced to sporulate and used for greenhouse screening on two differential rice varieties: Mahsuri (susceptible) and Pongsu Seribu 2 (resistant). Among the 6 isolates, isolate number 3 was found to be the most virulent showing high sporulation while isolate number 4 was very slow growing, and the least virulent.

  17. Genomic analysis of hybrid rice varieties reveals numerous superior alleles that contribute to heterosis.

    PubMed

    Huang, Xuehui; Yang, Shihua; Gong, Junyi; Zhao, Yan; Feng, Qi; Gong, Hao; Li, Wenjun; Zhan, Qilin; Cheng, Benyi; Xia, Junhui; Chen, Neng; Hao, Zhongna; Liu, Kunyan; Zhu, Chuanrang; Huang, Tao; Zhao, Qiang; Zhang, Lei; Fan, Danlin; Zhou, Congcong; Lu, Yiqi; Weng, Qijun; Wang, Zi-Xuan; Li, Jiayang; Han, Bin

    2015-02-05

    Exploitation of heterosis is one of the most important applications of genetics in agriculture. However, the genetic mechanisms of heterosis are only partly understood, and a global view of heterosis from a representative number of hybrid combinations is lacking. Here we develop an integrated genomic approach to construct a genome map for 1,495 elite hybrid rice varieties and their inbred parental lines. We investigate 38 agronomic traits and identify 130 associated loci. In-depth analyses of the effects of heterozygous genotypes reveal that there are only a few loci with strong overdominance effects in hybrids, but a strong correlation is observed between the yield and the number of superior alleles. While most parental inbred lines have only a small number of superior alleles, high-yielding hybrid varieties have several. We conclude that the accumulation of numerous rare superior alleles with positive dominance is an important contributor to the heterotic phenomena.

  18. Effect of arsenic on photosynthesis, growth and yield of five widely cultivated rice (Oryza sativa L.) varieties in Bangladesh.

    PubMed

    Azizur Rahman, M; Hasegawa, H; Mahfuzur Rahman, M; Nazrul Islam, M; Majid Miah, M A; Tasmen, A

    2007-04-01

    A glass house experiment was conducted to investigate the effect of soil arsenic on photosynthetic pigments, chlorophyll-a and -b, and their correlations with rice yield and growth. The experiment was designed with three replications of six arsenic treatments viz. control, 10, 20, 30, 60, 90 mg of As kg(-1) soil. Arsenic concentration in initial soil, to which the above mentioned concentrations of arsenic were added, was 6.44+/-0.24 mg kg(-1). Both chlorophyll-a and -b contents in rice leaf decreased significantly (p<0.05) with the increase of soil arsenic concentrations. No rice plant survived up to maturity stage in soil treated with 60 and 90 mg of As kg(-1). The highest chlorophyll-a and -b contents were observed in control treatment (2.62+/-0.24 and 2.07+/-0.14 mg g(-1) were the average values of chlorophyll-a and -b, respectively of the five rice varieties) while 1.50+/-0.20 and 1.04+/-0.08 mg g(-1) (average of five rice varieties) of chlorophyll-a and -b, respectively were the lowest. The content of photosynthetic pigments in these five rice varieties did not differ significantly (p>0.05) from each other in control treatment though they differed significantly (p<0.05) from each other in 30 mg of As kg(-1) soil treatment. Among the five rice varieties, chlorophyll content in BRRI dhan 35 was found to be mostly affected with the increase of soil arsenic concentration while BRRI hybrid dhan 1 was least affected. Well correlations were observed between chlorophyll content and rice growth and yield suggesting that arsenic toxicity affects the photosynthesis which ultimately results in the reduction of rice growth and yield.

  19. A comparative study on starch digestibility, glycemic index and resistant starch of pigmented ('Njavara' and 'Jyothi') and a non-pigmented ('IR 64') rice varieties.

    PubMed

    Deepa, G; Singh, Vasudeva; Naidu, K Akhilender

    2010-12-01

    In vitro starch digestibility and glycemic indices of three rice varieties- 'Njavara', 'Jyothi' (pigmented rice verities) and 'IR 64' (non-pigmented rice) with similar amylose content were studied. Starch digestibility studies showed differences in glycemic response in three types of rice. The rate of starch hydrolysis was maximum (67.3%) in 'Njavara' rice compared to other two rice varieties. 'Njavara' exhibited the lowest kinetic constant (k) indicating inherent resistance to enzymatic hydrolysis. The glycemic load (GL) and glycemic index (GI) of 'Njavara' were similar to 'Jyothi' and 'IR 64'. Resistant starch content was high in pigmented rice varieties compared to 'IR 64'. The resistant starch content of dehusked and cooked rice increased with the storage time at refrigeration temperature (4°C). 'Njavara' is an easily digestible rice and can be used for baby and geriatric foods.

  20. Traits and QTLs for development of dry direct-seeded rainfed rice varieties

    PubMed Central

    Sandhu, Nitika; Torres, Rolando O.; Sta Cruz, Ma. Teresa; Maturan, Paul Cornelio; Jain, Rajinder; Kumar, Arvind; Henry, Amelia

    2015-01-01

    The development of rice varieties for dry direct-seeded conditions can be accelerated by selecting suitable traits. In the present investigation, traits hypothesized to be important for direct-seeded conditions in rainfed systems, including seedling emergence, early vegetative vigour, nutrient uptake, nodal root number, and root hair length and density, were characterized to study the genetic control of these traits and their relationship with grain yield under seedling- and reproductive-stage drought stress. Two BC2F4 mapping populations derived from crosses of Aus276, a drought-tolerant aus variety, with MTU1010 and IR64, high-yielding indica mega-varieties, were developed and studied to identify quantitative trait loci (QTLs) that showed large and consistent effects. A total of 26 QTLs associated with 23 traits and 20 QTLs associated with 13 traits were mapped in the Aus276/3*IR64 and Aus276/3*MTU1010 populations, respectively. qGY6.1, qGY10.1, qGY1.1, and qEVV9.1 were found to be effective in both populations under a wide range of conditions. QTLs for several seedling-stage traits co-located with QTLs for grain yield, including early vegetative vigour and root hair length. On chromosome 5, several QTLs for nutrient uptake co-located with QTLs for root hair density and nematode gall rating. Six lines were selected from both populations based on grain yield and the presence of QTLs, and these lines typically showed improved seedling-stage traits (nodal root number, dry shoot weight, and root hair length and density). The co-located QTLs identified here can be used in research aimed at increasing the yield and adaptability of rainfed rice to direct-seeded conditions. PMID:25336682

  1. Trends in leaf photosynthesis in historical rice varieties developed in the Philippines since 1966.

    PubMed

    Hubbart, S; Peng, S; Horton, P; Chen, Y; Murchie, E H

    2007-01-01

    Crop improvement in terms of yield is rarely linked to leaf photosynthesis. However, in certain crop plants such as rice, it is predicted that an increase in photosynthetic rate will be required to support future grain yield potential. In order to understand the relationships between yield improvement and leaf photosynthesis, controlled environment conditions were used to grow 10 varieties which were released from the International Rice Research Institute (IRRI) between 1966 and 1995 and one newly developed line. Two growth light intensities were used: high light (1500 micromol m(-2) s(-1)) and low light (300 micromol m(-2) s(-1)). Gas exchange, leaf protein, chlorophyll, and leaf morphology were measured in the ninth leaf on the main stem. A high level of variation was observed among high light-grown plants for light-saturated photosynthetic rate per unit leaf area (P(max)), stomatal conductance (g), content of ribulose bisphosphate carboxylase-oxygenase (Rubisco), and total leaf protein content. Notably, between 1966 and 1980 there was a decline in P(max), g, leaf protein, chlorophyll, and Rubisco content. Values recovered in those varieties released after 1980. This striking trend coincides with a previous published observation that grain yield in IRRI varieties released prior to 1980 correlated with harvest index whereas that for those released after 1980 correlated with biomass. P(max) showed significant correlations with both g and Rubisco content. Large differences were observed between high light- and low light-grown plants (photoacclimation). The photoacclimation 'range' for P(max) correlated with P(max) in high light-grown plants. It is concluded that (i) leaf photosynthesis may be systematically affected by breeding strategy; (ii) P(max) is a useful target for yield improvements where yield is limited by biomass production rather than partitioning; and (iii) the capacity for photoacclimation is related to high P(max) values.

  2. Comparison of disease severity and yield potential of rice varieties in two organic cropping systems

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The market demand for organically produced rice has driven the steady increase in acreage of organic rice in the U. S., with Texas and California having the most acreage. Yield potential and disease management are among the principal challenges associated with organic rice production. Organic rice c...

  3. Acid diffusion into rice boluses is influenced by rice type, variety, and presence of α-amylase.

    PubMed

    Mennah-Govela, Yamile A; Bornhorst, Gail M; Singh, R Paul

    2015-02-01

    Breakdown of rice during gastric digestion may be influenced by rice structure, presence of salivary α-amylase, and hydrolysis by gastric acid. During mastication, saliva is mixed with rice, allowing α-amylase to begin starch hydrolysis. This hydrolysis may continue in the gastric environment depending on the rate at which gastric acid penetrates into the rice bolus. The objective of this study was to determine the acid uptake into rice boluses with and without α-amylase in saliva. Two types each of brown and white rice (medium and long grain), were formed into a cylindrical-shaped bolus. Each bolus was sealed on all sides except one to allow one-dimensional mass transfer, and incubated by immersion in simulated gastric juice at 37 °C under static conditions. Acidity of the boluses was measured by titration after 1 to 96 h of incubation. Effective diffusivity of the gastric juice through the bolus was estimated using MATLAB. Average acidity values ranged from 0.04 mg HCl/g dry matter (medium grain white rice, no incubation) to 10.01 mg HCl/g dry matter (long-grain brown rice, 72 h incubation). The rice type, presence of α-amylase, and incubation time all significantly influenced rice bolus acidity (P < 0.001). Effective diffusivity of gastric juice into the bolus was greater in brown rice than in white rice. These results indicate that starch hydrolysis by α-amylase may continue in the stomach before the gastric acid penetrates the rice bolus, and the rate of acid uptake will depend on the type of rice consumed.

  4. Analysis of SSH library of rice variety Aganni reveals candidate gall midge resistance genes.

    PubMed

    Divya, Dhanasekar; Singh, Y Tunginba; Nair, Suresh; Bentur, J S

    2016-03-01

    The Asian rice gall midge, Orseolia oryzae, is a serious insect pest causing extensive yield loss. Interaction between the gall midge and rice genotypes is known to be on a gene-for-gene basis. Here, we report molecular basis of HR- (hypersensitive reaction-negative) type of resistance in Aganni (an indica rice variety possessing gall midge resistance gene Gm8) through the construction and analysis of a suppressive subtraction hybridization (SSH) cDNA library. In all, 2,800 positive clones were sequenced and analyzed. The high-quality ESTs were assembled into 448 non-redundant gene sequences. Homology search with the NCBI databases, using BlastX and BlastN, revealed that 73% of the clones showed homology to genes with known function and majority of ESTs belonged to the gene ontology category 'biological process'. Validation of 27 putative candidate gall midge resistance genes through real-time PCR, following gall midge infestation, in contrasting parents and their derived pre-NILs (near isogenic lines) revealed induction of specific genes related to defense and metabolism. Interestingly, four genes, belonging to families of leucine-rich repeat (LRR), heat shock protein (HSP), pathogenesis related protein (PR), and NAC domain-containing protein, implicated in conferring HR+ type of resistance, were found to be up-regulated in Aganni. Two of the reactive oxygen intermediates (ROI)-scavenging-enzyme-coding genes Cytosolic Ascorbate Peroxidase1, 2 (OsAPx1 and OsAPx2) were found up-regulated in Aganni in incompatible interaction possibly suppressing HR. We suggest that Aganni has a deviant form of inducible, salicylic acid (SA)-mediated resistance but without HR.

  5. Comparative performance of hybrid and elite inbred rice varieties with respect to their source-sink relationship.

    PubMed

    Haque, Md Moinul; Pramanik, Habibur Rahman; Biswas, Jiban Krishna; Iftekharuddaula, K M; Hasanuzzaman, Mirza

    2015-01-01

    Hybrid rice varieties have higher yield potential over inbred varieties. This improvement is not always translated to the grain yield and its physiological causes are still unclear. In order to clarify it, two field experiments were conducted including two popular indica hybrids (BRRI hybrid dhan2 and Heera2) and one elite inbred (BRRI dhan45) rice varieties. Leaf area index, chlorophyll status, and photosynthetic rate of flag leaf, postheading crop growth rate, shoot reserve translocation, source-sink relation and yield, and its attributes of each variety were comprehensively analyzed. Both hybrid varieties outyielded the inbred. However, the hybrids and inbred varieties exhibited statistically identical yield in late planting. Both hybrids accumulated higher amount of biomass before heading and exhibited greater remobilization of assimilates to the grain in early plantings compared to the inbred variety. Filled grain (%) declined significantly at delayed planting in the hybrids compared to elite inbred due to increased temperature impaired-inefficient transport of assimilates. Flag leaf photosynthesis parameters were higher in the hybrid varieties than those of the inbred variety. Results suggest that greater remobilization of shoot reserves to the grain rendered higher yield of hybrid rice varieties.

  6. TALEN-mediated targeted mutagenesis produces a large variety of heritable mutations in rice.

    PubMed

    Zhang, Hui; Gou, Feng; Zhang, Jinshan; Liu, Wenshan; Li, Qianqian; Mao, Yanfei; Botella, José Ramón; Zhu, Jian-Kang

    2016-01-01

    CRISPR/Cas9 and TALEN are currently the two systems of choice for genome editing. We have studied the efficiency of the TALEN system in rice as well as the nature and inheritability of TALEN-induced mutations and found important features of this technology. The N287C230 TALEN backbone resulted in low mutation rates (0-6.6%), but truncations in its C-terminal domain dramatically increased efficiency to 25%. In most transgenic T0 plants, TALEN produced a single prevalent mutation accompanied by a variety of low-frequency mutations. For each independent T0 plant, the prevalent mutation was present in most tissues within a single tiller as well as in all tillers examined, suggesting that TALEN-induced mutations occurred very early in the development of the shoot apical meristem. Multigenerational analysis showed that TALEN-induced mutations were stably transmitted to the T1 and T2 populations in a normal Mendelian fashion. In our study, the vast majority of TALEN-induced mutations (~81%) affected multiple bases and ~70% of them were deletions. Our results contrast with published reports for the CRISPR/Cas9 system in rice, in which the predominant mutations affected single bases and deletions accounted for only 3.3% of the overall mutations.

  7. Overexpression of Rab16A gene in indica rice variety for generating enhanced salt tolerance.

    PubMed

    Ganguly, Moumita; Datta, Karabi; Roychoudhury, Aryadeep; Gayen, Dipak; Sengupta, Dibyendu N; Datta, Swapan K

    2012-04-01

    We report here the overexpression of Rab16A full length gene (promoter + ORF), from the salt-tolerant indica rice Pokkali, in the salt-susceptible indica rice variety Khitish, via particle bombardment. Molecular analysis of the transgenics revealed stable integration of the transgene upto T2 generation. High level of expression of the transgene (driven by its own stress-inducible promoter), as well as the protein, was detectable in the leaves under simulated salinity stress (250 mM NaCl, 24 h); the expression level being higher than wild type (WT) plants. The Rab16A transcript also increased gradually with seed maturity, with its maximal accumulation at 30 d after pollination (DAP) i.e., fully matured seeds, explaining the protective role of Rab16A gene during seed maturation. Enhanced tolerance to salinity was observed in the plants transformed with Rab16A. The superior physiological performances of the transgenics under salt treatment were also reflected in lesser shoot or root length inhibition, reduced chlorophyll damages, lesser accumulation of Na(+) and reduced loss of K(+), increased proline content as compared with the WT plants. All these results indicated that the overproduction of RAB16A protein in the transgenics enable them to display enhanced tolerance to salinity stress with improved physiological traits. Our work demonstrates the profound potential of Group 2 LEA proteins (to which RAB16A belongs to) in conferring stress tolerance in crop plants through their genetic manipulation.

  8. Seasoning ingredient variety, but not quality, is associated with greater intake of beans and rice among urban Costa Rican adults.

    PubMed

    Vadiveloo, Maya K; Campos, Hannia; Mattei, Josiemer

    2016-08-01

    Exposure to a variety of flavors may promote food enjoyment, but few studies have examined the relationship between food seasoning and food intake. We hypothesized that using a higher variety (number) of 11 seasonings to prepare 2 staple foods (beans, white rice) would be associated with intake of those foods in a population-based case-control study of Costa Rican adults in urban vs rural areas (n=1025), where cooking and dietary practices differ. Participants were surveyed about the variety of seasoning ingredients added when preparing beans or rice. Ingredients were also categorized by their dietary quality (healthfulness), and scores for seasoning variety and quality were created. Multivariable linear regression was used to determine the association between variety and quality scores (continuously and in tertiles (T)) and intake of each staple food. Seasoning variety was positively associated with daily servings of beans (β=.02, P=.01; 1.31 and 1.23 servings/day in T2 and T3 versus 1.02 servings/day in T1, P<.05) and rice (β=.04, P=.005) in the urban areas only. No differences in ingredient quality across increasing intakes of beans or rice were noted, and the joint associations between variety and quality were not significant. In conclusion, a greater variety, but not quality, of seasoning ingredients was positively associated with intakes of beans and rice in urban Costa Rican adults. Our results suggest that increasing the variety of seasonings added to beans may be a culturally-appropriate strategy to improve intake of this healthy staple food among urban Costa Rican adults.

  9. Effect of variety and moisture content on some engineering properties of paddy rice.

    PubMed

    Adebowale, Abdul-Rasaq A; Sanni, Lateef O; Owo, Hameed O; Karim, Olayinka R

    2011-10-01

    The effect of variety and moisture content on some engineering properties of five improved paddy rice varieties was investigated within moisture content range of 10% and 30% dry basis (d.b.). Increase in moisture content was found to increase the linear dimensions, mass of 100 seeds, surface area, apparent volume, true volume, arithmetic mean diameter, effective geometric diameter, sphericity, angle of repose, porosity and static coefficient of friction while bulk density and true density decreased with increase in moisture content. Static coefficient of friction was found to increase as moisture content increased from 0.34-0.46, 0.35-0.59, 0.36-0.46 and 0.34-0.45, respectively on plywood, galvanized steel, mild steel and glass structural surfaces. The highest static coefficient was found on galvanized steel. Angle of repose was found to increase as moisture content increases. The study concludes that variety and changes in moisture content significantly (P < 0.05) affected most of the engineering properties determined.

  10. Effect of polishing and cooking on the antioxidant activities of local rice

    NASA Astrophysics Data System (ADS)

    Rosnaini, Rahmah Mastura; Abdullah, Aminah

    2016-11-01

    The effect of polishing and cooking on the antioxidant activities of local rice was studied. Brown rice was polished to 2%, 4% and 6% of polishing degree using embryo rice machine to produce three levels of embryo rice. All rice sample (brown rice, embryo rice 1 (2%), embryo rice 2 (4%), embryo rice 3 (6%) and white rice) were cooked using electric rice cooker. The raw and cooked rice samples were analyzed for antioxidant by total phenolic content (TPC), ferric reducing antioxidant power (FRAP) and 2,2-diphenyl-1-picrylhydrazyl (DPPH) assays. Polishing degree and cooking treatment showed significant (p≤ 0.05) effects on both antioxidant activities (TPC, FRAP and DPPH radical scavenging values) of the raw and cooked rice samples. Results showed that raw brown rice and raw embryo rice 1 were significantly higher than the other type of rice samples for TPC and FRAP values. In DPPH radical scavenging activities, raw brown rice had the highest value while white rice indicated the otherwise. Cooked brown rice demonstrated significantly higher of FRAP values (p≤ 0.05) than embryo rice 1, followed by embryo rice 2, embryo rice 3 and white rice. No significant differences were observed either between TPC values of cooked brown rice and cooked embryo rice 1 or between the DPPH radical scavenging values of cooked embryo rice 2 and cooked embryo rice 3. High positive correlations were determined between TPC, FRAP and DPPH assays (R2 > 0.70) of the samples. In overall, moderate level of antioxidant activities were detected in the raw and cooked rice samples.

  11. Identification of Rice Varieties with High Tolerance or Sensitivity to Lead and Characterization of the Mechanism of Tolerance1

    PubMed Central

    Yang, Young-Yell; Jung, Ji-Young; Song, Won-Yong; Suh, Hak-Soo; Lee, Youngsook

    2000-01-01

    Pb inhibits plant growth. To study Pb tolerance in rice (Oryza sativa), we screened 229 varieties for Pb tolerance or sensitivity. Three-day-old seedlings were treated for 12 d with 20 μm Pb solution. Based on the dry weight of the root, three Pb-tolerant (var CH-55, var KH-2J, var Kumnung) and three Pb-sensitive (var Aixueru, var C-9491, var Milyang23) rice varieties were selected. The root biomasses of the tolerant varieties were approximately 10-fold higher than those of the sensitive ones. The greatest morphological difference between the two groups was in the growth of the adventitious roots, as tolerant lines were able to develop adventitious roots after 6 d of Pb treatment, whereas sensitive ones did not develop any even after 15 d. The growth of adventitious roots in the tolerant varieties was dependent on a mechanism, whereby Pb was altered to a form that cannot be taken up by the tissue, because (a) the solution in which the tolerant varieties of rice had grown still contained Pb but nevertheless did not affect the root growth of new rice seedlings, and (b) the adventitious roots of tolerant seedlings developed in Pb solution contained little Pb. The oxalate content in the root and root exudate increased upon Pb treatment in the tolerant varieties, whereas the opposite was observed for the sensitive ones. Oxalate added to the growth solution ameliorated the inhibition of root growth by Pb. These results suggest that compounds such as oxalate secreted from the root may reduce the bio-availability of Pb, and that this may constitute an important Pb tolerance mechanism in the tolerant rice varieties studied here. PMID:11080279

  12. Characterization of total antioxidant capacity and (poly)phenolic compounds of differently pigmented rice varieties and their changes during domestic cooking.

    PubMed

    Zaupa, Maria; Calani, Luca; Del Rio, Daniele; Brighenti, Furio; Pellegrini, Nicoletta

    2015-11-15

    In the recent years, the pigmented rice varieties are becoming more popular due to their antioxidant properties and phenolic content. In this study, we characterized the antioxidant capacity (TAC) and the phenolic profile in white, red and black rice varieties, and evaluated the effect of two cooking methods (i.e. "risotto" and boiling) on these compounds. Before the cooking, all the varieties contained several phenolic acids, whereas anthocyanins and flavonols were peculiar of black rice and flavan-3-ols of red rice. Among the rice varieties, the black had the highest TAC value. The content of (poly)phenolic compounds and TAC decreased after cooking in all three varieties, but to a lesser extent after the risotto method. As a consequence, the risotto cooking, which allows a complete absorption of water, would be a good cooking method to retain (poly)phenolic compounds and TAC in pigmented and non-pigmented whole-meal rice.

  13. Real-time and conventional PCR detection of Liberty Link rice varieties and transgenic soy in rice sampled in the Mexican and American retail markets.

    PubMed

    Quirasco, Maricarmen; Schoel, Bernd; Chhalliyil, Pradheep; Fagan, John; Gálvez, Amanda

    2008-10-01

    Samples of rice from Mexican and USA retail stores were analyzed for the presence of transgenic (GM) events using real-time PCR. In screening for the CaMV35S promoter sequence (35SP), positive results were found in 49 and 35% of the Mexican and American samples, respectively. In further investigations in Mexican samples, 43% were positive for P35S::bar, with two above the quantifiable limit; these were 0.07% and 0.05% GMO. Fourteen out of the sixteen positive samples were labeled as imported from the USA. In testing samples bought in American retail shops, 24% showed positive results, all below the quantifiable range. It could be deduced that P35S::bar positive samples were Liberty Link(R) (LL) rice. In distinguishing between LL601 and LL62, end-point PCR was used, corroborating the P35S::bar amplicon length difference of these events. LL62 was found in one rice sample purchased in Mexico and two in the USA samples. Its presence was verified with the 35S terminator sequence. All other LL positive samples contained LL601. None of the samples analyzed showed the presence of Bt63 rice. The LL rice varieties found have been identified as not being commercially cultivated, and so their presence requires further investigation. 35SP was also present in samples which did not have any LL rice. Maize sequences could not be detected in any of the samples; however, soybean DNA was found in Mexican and USA rice samples. The Roundup Ready(R) trait was detected in trace amounts in 16 and 6% of the rice samples bought in Mexico and the USA, respectively. Real-time PCR was shown to be the method of choice for the sensitive and rapid screening of commodities and retail samples for the detection of GM and other contamination.

  14. Feasibility study on variety identification of rice vinegars using visible and near infrared spectroscopy and multivariate calibration

    NASA Astrophysics Data System (ADS)

    Liu, Fei; He, Yong; Wang, Li

    2008-02-01

    The feasibility of visible and near infrared (Vis/NIR) spectroscopy, in combination with a hybrid multivariate methods of partial least squares (PLS) analysis and BP neural network (BPNN), was investigated to identify the variety of rice vinegars with different internal qualities. Five varieties of rice vinegars were prepared and 225 samples (45 for each variety) were selected randomly for the calibration set, while 75 samples (15 for each variety) for the validation set. After some pretreatments with moving average and standard normal variate (SNV), partial least squares (PLS) analysis was implemented for the extraction of principal components (PCs), which would be used as the inputs of BP neural network (BPNN) according to their accumulative reliabilities. Finally, a PLS-BPNN model with sigmoid transfer function was achieved. The performance was validated by the 75 unknown samples in validation set. The threshold error of prediction was set as +/-0.1 and an excellent precision and recognition ratio of 100% was achieved. Simultaneously, certain effective wavelengths for the identification of varieties were proposed by x-loading weights and regression coefficients. The prediction results indicated that Vis/NIR spectroscopy could be used as a rapid and high precision method for the identification of different varieties of rice vinegars.

  15. Methane emission from Indonesian rice fields with special references to the effects of yearly and seasonal variations, rice variety, soil type and water management

    NASA Astrophysics Data System (ADS)

    Lumbanraja, Jamalam; Ghani Nugroho, Sutopo; Niswati, Ainin; Sabe Ardjasa, Wayan; Subadiyasa, Netera; Arya, Nyoman; Haraguchi, Hiroki; Kimura, Makoto

    1998-10-01

    Total amounts of CH4 emission from a Sumatra rice field were in the ranges 29·5-48·2 and 43·0-64·6 g CH4 m-2 season-1 for the plots with chemical fertilizer (CF-plot) and those with rice straw application (RS-plot), respectively. Nearly the same amounts of CH4 were emitted in the first and second half of the growth period, irrespective of rice straw application. The increase in the amounts of CH4 emission by rice straw application were from 1·3 to 1·6 times. There was no significant difference in the mean CH4 emission rates between rainy and dry seasons. Rain-fed conditions decreased the CH4 emission by 27-37% compared with continuously flooded conditions. Total amounts of CH4 emission from a rice field growing eight popular modern rice varieties in Indonesia were in the ranges 32·6-41·7 and 51·3-64·6 g CH4 m-2 season-1 for CF- and RS-plots, respectively. Total amounts of CH4 emission from four Sumatra rice fields with different soil types (a Typic Paleudult, a Typic Sulfaquent, a Typic Tropohumult and a Typic Tropopsament) were in the range 22·1 (a Typic Sulfaquent) to 53·4 (a Typic Tropohumult) g CH4 m-2 season-1rice fields with soils of volcanic ash origin were very low; 3·5-7·7 and 5·3-14·3 g CHrice fields showed the specific productivity of grain production, and CHrice fields of volcanic ash origin to 83 and 121 g CHrice field for CF- and RS-plots, respectively. Water management was also an important factor in decreasing the CH

  16. The effect of apparent amylose content and dietary fibre on the glycemic response of different varieties of cooked milled and brown rice.

    PubMed

    Trinidad, Trinidad P; Mallillin, Aida C; Encabo, Rosario R; Sagum, Rosario S; Felix, Angelina D R; Juliano, Bienvenido O

    2013-02-01

    Brown rice is a good source of dietary fibre (DF) and contains higher vitamins/minerals than milled rice. The study determined the effect of amylose content (AC) and DF on glucose response (GR) from different varieties of milled and brown rice. Milled and brown rice were used as test foods. They were fed to 9-10 human volunteers containing 50 g available carbohydrate after an overnight fast. GR and the glycemic index (GI) were determined. Results found that Sinandomeng with the lowest AC had a high GI = 75, while PSBRc10 with the highest AC had a low GI = 50. Sinandomeng with a low DF had GI = 75, while its brown rice had GI = 55. Brown rice (IR64) with 23% AC and DF of 2.5 g/100 g had low GI = 51. In conclusion, the GR and GI of the different varieties of cooked milled and brown rice varied depending on its AC and DF contents.

  17. Effect of variety and cooking method on resistant starch content of white rice and subsequent postprandial glucose response and appetite in humans.

    PubMed

    Chiu, Yu-Ting; Stewart, Maria L

    2013-01-01

    Rice is a staple carbohydrate throughout much of the world. Previous work indicated that resistant starch (RS) content of rice consumed in India varied with rice variety and cooking method. This study quantified RS in 4 white rice varieties (jasmine, long grain, medium grain, and short grain) cooked in three manners (oven baked, conventional rice cooker, and pressure cooker), and analyzed for RS content immediately after preparation or after 3 days of refrigeration at 4°C. The rice varieties with the highest and lowest RS content were selected for a pilot- scale trial to characterize postprandial glycemic response and appetite ratings in healthy adults (n=21). Refrigerated long-grain rice cooked in a conventional rice cooker had the highest RS content (HRS, 2.55 g RS/100 g) and refrigerated short-grain rice cooked in a pressure cooker had the lowest RS content (LRS, 0.20 g RS/100 g). These rice samples were served reheated in the clinical trial. Glucose area under the curve (AUC) were significantly lower with HRS and LRS compared to glucose beverage; however, there was no difference between HRS and LRS. Glycemic indices did not differ significantly between HRS and LRS. Subjects reported an overall increased feeling of fullness and decreased desire to eat based on incremental area under the curve (iAUC) for both HRS and LRS compared to control. This study found that RS naturally occurring in rice had minimal impact on the postprandial glycemic response and appetite.

  18. Assessment of Relationship Between Bacterial Stripe Resistance And Leaf Protein Bands In Rice (Oryza sativa L.) Varieties.

    NASA Astrophysics Data System (ADS)

    Talei, D.; Fotokian, M. H.

    2008-01-01

    Bacterial stripe as a new rice disease in Iran is more frequent nowadays. The objective of this study was to assessment of resistance in rice varieties together with evaluating of zymogram bands resulted from SDS PAGE electrophoresis of leaf proteins. For this purpose, 30 lines were tested in a randomized complete block design with three replications. The analysis of variance showed that there was significant difference between genotypes for resistance. Mean compare based on field results revealed that Domsiyah had the lowest resistance while Nemat and 7162 demonstrated the highest resistance. Laboratory results showed that there were significant difference between protein bands resulted from sensitive and resistance verities. Twenty bands were observed through SDS PAGE electrophoresis of leaf proteins. The 9th and 12th bands were found in sensitive varieties while were not in resistance genotypes. According to the results of this study, 7162 variety can be considered as the sources of resistance in breeding programs. Meanwhile attending to existence of 9th and 12th bands in sensitive varieties, resistance against bacterial stripe of rice maybe influenced by absence of these proteins.

  19. Investigation the growth, yield and yield components of rice varieties in rotation with garlic, Faba bean, lettuce, pea and fallow in north of Iran.

    PubMed

    Nasiri, Morteza; Pirdashti, Hemmatollah; Tari, Davood Barari

    2007-08-15

    In order to investigating the effects of second crop cultivation on growth, yield and yield components of rice, a field experiment was conducted at the Rice Research Institute of Iran-Deputy of Mazandaran (Amol) during 2004 and 2005. Tarom as a traditional variety and Fajr as a improved variety were used in this research. Faba, pea, Lettuce and garlic were used as a second crop in rotation with rice. Second crop cultivation, variety and interaction between them had a significant effect on tiller number at 0.01 probability level. Results showed that rice yield after lettuce and garlic rotation was lower than with Faba bean, pea and fallow rotation. These results indicated that rice varieties had different reaction to second crop cultivation. For example, Tarom variety in rotation with lettuce and garlic had higher yield deficiency than Fajr variety. These results suggested that Lettuce and garlic can not be a permanent second crop in paddy field. According to results, pea and faba bean in rotation with rice for the best performance of yield attributes of rice varieties were recommended.

  20. Subcellular Localization of Rice Leaf Aryl Acylamidase Activity 1

    PubMed Central

    Gaynor, John J.; Still, Cecil C.

    1983-01-01

    The intracellular localization of aryl acylamidase (aryl-acylamide amidohydrolase, EC 3.5.1.13) in rice (Oryza sativa L. var Starbonnet) leaves was investigated. The enzyme hydrolyzes and detoxifies the herbicide propanil (3,4-dichloropropionanilide) thereby accounting for immunity of the rice plant to herbicidal action. Fractionation of mesophyll protoplasts by differential centrifugation yielded the highest specific activity of amidase in the crude mitochondrial fraction. Further separation of density gradients of the silica sol Percoll also indicated that this enzyme was mitochondrial. By the use of biochemical markers, the purified mitochondrial fraction was shown to be substantially free of contamination from nuclei, chloroplasts, golgi, and plasma membranes. Subfractionation of the purified mitochondria suggests that this enzyme is located on the outer membrane. PMID:16662987

  1. Transgenerational Variations in DNA Methylation Induced by Drought Stress in Two Rice Varieties with Distinguished Difference to Drought Resistance

    PubMed Central

    Li, Mingshou; Lou, Qiaojun; Xia, Hui; Wang, Pei; Li, Tiemei; Liu, Hongyan; Luo, Lijun

    2013-01-01

    Adverse environmental conditions have large impacts on plant growth and crop production. One of the crucial mechanisms that plants use in variable and stressful natural environments is gene expression modulation through epigenetic modification. In this study, two rice varieties with different drought resistance levels were cultivated under drought stress from tilling stage to seed filling stage for six successive generations. The variations in DNA methylation of the original generation (G0) and the sixth generation (G6) of these two varieties in normal condition (CK) and under drought stress (DT) at seedling stage were assessed by using Methylation Sensitive Amplification Polymorphism (MSAP) method. The results revealed that drought stress had a cumulative effect on the DNA methylation pattern of both varieties, but these two varieties had different responses to drought stress in DNA methylation. The DNA methylation levels of II-32B (sensitive) and Huhan-3 (resistant) were around 39% and 32%, respectively. Genome-wide DNA methylation variations among generations or treatments accounted for around 13.1% of total MSAP loci in II-32B, but was only approximately 1.3% in Huhan-3. In II-32B, 27.6% of total differentially methylated loci (DML) were directly induced by drought stress and 3.2% of total DML stably transmitted their changed DNA methylation status to the next generation. In Huhan-3, the numbers were 48.8% and 29.8%, respectively. Therefore, entrainment had greater effect on Huhan-3 than on II-32B. Sequence analysis revealed that the DML were widely distributed on all 12 rice chromosomes and that it mainly occurred on the gene’s promoter and exon region. Some genes with DML respond to environmental stresses. The inheritance of epigenetic variations induced by drought stress may provide a new way to develop drought resistant rice varieties. PMID:24244664

  2. Data set from a comprehensive phosphoproteomic analysis of rice variety IRBB5 in response to bacterial blight.

    PubMed

    Hou, Yuxuan; Tong, Xiaohong; Wang, Yifeng; Qiu, Jiehua; Li, Zhiyong; Zhang, Wen; Huang, Shiwen; Zhang, Jian

    2016-03-01

    Bacterial blight (BB) caused by Xanthomonas oryzae pv. oryzae (Xoo) has become one of the most devastating diseases for rice, a major food source for over half of the world populations. To investigate the roles of protein phosphorylation in rice bacterial blight resistance, a quantitative phosphoproteomic study was conducted in rice variety IRBB5 at 0 h and 24 h after Xoo infection. 2367 and 2223 phosphosites on 1334 and 1297 representative proteins were identified in 0 h and 24 h after Xoo infection, respectively, out of which 762 proteins were found to be differentially phosphorylated. In associated with the published article "A comprehensive quantitative phosphoproteome analysis of rice in response to bacterial blight" in BMC Plant Biology (Hou et al., 2015) [1], this dataset article provided the detailed information of experimental designing, methods, features as well as the raw data of mass spectrometry (MS) identification. The MS proteomics data could be fully accessed from the ProteomeXchange Consortium with the dataset identifier PXD002222.

  3. Studies on physico-chemical and cooking characteristics of rice bean varieties grown in NE region of India.

    PubMed

    Bepary, Rejaul Hoque; Wadikar, D D; Neog, Seuji Borah; Patki, P E

    2017-03-01

    Rice bean (Vigna umbellata) is grown in South and Southeast Asia, and the bean has gained importance due to its nutritional strength in terms of dietary fiber, quality protein and minerals. In current study, the nutritional and functional components, cooking and thermo-gravimetric properties of eleven rice bean varieties from NE India were investigated. Results revealed that the major nutrients among the varieties ranged as follows: 54.21-60.49% carbohydrates, 15.64-21.60% protein, 1.22-2.3% fat, 5.53-6.56% crude fibre, 3.34-3.8% ash; while the functional, anti-nutritional factors and mineral were present as 1189.32-1645.8 mg gallic acid equivalent (GAE)/100 g polyphenols, 205.38-432.14 mg/100 g phytic acid, 23.14-34.12 mg/100 g oxalate, 690.7-1589.5 mg/100 g saponins, 49.90-158.17 μg/100 g hydrocyanide, 111.51-168 calcium, 5.50-10.44 zinc, 3.72-8.37 iron. Principal component analysis revealed that varieties with higher calcium, iron and ash content had lower cooking time, swelling ratio, and cooked grain hardness. It is also revealed that varieties with higher weight loss at sixth stage in thermogravimetric graph had lower carbohydrate and higher protein content. Nagadal variety had higher fat, potassium, magnesium, calcium, sodium, iron, copper and chromium content and better cooking quality as compared to the other varieties. The study revealed that Nagadal variety was superior to other varieties with respect to mineral content, cooking and thermal properties and hence have better potential in the development of value added products.

  4. Preliminary results on yield and CO2 fluxes when using alternate wetting and drying on different varieties of European rice

    NASA Astrophysics Data System (ADS)

    Oliver, Viktoria; Monaco, Stefano; Volante, Andrea; Cochrane, Nicole; Gennaro, Massimo; Orasen, Gabriele; Valè, Giampiero; Price, Adam; Arn Teh, Yit

    2016-04-01

    In Europe, rice is grown (467 000 ha) under permanently flooded conditions (PF) using irrigation waters of major rivers. Climate change, which has led to a greater fluctuation in river flows, is a major challenge to rice production systems, which depend on large and consistent water supplies. This challenge will become more acute in the future, with more frequent extreme weather (e.g. drought) predicted under climate change and increased demands for rice. Alternate wetting and drying (AWD) is a system in where irrigation is applied to obtain 2-5 cm of field water depth, after which the soil is allowed to drain naturally to typically 15 cm below the surface before re-wetting once more. Preliminary studies suggest that AWD can reduce water use by up 30 %, with no net loss in yield but significantly reducing CH4 emissions. However, uncertainties still remain as to the impacts of AWD on CO2 exchange, N2O fluxes, and plant acclimation responses to a fluctuating water regime. For example, CO2 emissions could potentially increase in AWD due to higher rates of soil organic matter decomposition when the fields are drained. The work presented here evaluated the impacts of AWD on the productivity and yield of twelve varieties of European rice, whilst simultaneously measuring CO2 exchange, N2O fluxes, and plant biomass allocation patterns under different treatment regimes. Field experiments were conducted in the Piedmont region (northern Italy Po river plain) in a loamy soil during the growing season of 2015 in a 2-factor paired plot design, with water treatment (AWD, PF) and variety (12 European varieties) as factors (n=4 per variety per treatment). The varieties chosen were commercially important cultivars from across the rice growing regions of Europe (6 Italian, 3 French, 3 Spanish). Light and dark CO2 fluxes were measured six times over the growing season, using an infra-red gas analyzer. Environmental variables (soil moisture, temperature, water table depth, water

  5. Speciation And Distribution Of Arsenic And Localization Of Nutrients In Rice Grains

    EPA Science Inventory

    Arsenic (As) contamination of rice grains and the generally low concentration of micronutrients in rice have been recognized as a major concern for human health. Here, we investigated the speciation and localization of As and the distribution of (micro)nutrients in rice grains b...

  6. Whole genome sequencing and analysis of Swarna, a widely cultivated indica rice variety with low glycemic index

    PubMed Central

    Rathinasabapathi, Pasupathi; Purushothaman, Natarajan; VL, Ramprasad; Parani, Madasamy

    2015-01-01

    Swarna is a popular cultivated indica rice variety with low glycemic index (GI) but its genetic basis is not known. The whole genome of Swarna was sequenced using Illumina’s paired-end technology, and the reads were mapped to the Nipponbare reference genome. Overall, 65,984 non-synonymous SNPs were identified in 20,350 genes, and in silico analysis predicted that 4,847 of them in 2,214 genes may have deleterious effect on protein functions. Polymorphisms were found in all the starch biosynthesis genes, except the gene for branching enzyme IIa. It was found that T/G SNP at position 246, ‘A’ at position 2,386, and ‘C’ at position 3,378 in the granule bound starch synthase I gene, and C/T SNP at position 1,188 in the glucose-6-phosphate translocator gene may contribute to the low GI phenotype in Swarna. All these variants were also found in the genome of another low GI indica rice variety from Columbia, Fedearroz 50. The whole genome analysis of Swarna helped to understand the genetic basis of GI in rice, which is a complex trait involving multiple factors. PMID:26068787

  7. Whole genome sequencing and analysis of Swarna, a widely cultivated indica rice variety with low glycemic index.

    PubMed

    Rathinasabapathi, Pasupathi; Purushothaman, Natarajan; Ramprasad, V L; Parani, Madasamy

    2015-06-11

    Swarna is a popular cultivated indica rice variety with low glycemic index (GI) but its genetic basis is not known. The whole genome of Swarna was sequenced using Illumina's paired-end technology, and the reads were mapped to the Nipponbare reference genome. Overall, 65,984 non-synonymous SNPs were identified in 20,350 genes, and in silico analysis predicted that 4,847 of them in 2,214 genes may have deleterious effect on protein functions. Polymorphisms were found in all the starch biosynthesis genes, except the gene for branching enzyme IIa. It was found that T/G SNP at position 246, 'A' at position 2,386, and 'C' at position 3,378 in the granule bound starch synthase I gene, and C/T SNP at position 1,188 in the glucose-6-phosphate translocator gene may contribute to the low GI phenotype in Swarna. All these variants were also found in the genome of another low GI indica rice variety from Columbia, Fedearroz 50. The whole genome analysis of Swarna helped to understand the genetic basis of GI in rice, which is a complex trait involving multiple factors.

  8. Essential amino acids of starch synthase IIa differentiate amylopectin structure and starch quality between japonica and indica rice varieties.

    PubMed

    Nakamura, Yasunori; Francisco, Perigio B; Hosaka, Yuko; Sato, Aya; Sawada, Takayuki; Kubo, Akiko; Fujita, Naoko

    2005-05-01

    Four amino acids were variable between the 'active' indica-type and 'inactive' japonica-type soluble starch synthase IIa (SSIIa) of rice plants; Glu-88 and Gly-604 in SSIIa of indica-cultivars IR36 and Kasalath were replaced by Asp-88 and Ser-604, respectively, in both japonica cultivars Nipponbare and Kinmaze SSIIa, whereas Val-737 and Leu-781 in indica SSIIa were replaced by Met-737 in cv. Nipponbare and Phe-781 in cv. Kinmaze SSIIa, respectively. The SSIIa gene fragments shuffling experiments revealed that Val-737 and Leu-781 are essential not only for the optimal SSIIa activity, but also for the capacity to synthesize indica-type amylopectin. Surprisingly, however, a combination of Phe-781 and Gly-604 could restore about 44% of the SSIIa activity provided that Val-737 was conserved. The introduction of the 'active' indica-type SSIIa gene enabled the japonica-type cv. Kinmaze to synthesize indica-type amylopectin. The starch in the transformed japonica rice plants exhibited gelatinization-resistant properties that are characteristic of indica-rice starch. Transformed lines expressing different levels of the IR36 SSIIa protein produced a variety of starches with amylopectin chain-length distribution patterns that correlated well with their onset temperatures of gelatinization. The present study confirmed that the SSIIa activity determines the type of amylopectin structure of rice starch to be either the typical indica-type or japonica-type, by playing a specific role in the synthesis of the long B(1) chains by elongating short A and B(1) chains, notwithstanding the presence of functional two additional SSII genes, a single SSI gene, two SSIII genes, and two SSIV genes in rice plants.

  9. Effect of nitrogen application on the physicochemical properties of selected rice varieties

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Rice with high amylose concentration (AM), low breakdown and high setback, as measured by the Rapid Visco Analyzer (RVA), is best suited for use by the parboiling and canning industries as these properties correlates with reduced starch solids loss and improved grain integrity after processing. This...

  10. Photosynthesis enhanced oxidative stress tolerance in high-yield rice varieties (Oryza sativa var. japonica L.) in the field.

    PubMed

    Wei, X D

    2016-07-29

    The objective of this study was to understand varietal differences in photosynthetic characteristics, chlorophyll fluorescence, antioxidant capability, and yield of japonica rice varieties. Nanjing 44, Oryza sativa var. japonica (average yield of 12.7 t/ha), Nanjing 46, and Nanjing 5055 (average yields of 11.3 and 11.5 t/ha) were included as "super" and high-yield varieties, respectively, whereas Wuyunjing 7 (average yield of 10.2 t/ha) was included as a control variety. These varieties were grown under field conditions in Jiangsu Province, China, in 2010-2012. Different organs (panicle, grain, etc.) were measured, before and after flowering, to identify differences of dry matter accumulation and transformation properties. Photosynthesis, the chlorophyll content, and antioxidant enzyme activities of the flag leaf in the days after flowering (DAF) were also investigated. The results showed that, compared with the other three rice varieties, Nanjing 44 had the highest plant dry weight and number of grains per panicle. It also had a relatively high net flag leaf photosynthetic rate and showed the least inhibition of photosynthesis at noon in DAF, which probably explains the higher yield in this variety. Furthermore, Nanjing 44 also had the highest stem export and conversion rate from stem to grain, exhibiting a strong ability to convert and distribute photosynthetic products. After DAF 42, Nanjing 44 still maintained a high-soluble protein content and a high antioxidant ability in the leaves to clear peroxidation products, which could protect the photosynthetic apparatus of the flag leaves, and maintain the grain-filling activity for longer. The high-yield capability of Nanjing 44 was attributed to its photosynthetic advantages in the leaves during the late developmental stage.

  11. Natural herbicide resistance (HR) to broad-spectrum herbicide, glyphosate among traditional and inbred-cultivated rice (Oryza sativa L.) varieties in Sri Lanka.

    PubMed

    Weerakoon, S R; Somaratne, S; Wijeratne, R G D; Ekanyaka, E M S I

    2013-08-15

    Weeds along with insect pests and plant diseases are sources of biotic stress in crop systems. Weeds are responsible for serious problems in rice worldwide affecting growth and causing a considerable reduction in quality and quantity in yield. High concentrations of pre-emergent-broad-spectrum systemic herbicide, Glyphosate is prevalently applied to control rice weeds which intern causes severe damages to cultivated rice varieties, susceptible to Glyphosate. However, there may be rice varieties with natural Herbicide Resistance (HR) which are so far, has not been evaluated. In this study Six traditional and eighteen developed-cultivated rice varieties (Bg, Bw, At and Ld series developed by Rice Research Development Institute, Sri Lanka) were used to screen their natural HR. RCBD with five replicates and three blocks in each treatment-combination was used as the experimental design. As observations, time taken-to seed germination, time taken to flowering; plant height and number of leaves at 12-weeks after sawing, leaf-length, breadth, panicle-length, number of seeds/panicle of resistant plants and controls were recorded. Plants with > or = 40% resistance were considered as resistant to Glyphosate. Ten inbred-cultivated rice varieties (Bg250, Bg94-1, Bg304, Bg359, Bg406, Bg379-2, Bg366, Bg300, Bw364, At362) and three traditional rice varieties ("Kalu Heenati", "Sudu Heenati", "Pachchaperumal") were naturally resistant to 0.25 g L(-1) Glyphosate concentration and when increased the concentration (0.5 g L(-1)) resistance was reduced. This study showed the usefulness of modern statistical method, classification and regression tree analysis (CART) in exploring and visualizing the patterns reflected by a large number of rice varieties (larger experimental database) on herbicide resistance in future.

  12. Productivity of sodic soils can be enhanced through the use of salt tolerant rice varieties and proper agronomic practices

    PubMed Central

    Singh, Y.P.; Mishra, V.K.; Singh, Sudhanshu; Sharma, D.K.; Singh, D.; Singh, U.S.; Singh, R.K.; Haefele, S.M.; Ismail, A.M.

    2016-01-01

    Regaining the agricultural potential of sodic soils in the Indo-Gangetic plains necessitates the development of suitable salt tolerant rice varieties to provide an entry for other affordable agronomic and soil manipulation measures. Thus selection of high yielding rice varieties across a range of sodic soils is central. Evaluation of breeding lines through on-station and on-farm farmers’ participatory varietal selection (FPVS) resulted in the identification of a short duration (110–115 days), high yielding and disease resistant salt-tolerant rice genotype ‘CSR-89IR-8’, which was later released as ‘CSR43’ in 2011. Several agronomic traits coupled with good grain quality and market value contributed to commercialization and quick adoption of this variety in the sodic areas of the Indo-Gangetic plains of eastern India. Management practices required for rice production in salt affected soils are evidently different from those in normal soils and practices for a short duration salt tolerant variety differ from those for medium to long duration varieties. Experiments were conducted at the Indian Council of Agricultural Research-Central Soil Salinity Research Institute (ICAR-CSSRI), Regional Research Station, Lucknow, Uttar Pradesh, India during 2011 and 2013 wet seasons, to test the hypothesis that combining matching management practices (Mmp) with an improved genotype would enhance productivity and profitability of rice in sodic soils. Mmp were developed on-station by optimizing existing best management practices (Bmp) recommended for the region to match the requirements of CSR43. The results revealed that transplanting 4 seedlings hill−1 at a spacing of 15 × 20 cm produced significantly higher yield over other treatments. The highest additional net gain was US$ 3.3 at 90 kg ha−1 N, and the lowest was US$ 0.4 at 150 kg ha−1 N. Above 150 kg ha−1, the additional net gain became negative, indicating decreasing returns from additional N

  13. Productivity of sodic soils can be enhanced through the use of salt tolerant rice varieties and proper agronomic practices.

    PubMed

    Singh, Y P; Mishra, V K; Singh, Sudhanshu; Sharma, D K; Singh, D; Singh, U S; Singh, R K; Haefele, S M; Ismail, A M

    2016-04-01

    Regaining the agricultural potential of sodic soils in the Indo-Gangetic plains necessitates the development of suitable salt tolerant rice varieties to provide an entry for other affordable agronomic and soil manipulation measures. Thus selection of high yielding rice varieties across a range of sodic soils is central. Evaluation of breeding lines through on-station and on-farm farmers' participatory varietal selection (FPVS) resulted in the identification of a short duration (110-115 days), high yielding and disease resistant salt-tolerant rice genotype 'CSR-89IR-8', which was later released as 'CSR43' in 2011. Several agronomic traits coupled with good grain quality and market value contributed to commercialization and quick adoption of this variety in the sodic areas of the Indo-Gangetic plains of eastern India. Management practices required for rice production in salt affected soils are evidently different from those in normal soils and practices for a short duration salt tolerant variety differ from those for medium to long duration varieties. Experiments were conducted at the Indian Council of Agricultural Research-Central Soil Salinity Research Institute (ICAR-CSSRI), Regional Research Station, Lucknow, Uttar Pradesh, India during 2011 and 2013 wet seasons, to test the hypothesis that combining matching management practices (Mmp) with an improved genotype would enhance productivity and profitability of rice in sodic soils. Mmp were developed on-station by optimizing existing best management practices (Bmp) recommended for the region to match the requirements of CSR43. The results revealed that transplanting 4 seedlings hill(-1) at a spacing of 15 × 20 cm produced significantly higher yield over other treatments. The highest additional net gain was US$ 3.3 at 90 kg ha(-1) N, and the lowest was US$ 0.4 at 150 kg ha(-1) N. Above 150 kg ha(-1), the additional net gain became negative, indicating decreasing returns from additional N. Hence, 150

  14. Germination response of MR 219 rice variety to different exposure times and periods of 2450 MHz microwave frequency.

    PubMed

    Talei, Daryush; Valdiani, Alireza; Maziah, Mahmood; Mohsenkhah, Mohammad

    2013-01-01

    Germination is a key process in plants' phenological cycles. Accelerating this process could lead to improvment of the seedling growth as well as the cultivation efficiency. To achieve this, the effect of microwave frequency on the germination of rice seeds was examined. The physiological feedbacks of the MR 219 rice variety in terms of seed germination rate (GR), germination percentage (GP), and mean germination time (MGT) were analyzed by exposing its seeds to 2450 MHz of microwave frequency for one, four, seven, and ten hours. It was revealed that exposing the seeds to the microwave frequency for 10 hours resulted in the highest GP. This treatment led to 100% of germination after three days with a mean germination time of 2.1 days. Although the other exposure times of microwave frequency caused the moderate effects on germination with a GP(a3) ranged from 93% to 98%, they failed to reduce the MGT(a3). The results showed that ten-hour exposure times of microwave frequency for six days significantly facilitated and improved the germination indices (primary shoot and root length). Therefore, the technique is expected to benefit the improvement of rice seed germination considering its simplicity and efficacy in increasing the germination percentage and rate as well as the primary shoot and root length without causing any environmental toxicity.

  15. Germination Response of MR 219 Rice Variety to Different Exposure Times and Periods of 2450 MHz Microwave Frequency

    PubMed Central

    Valdiani, Alireza; Maziah, Mahmood; Mohsenkhah, Mohammad

    2013-01-01

    Germination is a key process in plants' phenological cycles. Accelerating this process could lead to improvment of the seedling growth as well as the cultivation efficiency. To achieve this, the effect of microwave frequency on the germination of rice seeds was examined. The physiological feedbacks of the MR 219 rice variety in terms of seed germination rate (GR), germination percentage (GP), and mean germination time (MGT) were analyzed by exposing its seeds to 2450 MHz of microwave frequency for one, four, seven, and ten hours. It was revealed that exposing the seeds to the microwave frequency for 10 hours resulted in the highest GP. This treatment led to 100% of germination after three days with a mean germination time of 2.1 days. Although the other exposure times of microwave frequency caused the moderate effects on germination with a GPa3 ranged from 93% to 98%, they failed to reduce the MGTa3. The results showed that ten-hour exposure times of microwave frequency for six days significantly facilitated and improved the germination indices (primary shoot and root length). Therefore, the technique is expected to benefit the improvement of rice seed germination considering its simplicity and efficacy in increasing the germination percentage and rate as well as the primary shoot and root length without causing any environmental toxicity. PMID:24307869

  16. Comparative biochemical and RAPD analysis in two varieties of rice (Oryza sativa) under arsenic stress by using various biomarkers.

    PubMed

    Ahmad, Mohd Anwar; Gaur, Rashmi; Gupta, Meetu

    2012-05-30

    Multiple biomarker systems have been frequently used to measure the genotoxic effects of environmental pollutants (including heavy metals) on living organisms. In this study, we used leaves of hydroponically grown 14 days old seedlings of rice (Oryza sativa) varieties (PB1 and IR64) treated with 50, 150 and 300 μM arsenite (As(III)) for 24 and 96 h duration. Reduction in seed germination, root-shoot length, chlorophyll and protein were observed with increasing As(III) concentration and duration in both varieties, being more in IR64. Increase/decrease of antioxidant enzymes and stress related parameters showed much changes at higher concentration for 24 and 96 h duration in both varieties. Eleven primers were found in RAPD analysis to produce polymorphic band pattern and produced a total of 51 (control), 79 (treated) and 42 (control) and 29 (treated) bands in PB1 and IR64 varieties, respectively. These results indicated that genomic template stability (GTS, changes in RAPD profile) was significantly affected at all tested As(III) concentration, when compared with other parameters. Differential response was observed in both varieties with PB1 being more tolerant. We concluded that DNA polymorphism detected by RAPD analysis in conjunction with other biochemical parameters could be a powerful eco-toxicological tool in bio-monitoring arsenic pollution.

  17. 2-Acetyl-1-pyrroline augmentation in scented indica rice (Oryza sativa L.) varieties through Δ(1)-pyrroline-5-carboxylate synthetase (P5CS) gene transformation.

    PubMed

    Kaikavoosi, Kayghobad; Kad, Trupti D; Zanan, Rahul L; Nadaf, Altafhusain B

    2015-12-01

    2-Acetyl-1-pyrroline (2AP) has been identified as a principal aroma compound in scented rice varieties. Δ(1)-Pyrroline-5-carboxylate synthetase (P5CS) gene is reported to regulate the proline synthesis in plants and acts as the precursor of 2AP. Two scented indica rice varieties, namely Ambemohar 157 and Indrayani, were subjected to Agrobacterium tumefaciens-mediated genetic transformation containing P5CS gene. Overexpression of P5CS led to a significant increase in proline, P5CS enzyme activity and 2AP levels in transgenic calli, vegetative plant parts, and seeds over control in both the varieties. 2AP level increased more than twofold in transgenic seeds in both varieties. This is the first report of enhancement in 2AP content through overexpression of using P5CS gene, indicating the role of proline as a precursor amino acid in the biosynthesis of 2AP in scented rice.

  18. Morphostructural Characterization of Rice Grain (Oryza sativa L.) Variety Morelos A-98 during Filling Stages

    PubMed Central

    Espinosa-Mendoza, Rosa Elena; Solorza-Feria, Javier; Arenas-Ocampo, Martha Lucía; Camacho-Díaz, Brenda Hildeliza; Del Villar-Martínez, Alma Angélica; Vanegas-Espinoza, Pablo Emilio; Jiménez-Aparicio, Antonio Ruperto

    2012-01-01

    The morphostructure of grain rice Morelos A-98 was characterized in five stages of physiological maturation, in order to generate morphometric information during the filling process. Micrographic images from optical and scanning electron microscopy coupled to a digital capture system were used. Images were digitally processed to measure different descriptors such as shape, fractal dimension, and surface texture. Results showed that, two weeks after anthesis, an accelerated grain filling was observed, particularly on those grains positioned in the distal panicle zone, compared to those located in the base of this one. As deposition of assimilates in the grain increased, the area and perimeter of the transversal cut of the grains also increased (P ≤ 0.05); meanwhile, the rounded shape factor tended to increase as well (P ≤ 0.05), while the elliptic shape factor decreased. As the dehydrated endosperm passed from “milky” to “doughy” stages, values of fractal dimension area and endosperm perimeter as well as surface texture values showed that grain borders tended to become smoother and that there was a greater structured endosperm area (P ≤ 0.05). PMID:22645473

  19. Isolation of lignin by organosolv process from different varieties of rice husk: Understanding their physical and chemical properties.

    PubMed

    Singh, Sandip K; Dhepe, Paresh L

    2016-12-01

    The aim of this work was to study the difference in properties of lignins, those (organosolv lignins (ORGLs, 12±3% yield and 93±5% mass balance) were isolated from diverse rice husk (RH) substrates using organosolv procedure (water:ethanol, H2SO4) carried out at 180°C for 1h. To identify the possible alterations in lignin structures several bulk and molecular level advanced characterization tools were employed. Even though lignins were extracted using common isolation procedure from three varieties of similar species of RH; from XRD, GPC, and elemental analysis it was found that those have comparable properties on bulk level. But molecular level analysis conducted using UV-vis, ATR, 1D/2D HSQC NMR techniques could help disclose that isolated lignins have varying concentrations of G, H, S and T substructures. Additionally, the double bond equivalence of 4.4-4.7 reveals that few of the aromatic rings are devoid of substituent.

  20. Changes in Endosymbiotic Bacteria of Brown Planthoppers During the Process of Adaptation to Different Resistant Rice Varieties.

    PubMed

    Hong-Xing, Xu; Xu-Song, Zheng; Ya-Jun, Yang; Jun-Ce, Tian; Qiang, Fu; Gong-Yin, Ye; Zhong-Xian, Lu

    2015-06-01

    The specific primers of five species of endosymbiotic bacteria were designed to determine their numbers in three virulent populations of brown planthopper, Nilapavata lugens Stål, and to assess changes during adaptation to different resistant varieties using fluorescent quantitative PCR. The results showed that Chryseobacterium was the dominant bacteria in all three populations of brown planthopper, followed by Acinetobacter in TN1 population, Arsenophonus and Serratia in Mudgo population, and Arthrobacter and Acinetobacter in ASD7 population. When the TN1 population of brown planthopper was transferred to ASD7 (with resistant gene bph2) rice plants, Chryseobacterium was still the dominant bacteria, but the originally subdominant Acinetobacter declined to a level that was not significantly different from that of other endosymbiotic bacteria. After they were transferred to Mudgo (with resistant gene Bph1), Serratia and Arsenophonus increased significantly and became the dominant bacteria. However, they declined to a level that was not significantly different from that of the three other species after two generations. When ASD7 and Mudgo populations of brown planthopper were transferred to the susceptible variety TN1, the community of endosymbiotic bacteria in the ASD7 population of brown planthopper showed no significant changes. However, the numbers of Acinetobacter and Arthrobacter in the Mudgo population of brown planthopper exhibited a transient increase and returned to their original levels after two generations. After the Mudgo population of brown planthopper was transferred to ASD7 rice plants, the quantity of endosymbiotic bacteria fluctuated, but the bacterial structure did not change significantly. However, after the ASD7 population of brown planthopper was transferred to the Mudgo rice plants, the bacterial structure changed significantly. Serratia and Arsenophonus increased significantly and became dominant. Although Serratia and Arsenophonus decreased

  1. Plasma membrane-localized transporter for aluminum in rice.

    PubMed

    Xia, Jixing; Yamaji, Naoki; Kasai, Tomonari; Ma, Jian Feng

    2010-10-26

    Aluminum (Al) is the most abundant metal in the Earth's crust, but its trivalent ionic form is highly toxic to all organisms at low concentrations. How Al enters cells has not been elucidated in any organisms. Herein, we report a transporter, Nrat1 (Nramp aluminum transporter 1), specific for trivalent Al ion in rice. Nrat1 belongs to the Nramp (natural resistance-associated macrophage protein) family, but shares a low similarity with other Nramp members. When expressed in yeast, Nrat1 transports trivalent Al ion, but not other divalent ions, such as manganese, iron, and cadmium, or the Al-citrate complex. Nrat1 is localized at the plasma membranes of all cells of root tips except epidermal cells. Knockout of Nrat1 resulted in decreased Al uptake, increased Al binding to cell wall, and enhanced Al sensitivity, but did not affect the tolerance to other metals. Expression of Nrat1 is up-regulated by Al in the roots and regulated by a C2H2 zinc finger transcription factor (ART1). We therefore concluded that Nrat1 is a plasma membrane-localized transporter for trivalent Al, which is required for a prior step of final Al detoxification through sequestration of Al into vacuoles.

  2. The Birth of a Black Rice Gene and Its Local Spread by Introgression

    PubMed Central

    Oikawa, Tetsuo; Maeda, Hiroaki; Oguchi, Taichi; Yamaguchi, Takuya; Tanabe, Noriko; Ebana, Kaworu; Yano, Masahiro; Izawa, Takeshi

    2015-01-01

    The origin and spread of novel agronomic traits during crop domestication are complex events in plant evolution. Wild rice (Oryza rufipogon) has red grains due to the accumulation of proanthocyanidins, whereas most cultivated rice (Oryza sativa) varieties have white grains induced by a defective allele in the Rc basic helix-loop-helix (bHLH) gene. Although the events surrounding the origin and spread of black rice traits remain unknown, varieties with black grains due to anthocyanin accumulation are distributed in various locations throughout Asia. Here, we show that the black grain trait originated from ectopic expression of the Kala4 bHLH gene due to rearrangement in the promoter region. Both the Rc and Kala4 genes activate upstream flavonol biosynthesis genes, such as chalcone synthase and dihydroflavonol-4-reductase, and downstream genes, such as leucoanthocyanidin reductase and leucoanthocyanidin dioxygenase, to produce the respective specific pigments. Genome analysis of 21 black rice varieties as well as red- and white-grained landraces demonstrated that black rice arose in tropical japonica and its subsequent spread to the indica subspecies can be attributed to the causal alleles of Kala4. The relatively small size of genomic fragments of tropical japonica origin in some indica varieties indicates that refined introgression must have occurred by natural crossbreeding in the course of evolution of the black trait in rice. PMID:26362607

  3. Effects of water-saving irrigation practices and drought resistant rice variety on greenhouse gas emissions from a no-till paddy in the central lowlands of China.

    PubMed

    Xu, Ying; Ge, Junzhu; Tian, Shaoyang; Li, Shuya; Nguy-Robertson, Anthony L; Zhan, Ming; Cao, Cougui

    2015-02-01

    As pressure on water resources increases, alternative practices to conserve water in paddies have been developed. Few studies have simultaneously examined the effectiveness of different water regimes on conserving water, mitigating greenhouse gases (GHG), and maintaining yields in rice production. This study, which was conducted during the drought of 2013, examined all three factors using a split-plot experiment with two rice varieties in a no-till paddy managed under three different water regimes: 1) continuous flooding (CF), 2) flooded and wet intermittent irrigation (FWI), and 3) flooded and dry intermittent irrigation (FDI). The Methane (CH₄) and nitrous oxide (N₂O) emissions were measured using static chamber-gas measurements, and the carbon dioxide (CO₂) emissions were monitored using a soil CO₂ flux system (LI-8100). Compared with CF, FWI and FDI irrigation strategies reduced CH₄ emissions by 60% and 83%, respectively. In contrast, CO₂ and N₂O fluxes increased by 65% and 9%, respectively, under FWI watering regime and by 104% and 11%, respectively, under FDI managed plots. Although CO₂ and N₂O emissions increased, the global warming potential (GWP) and greenhouse gas intensity (GHGI) of all three GHG decreased by up to 25% and 29% (p<0.01), respectively, using water-saving irrigation strategies. The rice variety also affected yields and GHG emissions in response to different water regimes. The drought-resistance rice variety (HY3) was observed to maintain yields, conserve water, and reduce GHG under the FWI irrigation management compared with the typical variety (FYY299) planted in the region. The FYY299 only had significantly lower GWP and GHGI when the yield was reduced under FDI water regime. In conclusion, FWI irrigation strategy could be an effective option for simultaneously saving water and mitigating GWP without reducing rice yields using drought-resistant rice varieties, such as HY3.

  4. Speciation and Localization of Arsenic in White and Brown Rice Grains

    SciTech Connect

    Meharg, Andrew A.; Lombi, Enzo; Williams, Paul N.; Scheckel, Kirk G.; Feldmann, Joerg; Raab, Andrea; Zhu, Yongguan; Islam, Rafiql

    2008-06-30

    Synchrotron-based X-ray fluorescence (S-XRF) was utilized to locate arsenic (As) in polished (white) and unpolished (brown) rice grains from the United States, China, and Bangladesh. In white rice As was generally dispersed throughout the grain, the bulk of which constitutes the endosperm. In brown rice As was found to be preferentially localized at the surface, in the region corresponding to the pericarp and aleurone layer. Copper, iron, manganese, and zinc localization followed that of arsenic in brown rice, while the location for cadmium and nickel was distinctly different, showing relatively even distribution throughout the endosperm. The localization of As in the outer grain of brown rice was confirmed by laser ablation ICP?MS. Arsenic speciation of all grains using spatially resolved X-ray absorption near edge structure (?-XANES) and bulk extraction followed by anion exchange HPLC?ICP?MS revealed the presence of mainly inorganic As and dimethylarsinic acid (DMA). However, the two techniques indicated different proportions of inorganic:organic As species. A wider survey of whole grain speciation of white (n = 39) and brown (n = 45) rice samples from numerous sources (field collected, supermarket survey, and pot trials) showed that brown rice had a higher proportion of inorganic arsenic present than white rice. Furthermore, the percentage of DMA present in the grain increased along with total grain arsenic.

  5. Physiological Mechanisms Underlying the High-Grain Yield and High-Nitrogen Use Efficiency of Elite Rice Varieties under a Low Rate of Nitrogen Application in China

    PubMed Central

    Wu, Lilian; Yuan, Shen; Huang, Liying; Sun, Fan; Zhu, Guanglong; Li, Guohui; Fahad, Shah; Peng, Shaobing; Wang, Fei

    2016-01-01

    Selecting rice varieties with a high nitrogen (N) use efficiency (NUE) is the best approach to reduce N fertilizer application in rice production and is one of the objectives of the Green Super Rice (GSR) Project in China. However, the performance of elite candidate GSR varieties under low N supply remains unclear. In the present study, differences in the grain yield and NUE of 13 and 14 candidate varieties with two controls were determined at a N rate of 100 kg ha−1 in field experiments in 2014 and 2015, respectively. The grain yield for all of the rice varieties ranged from 8.67 to 11.09 t ha−1, except for a japonica rice variety YG29, which had a grain yield of 6.42 t ha−1. HY549 and YY4949 produced the highest grain yield, reflecting a higher biomass production and harvest index in 2014 and 2015, respectively. Total N uptake at maturity (TNPM) ranged from 144 to 210 kg ha−1, while the nitrogen use efficiency for grain production (NUEg) ranged from 35.2 to 62.0 kg kg−1. Both TNPM and NUEg showed a significant quadratic correlation with grain yield, indicating that it is possible to obtain high grain yield and NUEg with the reduction of TNPM. The correlation between N-related parameters and yield-related traits suggests that promoting pre-heading growth could increase TNPM, while high biomass accumulation during the grain filling period and large panicles are important for a higher NUEg. In addition, there were significant and negative correlations between the NUEg and N concentrations in leaf, stem, and grain tissues at maturity. Further improvements in NUEg require a reduction in the stem N concentration but not the leaf N concentration. The daily grain yield was the only parameter that significantly and positively correlated with both TNPMand NUEg. This study determined variations in the grain yield and NUE of elite candidate GSR rice varieties and provided plant traits that could be used as selection criteria in breeding N-efficient rice varieties

  6. High concentrations of anthocyanins in genuine cherry-juice of old local Austrian Prunus avium varieties.

    PubMed

    Schüller, Elisabeth; Halbwirth, Heidi; Mikulic-Petkovsek, Maja; Slatnar, Ana; Veberic, Robert; Forneck, Astrid; Stich, Karl; Spornberger, Andreas

    2015-04-15

    Antioxidant activity and polyphenols were quantified in vapour-extracted juice of nine Austrian, partially endemic varieties of sweet cherry (Prunus avium): cv. 'Spätbraune von Purbach', cv. 'Early Rivers', cv. 'Joiser Einsiedekirsche', cv. 'Große Schwarze Knorpelkirsche' and four unidentified local varieties. Additionally the effect of storage was evaluated for six of the varieties. A variety showing the highest antioxidant capacity (9.64 μmol Trolox equivalents per mL), total polyphenols (2747 mg/L) and total cyanidins (1085 mg/L) was suitable for mechanical harvest and its juice did not show any losses of antioxidant capacity and total anthocyanin concentration during storage. The juice of cv. 'Große Schwarze Knorpelkirsche' had also high concentrations of total anthocyanins (873 mg/L), but showed substantial losses through storage. The local Austrian sweet cherry varieties from the Pannonian climate zone are particularly suitable for the production of processed products like cherry juice with high content of anthocyanins and polyphenols.

  7. Genetic, Physiological, and Gene Expression Analyses Reveal That Multiple QTL Enhance Yield of Rice Mega-Variety IR64 under Drought

    PubMed Central

    Swamy B. P., Mallikarjuna; Ahmed, Helal Uddin; Henry, Amelia; Mauleon, Ramil; Dixit, Shalabh; Vikram, Prashant; Tilatto, Ram; Verulkar, Satish B.; Perraju, Puvvada; Mandal, Nimai P.; Variar, Mukund; S., Robin; Chandrababu, Ranganath; Singh, Onkar N.; Dwivedi, Jawaharlal L.; Das, Sankar Prasad; Mishra, Krishna K.; Yadaw, Ram B.; Aditya, Tamal Lata; Karmakar, Biswajit; Satoh, Kouji; Moumeni, Ali; Kikuchi, Shoshi; Leung, Hei; Kumar, Arvind

    2013-01-01

    Background Rice (Oryza sativa L.) is a highly drought sensitive crop, and most semi dwarf rice varieties suffer severe yield losses from reproductive stage drought stress. The genetic complexity of drought tolerance has deterred the identification of agronomically relevant quantitative trait loci (QTL) that can be deployed to improve rice yield under drought in rice. Convergent evidence from physiological characterization, genetic mapping, and multi-location field evaluation was used to address this challenge. Methodology/Principal Findings Two pairs of backcross inbred lines (BILs) from a cross between drought-tolerant donor Aday Sel and high-yielding but drought-susceptible rice variety IR64 were produced. From six BC4F3 mapping populations produced by crossing the +QTL BILs with the −QTL BILs and IR64, four major-effect QTL - one each on chromosomes 2, 4, 9, and 10 - were identified. Meta-analysis of transcriptome data from the +QTL/−QTL BILs identified differentially expressed genes (DEGs) significantly associated with QTL on chromosomes 2, 4, 9, and 10. Physiological characterization of BILs showed increased water uptake ability under drought. The enrichment of DEGs associated with root traits points to differential regulation of root development and function as contributing to drought tolerance in these BILs. BC4F3-derived lines with the QTL conferred yield advantages of 528 to 1875 kg ha−1 over IR64 under reproductive-stage drought stress in the targeted ecosystems of South Asia. Conclusions/Significance Given the importance of rice in daily food consumption and the popularity of IR64, the BC4F3 lines with multiple QTL could provide higher livelihood security to farmers in drought-prone environments. Candidate genes were shortlisted for further characterization to confirm their role in drought tolerance. Differential yield advantages of different combinations of the four QTL reported here indicate that future research should include optimizing QTL

  8. Characterization of near-isogenic lines carrying QTL for high spikelet number with the genetic background of an indica rice variety IR64 (Oryza sativa L.)

    PubMed Central

    Fujita, Daisuke; Tagle, Analiza G.; Ebron, Leodegario A.; Fukuta, Yoshimichi; Kobayashi, Nobuya

    2012-01-01

    Total spikelet number per panicle (TSN) is one of the most important traits associated with rice yield potential. This trait was assessed in a set of 334 chromosomal segment introgression lines (ILs: BC3-derived lines), developed from new plant type (NPT) varieties as donor parents and having the genetic background of an indica-type rice variety IR64. Among the 334 ILs, five lines which had different donor parents and showed significantly higher TSN than IR64 were used for genetic analysis. Quantitative trait locus (QTL) analysis was conducted using F2 populations derived from crosses between IR64 and these ILs. As a result, a QTL for high TSN (one from each NPT donor variety) was detected on common region of the long arm of chromosome 4. The effect of the QTL was confirmed by an increase in TSN of five near-isogenic lines (NILs) developed in the present study. The variation in TSN was found among these NILs, attributing to the panicle architecture in the numbers of primary, secondary and tertiary branches. The NILs for TSN and the SSR markers linked to the TSN QTLs are expected to be useful materials for research and breeding to enhance the yield potential of rice varieties. PMID:23136510

  9. Characterization of near-isogenic lines carrying QTL for high spikelet number with the genetic background of an indica rice variety IR64 (Oryza sativa L.).

    PubMed

    Fujita, Daisuke; Tagle, Analiza G; Ebron, Leodegario A; Fukuta, Yoshimichi; Kobayashi, Nobuya

    2012-03-01

    Total spikelet number per panicle (TSN) is one of the most important traits associated with rice yield potential. This trait was assessed in a set of 334 chromosomal segment introgression lines (ILs: BC(3)-derived lines), developed from new plant type (NPT) varieties as donor parents and having the genetic background of an indica-type rice variety IR64. Among the 334 ILs, five lines which had different donor parents and showed significantly higher TSN than IR64 were used for genetic analysis. Quantitative trait locus (QTL) analysis was conducted using F(2) populations derived from crosses between IR64 and these ILs. As a result, a QTL for high TSN (one from each NPT donor variety) was detected on common region of the long arm of chromosome 4. The effect of the QTL was confirmed by an increase in TSN of five near-isogenic lines (NILs) developed in the present study. The variation in TSN was found among these NILs, attributing to the panicle architecture in the numbers of primary, secondary and tertiary branches. The NILs for TSN and the SSR markers linked to the TSN QTLs are expected to be useful materials for research and breeding to enhance the yield potential of rice varieties.

  10. Assessment of arsenic in Australian grown and imported rice varieties on sale in Australia and potential links with irrigation practises and soil geochemistry.

    PubMed

    Fransisca, Yunnita; Small, Darryl M; Morrison, Paul D; Spencer, Michelle J S; Ball, Andrew S; Jones, Oliver A H

    2015-11-01

    Chronic dietary exposure to arsenic, particularly the inorganic forms (defined as elemental arsenic, predominantly As(3+) and As(5+), and all its inorganic compounds except arsine), is a matter of concern for human health. Ingestion of arsenic usually occurs via contaminated water but recent studies show there is also a risk of exposure from food, particularly Asian rice (Oryza sativa). Australia is a rice growing country, contributing around 2% of the world rice trade, and a large proportion of the population consumes rice regularly. In the present study we investigated concentrations of arsenic in both Australian grown and imported rice on sale in Australia and examined the potential links with irrigation practises and soil geochemistry. The results indicated a wide spread of arsenic levels of 0.09-0.33 mg kg(-1), with Australian grown Arborio and sushi varieties of O. sativa containing the highest mean value of ∼0.22 mg kg(-1). Arsenic levels in all samples were below the 1 mg kg(-1) limit set by Food Standards Australia New Zealand.

  11. Determination of Optimal Harvest Time of Chuchung Variety Green Rice® (Oryza sativa L.) with High Contents of GABA, γ-Oryzanol, and α-Tocopherol

    PubMed Central

    Kim, Hoon; Kim, Oui-Woung; Ha, Ae Wha; Park, Soojin

    2016-01-01

    In our previous study, an early-maturing variety of rice (Oryza sativa L.), Jinbu can have feature with unique green color, various phytochemicals as well as nutritive components by the optimal early harvesting, called Green Rice® (GR). The aims of the present field experiments were to evaluate the changes in the weight of 1,000 kernels, yield, and contents of proximate and bioactive compounds in Chuchung, a mid-late maturing variety, during the pre-harvest maturation of rough rice and to research the appropriate harvest time and potent bioactivity of Chuchung GR. The weights of 1,000 kernels of Chuchung GR dramatically increased until 27 days after heading (DAH). The yields of Chuchung GR declined after 27 DAH and significantly declined to 0.0% after 45 DAH. The caloric value and total mineral contents were higher in the GR than in the full ripe stage, the brown rice (BR). In the GR, the contents of bioactive compounds, such as γ-aminobutyric acid, γ-oryzanol, and α-tocopherol, were much higher (P<0.05) than those in the BR, specifically during 24~27 DAH. Therefore, bioactive Chuchung GR can be produced with a reasonable yield at 24~27 DAH and it could be useful for applications in various nutritive and functional food products. PMID:27390725

  12. Arsenic concentrations in local aromatic and high-yielding hybrid rice cultivars and the potential health risk: a study in an arsenic hotspot.

    PubMed

    Sandhi, Arifin; Greger, Maria; Landberg, Tommy; Jacks, Gunnar; Bhattacharya, Prosun

    2017-04-01

    The presence of high levels of arsenic (As) in rice fields has negative effects on the health of those consuming rice as their subsistence food. This study determined the variation in total As concentration in local aromatic rice (LAR) (kalijira) and two high-yielding varieties (HYVs) (BRRI dhan 32 and BRRI dhan 28) grown in paddy fields in Matlab, Bangladesh, an As hotspot with elevated As levels in groundwater. Mature rice grain samples and soil samples were collected from different paddy fields, and the As concentrations in both the de-husked grains and the husks of the three rice cultivars were analysed to identify the safest of the three cultivars for human consumption. The results showed that the total As concentration was higher (0.09-0.21 mg As kg(-1)) in the de-husked grains of LAR than in the husks, while the opposite was found for the HYV rice. Moreover, the As concentration in soil samples was 2 to 5-fold higher for the LAR than for the HYVs, but the As accumulation factor (AF) was lower in the LAR (0.2-0.4%) than in the HYVs (0.9-1%). Thus, LAR can be considered the safest of the three cultivars for human consumption owing to its low AF value. Furthermore, due to the low AF, growing LAR instead of HYVs in soils with slightly elevated As levels could help improve the food safety level in the food chain.

  13. Modern maize varieties going local in the semi-arid zone in Tanzania

    PubMed Central

    2014-01-01

    Background Maize is the most produced crop in Sub-Saharan Africa, but yields are low and climate change is projected to further constrain smallholder production. The current efforts to breed and disseminate new high yielding and climate ready maize varieties are implemented through the formal seed system; the chain of public and private sector activities and institutions that produce and release certified seeds. These efforts are taking place in contexts currently dominated by informal seed systems; local and informal seed management and exchange channels with a long history of adapting crops to local conditions. We here present a case study of the genetic effects of both formal and informal seed management from the semi-arid zone in Tanzania. Results Two open pollinated varieties (OPVs), Staha and TMV1, first released by the formal seed system in the 1980s are cultivated on two-thirds of the maize fields among the surveyed households. Farmer-recycling of improved varieties and seed selection are common on-farm seed management practices. Drought tolerance and high yield are the most important characteristics reported as reason for cultivating the current varieties as well as the most important criteria for farmers’ seed selection. Bayesian cluster analysis, PCA and FST analyses based on 131 SNPs clearly distinguish between the two OPVs, and despite considerable heterogeneity between and within seed lots, there is insignificant differentiation between breeder’s seeds and commercial seeds in both OPVs. Genetic separation increases as the formal system varieties enter the informal system and both hybridization with unrelated varieties and directional selection probably play a role in the differentiation. Using a Bayesian association approach we identify three loci putatively under selection in the informal seed system. Conclusions Our results suggest that the formal seed system in the study area distributes seed lots that are true to type. We suggest that

  14. Extensive sequence divergence between the reference genomes of two elite indica rice varieties Zhenshan 97 and Minghui 63

    PubMed Central

    Zhang, Jianwei; Chen, Ling-Ling; Xing, Feng; Kudrna, David A.; Yao, Wen; Copetti, Dario; Mu, Ting; Li, Weiming; Song, Jia-Ming; Lee, Seunghee; Talag, Jayson; Shao, Lin; An, Yue; Zhang, Chun-Liu; Ouyang, Yidan; Sun, Shuai; Jiao, Wen-Biao; Lv, Fang; Du, Bogu; Luo, Meizhong; Maldonado, Carlos Ernesto; Goicoechea, Jose Luis; Xiong, Lizhong; Wu, Changyin; Xing, Yongzhong; Zhou, Dao-Xiu; Yu, Sibin; Zhao, Yu; Wang, Gongwei; Yu, Yeisoo; Luo, Yijie; Zhou, Zhi-Wei; Hurtado, Beatriz Elena Padilla; Danowitz, Ann; Wing, Rod A.; Zhang, Qifa

    2016-01-01

    Asian cultivated rice consists of two subspecies: Oryza sativa subsp. indica and O. sativa subsp. japonica. Despite the fact that indica rice accounts for over 70% of total rice production worldwide and is genetically much more diverse, a high-quality reference genome for indica rice has yet to be published. We conducted map-based sequencing of two indica rice lines, Zhenshan 97 (ZS97) and Minghui 63 (MH63), which represent the two major varietal groups of the indica subspecies and are the parents of an elite Chinese hybrid. The genome sequences were assembled into 237 (ZS97) and 181 (MH63) contigs, with an accuracy >99.99%, and covered 90.6% and 93.2% of their estimated genome sizes. Comparative analyses of these two indica genomes uncovered surprising structural differences, especially with respect to inversions, translocations, presence/absence variations, and segmental duplications. Approximately 42% of nontransposable element related genes were identical between the two genomes. Transcriptome analysis of three tissues showed that 1,059–2,217 more genes were expressed in the hybrid than in the parents and that the expressed genes in the hybrid were much more diverse due to their divergence between the parental genomes. The public availability of two high-quality reference genomes for the indica subspecies of rice will have large-ranging implications for plant biology and crop genetic improvement. PMID:27535938

  15. Rice OsVAMP714, a membrane-trafficking protein localized to the chloroplast and vacuolar membrane, is involved in resistance to rice blast disease.

    PubMed

    Sugano, Shoji; Hayashi, Nagao; Kawagoe, Yasushi; Mochizuki, Susumu; Inoue, Haruhiko; Mori, Masaki; Nishizawa, Yoko; Jiang, Chang-Jie; Matsui, Minami; Takatsuji, Hiroshi

    2016-05-01

    Membrane trafficking plays pivotal roles in many cellular processes including plant immunity. Here, we report the characterization of OsVAMP714, an intracellular SNARE protein, focusing on its role in resistance to rice blast disease caused by the fungal pathogen Magnaporthe oryzae. Disease resistance tests using OsVAMP714 knockdown and overexpressing rice plants demonstrated the involvement of OsVAMP714 in blast resistance. The overexpression of OsVAMP7111, whose product is highly homologous to OsVAMP714, did not enhance blast resistance to rice, implying a potential specificity of OsVAMP714 to blast resistance. OsVAMP714 was localized to the chloroplast in mesophyll cells and to the cellular periphery in epidermal cells of transgenic rice plant leaves. We showed that chloroplast localization is critical for the normal OsVAMP714 functioning in blast resistance by analyzing the rice plants overexpressing OsVAMP714 mutants whose products did not localize in the chloroplast. We also found that OsVAMP714 was located in the vacuolar membrane surrounding the invasive hyphae of M. oryzae. Furthermore, we showed that OsVAMP714 overexpression promotes leaf sheath elongation and that the first 19 amino acids, which are highly conserved between animal and plant VAMP7 proteins, are crucial for normal rice plant growths. Our studies imply that the OsVAMP714-mediated trafficking pathway plays an important role in rice blast resistance as well as in the vegetative growth of rice.

  16. Role of plant volatiles in resistance of selected rice varieties to brown planthopper,Nilaparvata lugens (Stål) (Homoptera: Delphacidae).

    PubMed

    Saxena, R C; Okech, S H

    1985-12-01

    Rice plant volatiles extracted as steam distillates significantly affected the behavior and biology of the brown planthopper,Nilaparvata lugens (Stål). In a multichoice test, more females settled and fed on tillers of a susceptible rice variety "Taichung Native 1" (TN1), sprayed with its own extract or acetone than on TN1 tillers sprayed with the extract of the resistant variety "ARC6650" or "Ptb33." In another test,N. lugens females ingested significantly more of a 10% sucrose solution mixed with TN1 steam distillate extract than of plain sucrose solution or that mixed with extracts of resistant varieties. Topical application of the extracts of resistant varieties "Mudgo," "ASD7," "Rathu Heenati," "Babawee," Ptb33, and ARC6650 caused significantly higher mortality of females than did the TN1 extract. Likewise, significantly more first-instar nymphs died when they were caged on susceptible TN1 plants sprayed with the extracts of resistant varieties than on plants sprayed with TN1 extract. The extract of 60-day-old resistant plants was more toxic than the extract of 30-, 45-, or 100-day-old plants. However, toxicity of the extract from susceptible TN1 remained low at all plant growth stages.

  17. Bran data of total flavonoid and total phenolic contents, oxygen radical absorbance capacity, and profiles of proanthocyanidins and whole grain physical traits of 32 red and purple rice varieties

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Phytochemicals in red and purple bran rice have potential health benefit to humans. We determined the phytochemicals in brans of 32 red and purple global rice varieties. The description of the origin and physical traits of the whole grain (color, length, width, thickness and 100-kernel weight) of th...

  18. Cytogenetic studies on two F1 hybrids of autotetraploid rice varieties showing extremely high level of heterosis

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Mechanisms of two F1 hybrids (D46AxDTP-4 and D46Ax Dminghui63) of auototetraploid rice (2n=4x=48) showing extremely high pollen fertility 87.40% and 85.97%, respectively, seed set 82.00% and 79%, respectively and extremely high level of heterosis were analyzed cytologically. Chromosome pairing of th...

  19. Metabolic Differences Found In Seedlings of Rice Varieties That Produce Grains Low Versus High in Arsenic Concentration

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Arsenic (As) occurs naturally in air, water and soil and is also present to some degree in all edible and non-edible plant tissues. Because As becomes more available for plant uptake when soils are flooded, there is more concern about As in rice than other grain crops. Our research objective was t...

  20. What might rice piles tell us about non-local sediment transport?

    NASA Astrophysics Data System (ADS)

    Longjas, A.; Voller, V. R.; Paola, C.; Filipovitch, N.

    2014-12-01

    Our research objective is to identify sediment transport systems that exhibit non local signals, such as those seen in the long-profile of fluvial surfaces. In previous work we have shown that appropriate nonlocal models of sediment transport under various tectonic forcing, can lead to fluvial surface shapes that are distinct from those obtained with local models. For example, in the study of a sediment bypass system, a nonlocal model for the sediment flux predicts a concave down fluvial surface in contrast to the linear surface predicted with a local flux model. It is well known that hold ups and fast paths in transport systems lead to non-local behaviors. And we think that the mechanism that creates the unexpected curvatures in fluvial profiles is one of "storage and release". Perhaps the classic storage and release system is that seen in rice pile experiments. One set up for this experiment involves the formation of a rice pile in the gap (~25mm) between two vertical glass plates resting on a solid surface. In this system rice is added at a constant rate at the left and allowed to freely exit a distance (~0.5m) downstream; the system is run until a steady state is approached. Of course, an exact steady state is not reached because the rice does not move steadily down the pile surface but rather advances in a series of avalanches, with multiple length scales, separated by waiting times; in other words is transported via storage and release. The naive expectancy is that at the steady state the surface of the rice pile will exhibit a constant angle of repose. Our experiments with the system, however, indicate that while the storage and release mechanism invokes large temporal fluctuations in the pile its surface exhibits a persistent concave down shape. In this paper, we present the main findings of our rice pile experiment, explore models that might explain the persistence of the curved surface, and uncover the behavioral links between the rice pile model and non-local

  1. Effect of methyl salicylate (MeSA), an elicitor on growth, physiology and pathology of resistant and susceptible rice varieties

    PubMed Central

    Kalaivani, Kandaswamy; Kalaiselvi, Marimuthu Maruthi; Senthil-Nathan, Sengottayan

    2016-01-01

    Methyl salicylate (MeSA) is a volatile organic compound synthesized from salicylic acid (SA) a plant hormone that helps to fight against plant disease. Seed treatment with MeSA, is an encouraging method to the seed industry to produce more growth and yield. The aim of our study is to find out the growth, development and disease tolerance of rice seed treated with different concentrations of MeSA. Also the seed treatments were studied to determine whether they directly influenced seedling emergence and growth in rice (Oryza sativa L) cultivars ‘IR 20, IR 50, IR 64, ASD 16, ASD 19 and ADT 46’ under greenhouse condition. MeSA seed treatments at 25, 50, 75 and 100 mg/L significantly increased seedling emergence. Effects were stronger in IR 50, and IR 64 and the effects were dose dependent, although the relationship between dose and effect was not always linear. MeSA seed treated rice plant against bacterial blight were analyzed. Bacterial blight was more effectively controlled by the seed treated with 100 mg/L than others. These results suggest that seed treatment with MeSA alters plant physiology in ways that may be useful for crop production as well as protection. PMID:27725719

  2. Transcriptome-Based Identification of Differently Expressed Genes from Xanthomonas oryzae pv. oryzae Strains Exhibiting Different Virulence in Rice Varieties

    PubMed Central

    Noh, Tae-Hwan; Song, Eun-Sung; Kim, Hong-Il; Kang, Mi-Hyung; Park, Young-Jin

    2016-01-01

    Xanthomonas oryzae pv. oryzae (Xoo) causes bacterial blight (BB) in rice (Oryza sativa L.). In this study, we investigated the genome-wide transcription patterns of two Xoo strains (KACC10331 and HB1009), which showed different virulence patterns against eight rice cultivars, including IRBB21 (carrying Xa21). In total, 743 genes showed a significant change (p-value < 0.001 in t-tests) in their mRNA expression levels in the HB1009 (K3a race) strain compared with the Xoo KACC10331 strain (K1 race). Among them, four remarkably enriched GO terms, DNA binding, transposition, cellular nitrogen compound metabolic process, and cellular macromolecule metabolic process, were identified in the upregulated genes. In addition, the expression of 44 genes was considerably higher (log2 fold changes > 2) in the HB1009 (K3a race) strain than in the Xoo KACC10331 (K1 race) strain. Furthermore, 13 and 12 genes involved in hypersensitive response and pathogenicity (hrp) and two-component regulatory systems (TCSs), respectively, were upregulated in the HB1009 (K3a race) strain compared with the Xoo KACC10331 (K1 race) strain, which we determined using either quantitative real-time PCR analysis or next-generation RNA sequencing. These results will be helpful to improve our understanding of Xoo and to gain a better insight into the Xoo–rice interactions. PMID:26907259

  3. Effect of timing and duration of salt treatment during growth of a fragrant rice variety on yield and 2-acetyl-1-pyrroline, proline, and GABA Levels.

    PubMed

    Poonlaphdecha, Janchai; Maraval, Isabelle; Roques, Sandrine; Audebert, Alain; Boulanger, Renaud; Bry, Xavier; Gunata, Ziya

    2012-04-18

    In greenhouse experiments, Aychade, a fragrant rice variety, was grown under one level of salt solution (EC of 3800 ± 400 μS·cm(-1)) sufficient to induce salt stress in rice. Timing and duration of salt solution application varied according to the growth stages. 2-Acetyl-1-pyrroline (2AP), a characteristic flavor compound of fragrant rice as well as biogenetically related compounds, proline, and γ-aminobutyric acid (GABA) were quantified. Salt treatments induced 2AP synthesis in the leaves, but the increase was often higher in the vegetative phase. This increase was correlated with proline level but not with that of GABA. Interestingly the grains from all the salt treated plants contained significantly higher levels of 2AP (733-998 μg·kg(-1)) than those from the control (592 μg·kg(-1)). The highest 2AP synthesis occurred when the plants were subjected to salt treatment during whole vegetative or reproductive phases. However in the latter case crop yield decreased significantly.

  4. A rice chloroplast transit peptide sequence does not alter the cytoplasmic localization of sheep serotonin N-acetyltransferase expressed in transgenic rice plants.

    PubMed

    Byeon, Yeong; Lee, Hyoung Yool; Lee, Kyungjin; Back, Kyoungwhan

    2014-09-01

    Ectopic overexpression of melatonin biosynthetic genes of animal origin has been used to generate melatonin-rich transgenic plants to examine the functional roles of melatonin in plants. However, the subcellular localization of these proteins expressed in the transgenic plants remains unknown. We studied the localization of sheep (Ovis aries) serotonin N-acetyltransferase (OaSNAT) and a translational fusion of a rice SNAT transit peptide to OaSNAT (TS:OaSNAT) in plants. Laser confocal microscopy analysis revealed that both OaSNAT and TS:OaSNAT proteins were localized to the cytoplasm even with the addition of the transit sequence to OaSNAT. Transgenic rice plants overexpressing the TS:OaSNAT fusion transgene exhibited high SNAT enzyme activity relative to untransformed wild-type plants, but lower activity than transgenic rice plants expressing the wild-type OaSNAT gene. Melatonin levels in both types of transgenic rice plant corresponded well with SNAT enzyme activity levels. The TS:OaSNAT transgenic lines exhibited increased seminal root growth relative to wild-type plants, but less than in the OaSNAT transgenic lines, confirming that melatonin promotes root growth. Seed-specific OaSNAT expression under the control of a rice prolamin promoter did not confer high levels of melatonin production in transgenic rice seeds compared with seeds from transgenic plants expressing OaSNAT under the control of the constitutive maize ubiquitin promoter.

  5. Complexity of Language Ideologies in Transnational Movement: Korean "Jogi Yuhak" Families' Ambivalent Attitudes towards Local Varieties of English in Singapore

    ERIC Educational Resources Information Center

    Bae, So Hee

    2015-01-01

    This paper discusses the complex and competing language ideologies that Korean educational migrant families in Singapore hold about the normativity and legitimacy of English language varieties. During their educational migration in Singapore, Korean families show ambivalent attitudes toward the local variety of English in Singapore, Singlish.…

  6. Speciation and distribution of arsenic and localization of nutrients in rice grains

    SciTech Connect

    Lombi, E.; Scheckel, K.G.; Pallon, J.; Carey, A.M.; Zhu, Y.G.; Meharg, A.A.

    2012-09-05

    Arsenic (As) contamination of rice grains and the generally low concentration of micronutrients in rice have been recognized as a major concern for human health. Here, we investigated the speciation and localization of As and the distribution of (micro)nutrients in rice grains because these are key factors controlling bioavailability of nutrients and contaminants. Bulk total and speciation analyses using high-pressure liquid chromatography (HPLC)-inductively coupled plasma mass spectrometry (ICP-MS) and X-ray absorption near-edge spectroscopy (XANES) was complemented by spatially resolved microspectroscopic techniques ({mu}-XANES, {mu}-X-ray fluorescence ({mu}-XRF) and particle induced X-ray emission (PIXE)) to investigate both speciation and distribution of As and localization of nutrients in situ. The distribution of As and micronutrients varied between the various parts of the grains (husk, bran and endosperm) and was characterized by element-specific distribution patterns. The speciation of As in bran and endosperm was dominated by As(III)-thiol complexes. The results indicate that the translocation from the maternal to filial tissues may be a bottleneck for As accumulation in the grain. Strong similarities between the distribution of iron (Fe), manganese (Mn) and phosphorus (P) and between zinc (Zn) and sulphur (S) may be indicative of complexation mechanisms in rice grains.

  7. Speciation and distribution of arsenic and localization of nutrients in rice grains.

    PubMed

    Lombi, E; Scheckel, K G; Pallon, J; Carey, A M; Zhu, Y G; Meharg, A A

    2009-01-01

    Arsenic (As) contamination of rice grains and the generally low concentration of micronutrients in rice have been recognized as a major concern for human health. Here, we investigated the speciation and localization of As and the distribution of (micro)nutrients in rice grains because these are key factors controlling bioavailability of nutrients and contaminants. Bulk total and speciation analyses using high-pressure liquid chromatography (HPLC)-inductively coupled plasma mass spectrometry (ICP-MS) and X-ray absorption near-edge spectroscopy (XANES) was complemented by spatially resolved microspectroscopic techniques (micro-XANES, micro-X-ray fluorescence (micro-XRF) and particle induced X-ray emission (PIXE)) to investigate both speciation and distribution of As and localization of nutrients in situ. The distribution of As and micronutrients varied between the various parts of the grains (husk, bran and endosperm) and was characterized by element-specific distribution patterns. The speciation of As in bran and endosperm was dominated by As(III)-thiol complexes. The results indicate that the translocation from the maternal to filial tissues may be a bottleneck for As accumulation in the grain. Strong similarities between the distribution of iron (Fe), manganese (Mn) and phosphorus (P) and between zinc (Zn) and sulphur (S) may be indicative of complexation mechanisms in rice grains.

  8. Expression Pattern and Subcellular Localization of the Ovate Protein Family in Rice

    PubMed Central

    Yu, Hui; Jiang, Wenzhu; Liu, Qing; Zhang, Hui; Piao, Mingxin; Chen, Zhengdao; Bian, Mingdi

    2015-01-01

    The Arabidopsis ovate family proteins (AtOFPs) have been shown to function as transcriptional repressors and regulate multiple aspects of plant growth and development. There are 31 genes that encode the full-length OVATE-domain containing proteins in the rice genome. In this study, the gene structure analysis revealed that OsOFPs are intron poor. Phylogenetic analysis suggested that OVATE proteins from rice, Arabidopsis and tomato can be divided into 4 groups (I–IV). Real-time quantitative polymerase chain reaction (RT-qPCR) analysis identified OsOFPs with different tissue-specific expression patterns at all stages of development in the rice plant. Interestingly, nearly half of the total number of OsOFP family was more highly expressed during the seed developmental stage. In addition, seed developmental cis-elements were found in the promoter region of the OsOFPs. Subcellular localization analysis revealed that YFP-OsOFP fusion proteins predominantly localized in the nucleus. Our results suggest that OsOFPs may act as regulatory proteins and play pivotal roles in the growth and development of rice. PMID:25760462

  9. Molecular and Functional Characterization of GR2-R1 Event Based Backcross Derived Lines of Golden Rice in the Genetic Background of a Mega Rice Variety Swarna.

    PubMed

    Bollinedi, Haritha; S, Gopala Krishnan; Prabhu, Kumble Vinod; Singh, Nagendra Kumar; Mishra, Sushma; Khurana, Jitendra P; Singh, Ashok Kumar

    2017-01-01

    Homozygous Golden Rice lines developed in the background of Swarna through marker assisted backcross breeding (MABB) using transgenic GR2-R1 event as a donor for the provitamin A trait have high levels of provitamin A (up to 20 ppm) but are dwarf with pale green leaves and drastically reduced panicle size, grain number and yield as compared to the recurrent parent, Swarna. In this study, we carried out detailed morphological, biochemical and molecular characterization of these lines in a quest to identify the probable reasons for their abnormal phenotype. Nucleotide blast analysis with the primer sequences used to amplify the transgene revealed that the integration of transgene disrupted the native OsAux1 gene, which codes for an auxin transmembrane transporter protein. Real time expression analysis of the transgenes (ZmPsy and CrtI) driven by endosperm-specific promoter revealed the leaky expression of the transgene in the vegetative tissues. We propose that the disruption of OsAux1 disturbed the fine balance of plant growth regulators viz., auxins, gibberellic acid and abscisic acid, leading to the abnormalities in the growth and development of the lines homozygous for the transgene. The study demonstrates the conserved roles of OsAux1 gene in rice and Arabidopsis.

  10. Molecular and Functional Characterization of GR2-R1 Event Based Backcross Derived Lines of Golden Rice in the Genetic Background of a Mega Rice Variety Swarna

    PubMed Central

    Bollinedi, Haritha; S., Gopala Krishnan; Prabhu, Kumble Vinod; Singh, Nagendra Kumar; Mishra, Sushma; Khurana, Jitendra P.; Singh, Ashok Kumar

    2017-01-01

    Homozygous Golden Rice lines developed in the background of Swarna through marker assisted backcross breeding (MABB) using transgenic GR2-R1 event as a donor for the provitamin A trait have high levels of provitamin A (up to 20 ppm) but are dwarf with pale green leaves and drastically reduced panicle size, grain number and yield as compared to the recurrent parent, Swarna. In this study, we carried out detailed morphological, biochemical and molecular characterization of these lines in a quest to identify the probable reasons for their abnormal phenotype. Nucleotide blast analysis with the primer sequences used to amplify the transgene revealed that the integration of transgene disrupted the native OsAux1 gene, which codes for an auxin transmembrane transporter protein. Real time expression analysis of the transgenes (ZmPsy and CrtI) driven by endosperm-specific promoter revealed the leaky expression of the transgene in the vegetative tissues. We propose that the disruption of OsAux1 disturbed the fine balance of plant growth regulators viz., auxins, gibberellic acid and abscisic acid, leading to the abnormalities in the growth and development of the lines homozygous for the transgene. The study demonstrates the conserved roles of OsAux1 gene in rice and Arabidopsis. PMID:28068433

  11. CH₄ and N₂O emissions from different varieties of forage rice (Oryza sativa L.) treating liquid cattle waste.

    PubMed

    Riya, Shohei; Zhou, Sheng; Watanabe, Yoichi; Sagehashi, Masaki; Terada, Akihiko; Hosomi, Masaaki

    2012-03-01

    To evaluate global warming potential (GWP) on livestock waste treatment and biomass production in rice field, methane (CH(4)) and nitrous oxide (N(2)O) fluxes from forage rice fields planted with 4 different cultivars (Oryza sativa L. cv. Hamasari, Leafstar, Kusahonami and Takanari) were measured. Each of the cultivars were subjected either to basal fertilization alone (control plots) (84 kg N ha(-1)), or to basal fertilization plus topdressing with liquid cattle waste or LCW (treatment plots) (567 kg N ha(-1)). Liquid cattle waste application to the rice field resulted in peak CH(4) fluxes ranging from 22.0 to 32.1 mg m(-1)h(-1) during flooded conditions and large N(2)O fluxes ranging from 526 to 8591 μg m(-1)h(-1) after midsummer drainage and final drainage. The GWP of the control plots was between 1358 and 3872 kg CO(2)eq ha(-1), while the treatment plots ranged between 4503 and 8426 kg CO(2)eq ha(-1) and more than 60% of the GWP was from the N(2)O emission in treatment plots. In both the control and treatment plots, the lowest GWPs per ton of above-ground biomass were found to be from the Leafstar cultivar, which had a higher aboveground biomass than other cultivars; 117 kg CO(2)eq t(-1) from the control and 257 kg CO(2)eq t(-1) from the treatment plots. Thus, both forage production and suitable disposal of the LCW may be able to be achieved concomitantly with lower levels of GWP by cultivation of Leafstar in our field.

  12. Hydraulic conductance as well as nitrogen accumulation plays a role in the higher rate of leaf photosynthesis of the most productive variety of rice in Japan

    PubMed Central

    Taylaran, Renante D.; Adachi, Shunsuke; Ookawa, Taiichiro; Usuda, Hideaki; Hirasawa, Tadashi

    2011-01-01

    An indica variety Takanari is known as one of the most productive rice varieties in Japan and consistently produces 20–30% heavier dry matter during ripening than Japanese commercial varieties in the field. The higher rate of photosynthesis of individual leaves during ripening has been recognized in Takanari. By using pot-grown plants under conditions of minimal mutual shading, it was confirmed that the higher rate of leaf photosynthesis is responsible for the higher dry matter production after heading in Takanari as compared with a japonica variety, Koshihikari. The rate of leaf photosynthesis and shoot dry weight became larger in Takanari after the panicle formation and heading stages, respectively, than in Koshihikari. Roots grew rapidly in the panicle formation stage until heading in Takanari compared with Koshihikari. The higher rate of leaf photosynthesis in Takanari resulted not only from the higher content of leaf nitrogen, which was caused by its elevated capacity for nitrogen accumulation, but also from higher stomatal conductance. When measured under light-saturated conditions, stomatal conductance was already decreased due to the reduction in leaf water potential in Koshihikari even under conditions of a relatively small difference in leaf–air vapour pressure difference. In contrast, the higher stomatal conductance was supported by the maintenance of higher leaf water potential through the higher hydraulic conductance in Takanari with the larger area of root surface. However, no increase in root hydraulic conductivity was expected in Takanari. The larger root surface area of Takanari might be a target trait in future rice breeding for increasing dry matter production. PMID:21527630

  13. Hydraulic conductance as well as nitrogen accumulation plays a role in the higher rate of leaf photosynthesis of the most productive variety of rice in Japan.

    PubMed

    Taylaran, Renante D; Adachi, Shunsuke; Ookawa, Taiichiro; Usuda, Hideaki; Hirasawa, Tadashi

    2011-07-01

    An indica variety Takanari is known as one of the most productive rice varieties in Japan and consistently produces 20-30% heavier dry matter during ripening than Japanese commercial varieties in the field. The higher rate of photosynthesis of individual leaves during ripening has been recognized in Takanari. By using pot-grown plants under conditions of minimal mutual shading, it was confirmed that the higher rate of leaf photosynthesis is responsible for the higher dry matter production after heading in Takanari as compared with a japonica variety, Koshihikari. The rate of leaf photosynthesis and shoot dry weight became larger in Takanari after the panicle formation and heading stages, respectively, than in Koshihikari. Roots grew rapidly in the panicle formation stage until heading in Takanari compared with Koshihikari. The higher rate of leaf photosynthesis in Takanari resulted not only from the higher content of leaf nitrogen, which was caused by its elevated capacity for nitrogen accumulation, but also from higher stomatal conductance. When measured under light-saturated conditions, stomatal conductance was already decreased due to the reduction in leaf water potential in Koshihikari even under conditions of a relatively small difference in leaf-air vapour pressure difference. In contrast, the higher stomatal conductance was supported by the maintenance of higher leaf water potential through the higher hydraulic conductance in Takanari with the larger area of root surface. However, no increase in root hydraulic conductivity was expected in Takanari. The larger root surface area of Takanari might be a target trait in future rice breeding for increasing dry matter production.

  14. Vinegar production from Togolese local variety Mangovi of Mango mangifera indica Linn. (Anacardiaceae).

    PubMed

    Ameyapoh, Y; Leveau, Jean-Yves; Karou, Simplice D; Bouix, M; Sossou, Seyram K; De Souza, C

    2010-02-01

    The present study aimed to access for the physiochemical parameters of vinegar production through Togolese local variety Mangovi of mango Mangifera indica juice fermentation. The juice was fermented successively by Saccharomyces cerevisisae and acetic bacteria. The levels of ethanol and acetic acid in the juice during the production of vinegar were monitored by gas chromatography and titrimetry methods, respectively. The physiological state of the yeast Saccharomyces cerevisiae L2056 was determined by flow cytometry using a dual fluorescent labeling of diacetate carboxy-fluorescein (CFDA) and propidium iodide. The results indicated that 200 mL of mango juice, sugar content 20 Brix, set in alcoholic fermentation with 10(6) yeast cells produced 22.4 g L(-1) ethanol in 72 h. Acetic fermentation transformed 93% of this ethanol to acetic acid in 288 h. Twenty-four hours after the beginning of alcoholic fermentation, 91% of cells were viable, 8.85% were stressed and 0.05% died. After 24 h of acetic fermentation, viable, stressed and dead cells were 45, 12 and 39%, respectively; corresponding to the passage of acetic vinegar level from 0.9 to 2.1 degrees. At the end of the acetic fermentation, dead cells were estimated to 98% at and acetic acid to 4.7 degrees. Using consecutive fermentations is suitable technique for vinegar production from mango juice. The application of the present results may contribute to avoid fruits post harvest losses.

  15. Stress Tolerance Profiling of a Collection of Extant Salt-Tolerant Rice Varieties and Transgenic Plants Overexpressing Abiotic Stress Tolerance Genes.

    PubMed

    Kurotani, Ken-ichi; Yamanaka, Kazumasa; Toda, Yosuke; Ogawa, Daisuke; Tanaka, Maiko; Kozawa, Hirotsugu; Nakamura, Hidemitsu; Hakata, Makoto; Ichikawa, Hiroaki; Hattori, Tsukaho; Takeda, Shin

    2015-10-01

    Environmental stress tolerance is an important trait for crop improvement. In recent decades, numerous genes that confer tolerance to abiotic stress such as salinity were reported. However, the levels of salt tolerance differ greatly depending on growth conditions, and mechanisms underlying the complicated nature of stress tolerance are far from being fully understood. In this study, we investigated the profiles of stress tolerance of nine salt-tolerant rice varieties and transgenic rice lines carrying constitutively expressed genes that are potentially involved in salt tolerance, by evaluating their growth and viability under salt, heat, ionic and hyperosmotic stress conditions. Profiling of the extant varieties and selected chromosome segment substitution lines showed that salt tolerance in a greenhouse condition was more tightly correlated with ionic stress tolerance than osmotic stresses. In Nona Bokra, one of the most salt-tolerant varieties, the contribution of the previously identified sodium transporter HKT1;5 to salt tolerance was fairly limited. In addition, Nona Bokra exhibited high tolerance to all the stresses imposed. More surprisingly, comparative evaluation of 74 stress tolerance genes revealed that the most striking effect to enhance salt tolerance was conferred by overexpressing CYP94C2b, which promotes deactivation of jasmonate. In contrast, genes encoding ABA signaling factors conferred multiple stress tolerance. Genes conferring tolerance to both heat and hyperosmotic stresses were preferentially linked to functional categories related to heat shock proteins, scavenging of reactive oxygen species and Ca(2+) signaling. These comparative profiling data provide a new basis for understanding the ability of plants to grow under harsh environmental conditions.

  16. Apoplasmic loading in the rice phloem supported by the presence of sucrose synthase and plasma membrane-localized proton pyrophosphatase

    PubMed Central

    Regmi, Kamesh C.; Zhang, Shangji; Gaxiola, Roberto A.

    2016-01-01

    Background and Aims Although Oryza sativa (rice) is one of the most important cereal crops, the mechanism by which sucrose, the major photosynthate, is loaded into its phloem is still a matter of debate. Current opinion holds that the phloem loading pathway in rice could involve either a symplasmic or an apoplasmic route. It was hypothesized, on the basis of a complementary body of evidence from arabidopsis, which is an apoplasmic loader, that the membrane specificity of proton pyrophosphatases (H+-PPases; OVPs) in the sieve element–companion cell (SE-CC) complexes of rice source leaves would support the existence of either of the aforementioned phloem loading mechanisms. Additionally, it was contended that the presence of sucrose synthase in the SE-CC complexes would be consistent with an apoplasmic sucrose loading route in rice. Methods Conventional chemical fixation methods were used for immunohistochemical localization of H+-PPases and sucrose synthase in rice and arabidopsis at the light microscopy level, while ultrastructural immunogold labelling of H+-PPases and sucrose synthase was performed on high-pressure frozen source leaves of rice. Key Results Using immunogold labelling, it was found that OVPs predominantly localize at the plasma membrane (PM) of the SE-CC complexes in rice source leaf minor veins, while in the root meristematic cells, OVPs preferentially localize at the vacuoles. The PM specificity of OPVs in the SE-CC complexes was deemed to support apoplasmic loading in the rice phloem. Further backing for this interpretation came from the sucrose synthase-specific immunogold labelling at the SE-CC complexes of rice source leaves. Conclusion These findings are consistent with the idea that, in the same way as in arabidopsis and a majority of grasses, sucrose is actively loaded into the SE-CC complexes of rice leaves using an apoplasmic step. PMID:26614751

  17. Characterization and subcellular localization of an RNA silencing suppressor encoded by Rice stripe tenuivirus

    SciTech Connect

    Xiong Ruyi; Wu Jianxiang; Zhou Yijun; Zhou Xueping

    2009-04-25

    Rice stripe virus (RSV) is a single-stranded (ss) RNA virus belonging to the genus Tenuivirus. RSV is present in many East Asian countries and causes severe diseases in rice fields, especially in China. In this study, we analyzed six proteins encoded by the virus for their abilities to suppress RNA silencing in plant using a green fluorescent protein (GFP)-based transient expression assay. Our results indicate that NS3 encoded by RSV RNA3, but not other five RSV encoded proteins, can strongly suppress local GFP silencing in agroinfiltrated Nicotiana benthamiana leaves. NS3 can reverse the GFP silencing, it can also prevent long distance spread of silencing signals which have been reported to be necessary for inducing systemic silencing in host plants. The NS3 protein can significantly reduce the levels of small interfering RNAs (siRNAs) in silencing cells, and was found to bind 21-nucleotide ss-siRNA, siRNA duplex and long ssRNA but not long double-stranded (ds)-RNA. Both N and C terminal of the NS3 protein are critical for silencing suppression, and mutation of the putative nuclear localization signal decreases its local silencing suppression efficiency and blocks its systemic silencing suppression. The NS3-GFP fusion protein and NS3 were shown to accumulate predominantly in nuclei of onion, tobacco and rice cells through transient expression assay or immunocytochemistry and electron microscopy. In addition, transgenic rice and tobacco plants expressing the NS3 did not show any apparent alteration in plant growth and morphology, although NS3 was proven to be a pathogenicity determinant in the PVX heterogenous system. Taken together, our results demonstrate that RSV NS3 is a suppressor of RNA silencing in planta, possibly through sequestering siRNA molecules generated in cells that are undergoing gene silencing.

  18. Tissue Localization of a Submergence-Induced 1-Aminocyclopropane-1-Carboxylic Acid Synthase in Rice1

    PubMed Central

    Zhou, Zhongyi; de Almeida Engler, Janice; Rouan, Dominique; Michiels, Frank; Van Montagu, Marc; Van Der Straeten, Dominique

    2002-01-01

    At least two 1-aminocyclopropane-1-carboxylic acid synthase genes (ACS) are implicated in the submergence response of rice (Oryza sativa). Previously, the OS-ACS5 gene has been shown to be induced during short- as well as long-term complete submergence of seedlings and to be controlled by a balance of gibberellin and abscisic acid in both lowland and deepwater rice. This study demonstrates that OS-ACS5 mRNA is localized in specific tissues and cells both during normal development and in response to complete submergence. The temporal and spatial regulation of OS-ACS5 expression is presented by in situ hybridization and histochemical analysis of β-glucuronidase (GUS) activity in transgenic rice carrying an OS-ACS5-gus fusion. Whole-mount in situ hybridization revealed that in air-grown rice seedlings, OS-ACS5 was expressed at a low level in the shoot apex, meristems, leaf, and adventitious root primordia, and in vascular tissues of nonelongated stems and leaf sheaths. In response to complete submergence, the expression in vascular bundles of young stems and leaf sheaths was strongly induced. The results of histochemical GUS assays were consistent with those found by whole-mount in situ hybridization. Our findings suggest that OS-ACS5 plays a role in vegetative growth of rice under normal conditions and is also recruited for enhanced growth upon complete submergence. The possible implication of OS-ACS5 in root-shoot communication during submergence stress and its putative role in aerenchyma formation upon low-oxygen stress are discussed. PMID:12011339

  19. RSLpred: an integrative system for predicting subcellular localization of rice proteins combining compositional and evolutionary information.

    PubMed

    Kaundal, Rakesh; Raghava, Gajendra P S

    2009-05-01

    The attainment of complete map-based sequence for rice (Oryza sativa) is clearly a major milestone for the research community. Identifying the localization of encoded proteins is the key to understanding their functional characteristics and facilitating their purification. Our proposed method, RSLpred, is an effort in this direction for genome-scale subcellular prediction of encoded rice proteins. First, the support vector machine (SVM)-based modules have been developed using traditional amino acid-, dipeptide- (i+1) and four parts-amino acid composition and achieved an overall accuracy of 81.43, 80.88 and 81.10%, respectively. Secondly, a similarity search-based module has been developed using position-specific iterated-basic local alignment search tool and achieved 68.35% accuracy. Another module developed using evolutionary information of a protein sequence extracted from position-specific scoring matrix achieved an accuracy of 87.10%. In this study, a large number of modules have been developed using various encoding schemes like higher-order dipeptide composition, N- and C-terminal, splitted amino acid composition and the hybrid information. In order to benchmark RSLpred, it was tested on an independent set of rice proteins where it outperformed widely used prediction methods such as TargetP, Wolf-PSORT, PA-SUB, Plant-Ploc and ESLpred. To assist the plant research community, an online web tool 'RSLpred' has been developed for subcellular prediction of query rice proteins, which is freely accessible at http://www.imtech.res.in/raghava/rslpred.

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

    PubMed

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

    2014-08-01

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

  1. Investigating the impact of rice blast disease on the livelihood of the local farmers in greater Mwea region of Kenya.

    PubMed

    Kihoro, Joseph; Bosco, Njoroge J; Murage, Hunja; Ateka, Elijah; Makihara, Daigo

    2013-12-01

    Rice is the most important cereal crop in Kenya coming third after maize and wheat. It forms a very important diet for a majority of families in Kenya. The demand for rice in Kenya has seen a dramatic increase over the last few years while production has remained low. This is because rice production has been faced by serious constraints notably plant diseases of which the most devastating is rice blast. Rice blast is known to cause approximately 60% -100% yield losses. It is caused by an Ascomycete fungus called Magnaporthe Oryzae. The aim of this study was to investigate the impact of rice blast disease on the livelihood of the local farmers in Greater Mwea region and develop a rice blast disease distribution map using GIS approach. The study methodology employed a questionnaire survey which were subjected to sample population of households in the 7 sections with 70 blocks within Mwea region. The collected data was analysed using SAS Version 9.1. Descriptive statistics were used to summarize the household characteristics, the farm characteristics and the farmers' perceptions of rice blast disease. In the questionnaire, farmers' response on whether they had been affected by rice blast disease and the total production per acreage was used to develop an attribute table with GPS points. The GPS points were interpolated to create a geographical distribution map of rice blast disease. From the research findings almost all the farmers' had awareness and knowledge of rice blast disease, 98% of the farmers interviewed were aware of rice blast disease. Out of the 98% with knowledge and awareness 76% have been affected by the disease, while 24% have never been affected. Farmers attributed rice blast disease to a range of different causes, including excessive use of nitrogen fertilizer, water shortage, lack of proper drainage canal and due to climate change. Majority of the farmers interviewed (72%) did not engage themselves in any other socio-economic activity even after

  2. Varieties of Organizational Learning: Investigating Learning in Local Level Public Sector Organizations

    ERIC Educational Resources Information Center

    Pokharel, Mohan P.; Hult, Karen M.

    2010-01-01

    Purpose: The purpose of this paper is to explore the learning dynamics in the local level public organizations due to a policy intervention in collaboration with university. This study aims to identify the existence of four different types of organizational learning in different localities and to explain their implications to public sector…

  3. Proteomic Analysis of Copper-Binding Proteins in Excess Copper-Stressed Roots of Two Rice (Oryza sativa L.) Varieties with Different Cu Tolerances

    PubMed Central

    Zhuang, Kai; Li, Lu; Xia, Yan; Shen, Zhenguo

    2015-01-01

    To better understand the mechanisms involved in the heavy metal stress response and tolerance in plants, a proteomic approach was used to investigate the differences in Cu-binding protein expression in Cu-tolerant and Cu-sensitive rice varieties. Cu-binding proteins from Cu-treated rice roots were separated using a new IMAC method in which an IDA-sepharose column was applied prior to the Cu-IMAC column to remove metal ions from protein samples. More than 300 protein spots were reproducibly detected in the 2D gel. Thirty-five protein spots exhibited changes greater than 1.5-fold in intensity compared to the control. Twenty-four proteins contained one or more of nine putative metal-binding motifs reported by Smith et al., and 19 proteins (spots) contained one to three of the top six motifs reported by Kung et al. The intensities of seven protein spots were increased in the Cu-tolerant variety B1139 compared to the Cu-sensitive variety B1195 (p<0.05) and six protein spots were markedly up-regulated in B1139, but not detectable in B1195. Four protein spots were significantly up-regulated in B1139, but unchanged in B1195 under Cu stress. In contrast, two protein spots were significantly down-regulated in B1195, but unchanged in B1139. These Cu-responsive proteins included those involved in antioxidant defense and detoxification (spots 5, 16, 21, 22, 28, 29 and 33), pathogenesis (spots 5, 16, 21, 22, 28, 29 and 33), regulation of gene transcription (spots 8 and 34), amino acid synthesis (spots 8 and 34), protein synthesis, modification, transport and degradation (spots 1, 2, 4, 10, 15, 19, 30, 31, 32 and 35), cell wall synthesis (spot 14), molecular signaling (spot 3), and salt stress (spots 7, 9 and 27); together with other proteins, such as a putative glyoxylate induced protein, proteins containing dimeric alpha-beta barrel domains, and adenosine kinase-like proteins. Our results suggest that these proteins, together with related physiological processes, play an

  4. Gel Sonovaginography: A New Way of Evaluating a Variety of Local Vaginal and Cervical Disorders.

    PubMed

    Sibal, Mala

    2016-12-01

    Gel sonovaginography is a new way of assessing local cervical and vaginal disorders, in which regular transvaginal sonography is known to have limitations. In gel sonovaginography, 20 mL of ultrasound gel is instilled into the vagina, followed by examination with a transvaginal transducer. In a study involving 28 women with known or suspected disorders such as cervical and vaginal cancer, cervical polyps, vaginal septa, and deep infiltrating endometriosis, a substantial improvement in visualization and assessment of local lesions and structures was noted with gel sonovaginography. This simple technique appears to be valuable for accurate diagnosis of local cervical and vaginal disorders.

  5. Genome-wide DNA polymorphism in the indica rice varieties RGD-7S and Taifeng B as revealed by whole genome re-sequencing.

    PubMed

    Fu, Chong-Yun; Liu, Wu-Ge; Liu, Di-Lin; Li, Ji-Hua; Zhu, Man-Shan; Liao, Yi-Long; Liu, Zhen-Rong; Zeng, Xue-Qin; Wang, Feng

    2016-03-01

    Next-generation sequencing technologies provide opportunities to further understand genetic variation, even within closely related cultivars. We performed whole genome resequencing of two elite indica rice varieties, RGD-7S and Taifeng B, whose F1 progeny showed hybrid weakness and hybrid vigor when grown in the early- and late-cropping seasons, respectively. Approximately 150 million 100-bp pair-end reads were generated, which covered ∼86% of the rice (Oryza sativa L. japonica 'Nipponbare') reference genome. A total of 2,758,740 polymorphic sites including 2,408,845 SNPs and 349,895 InDels were detected in RGD-7S and Taifeng B, respectively. Applying stringent parameters, we identified 961,791 SNPs and 46,640 InDels between RGD-7S and Taifeng B (RGD-7S/Taifeng B). The density of DNA polymorphisms was 256.8 SNPs and 12.5 InDels per 100 kb for RGD-7S/Taifeng B. Copy number variations (CNVs) were also investigated. In RGD-7S, 1989 of 2727 CNVs were overlapped in 218 genes, and 1231 of 2010 CNVs were annotated in 175 genes in Taifeng B. In addition, we verified a subset of InDels in the interval of hybrid weakness genes, Hw3 and Hw4, and obtained some polymorphic InDel markers, which will provide a sound foundation for cloning hybrid weakness genes. Analysis of genomic variations will also contribute to understanding the genetic basis of hybrid weakness and heterosis.

  6. Cellular localization and kinetics of the rice melatonin biosynthetic enzymes SNAT and ASMT.

    PubMed

    Byeon, Yeong; Lee, Hyoung Yool; Lee, Kyungjin; Park, Sangkyu; Back, Kyoungwhan

    2014-01-01

    Serotonin N-acetyltransferase (SNAT) and N-acetylserotonin methyltransferase (ASMT) are the final two enzymes in the melatonin synthesis pathway in plants. Although their corresponding genes have been cloned, their cellular localization and enzymatic characteristics are unknown. Using confocal microscopy, we showed that SNAT protein is localized in chloroplasts, whereas ASMT is expressed in the cytoplasm. In vitro measurement of ASMT enzyme activity revealed a peak of activity in roots, but SNAT enzyme activity was not detected in any plant tissues. This may be attributed in part to an effect of chlorophyll because SNAT enzyme activity was greatly inhibited by chlorophyll in a dose-dependent manner. Because the SNAT protein of cyanobacteria is thermophilic, we examined the effect of temperature on the activity of the rice SNAT and ASMT enzymes. Purified recombinant rice SNAT and ASMT enzymes had an optimum temperature for activity of 55°C. The Km and Vmax values for SNAT at 55°C were 270 μm and 3.3 nmol/min/mg protein, whereas the Km and Vmax for ASMT were 222 μm and 9 nmol/min/mg protein, respectively. The catalytic efficiency (Vmax /Km ) values of SNAT and ASMT were 16-fold and 4054-fold higher at 55°C than at 30°C suggestive of increased melatonin production at high temperature in plants.

  7. Distribution, management and diversity of yam local varieties in Brazil: a study on Dioscorea alata L.

    PubMed

    Siqueira, M V B M; Nascimento, W F; Silva, L R G; Ferreira, A B; Silva, E F; Ming, L C; Veasey, E A

    2014-02-01

    Widely spread in the tropics, yams were introduced into Brazil during the colonial period and are currently grown throughout the country. Despite its importance as a pharmacological and food source, there is a lack of studies describing how and where this tuber is grown in Brazil. The aim of this study was to provide an overview of the cultivation and distribution of Dioscorea alata in different Brazilian regions. A total of 63 farmers were visited in different municipalities and communities in four regions in the country: South, Southeast, Northeast and Midwest. Semi-structured interviews were conducted to collect socio-economic, use, management and diversity data for this crop. The majority of interviewers were men, married, with children, using retirement benefits and agriculture as income and family labour as the main support in the yam cultivation. A wide distribution of this species was found, with the occurrence of D. alata in the four sampled regions. A variety of vernacular names for this species was collected, differing according to the region where it is cultivated. Most farmers cultivate yams in fields, however an increased usage of home gardens for the cultivation of this tuber was found. Also, most farmers cultivate yams in association with other crops in areas of different sizes and slash and burn practices, although mostly disappearing, are still being used by many farmers. The results of this study provide more concrete data on the distribution and diversity of this important crop.

  8. Expression of a betaine aldehyde dehydrogenase gene in rice, a glycinebetaine nonaccumulator, and possible localization of its protein in peroxisomes.

    PubMed

    Nakamura, T; Yokota, S; Muramoto, Y; Tsutsui, K; Oguri, Y; Fukui, K; Takabe, T

    1997-05-01

    Betaine aldehyde dehydrogenase (BADH) catalyzes the last step in the plant biosynthetic pathway that leads to glycinebetaine. Rice plants (Oryza sativa L.), albeit considered a typical non-glycinebetaine accumulating species, have been found to express this enzyme at low levels. This observation evokes an interest in phylogenic evolution of the enzyme in the plant kingdom. It is reported here that rice plants possess the ability to take up exogenously added betaine aldehyde through the roots and convert it to glycinebetaine, resulting in an enhanced salt-tolerance of the plants. A gene encoding a putative BADH from the rice genome was also cloned and sequenced. The gene was found to contain 14 introns, and the overall nucleotide sequence of the coding region is c. 78% identical to that of the barley BADH cDNA. Cloning of a partial BADH cDNA from rice was accomplished by reverse transcription-polymerase chain reaction (RT-PCR). The nucleotide sequence of the cloned fragment was found to be identical to the corresponding exon regions of the rice genomic BADH gene. The deduced amino acid sequences of rice and barley BADH both contain a C-terminal tripeptide SKL, a signal known to target preproteins to microbodies. This localization was confirmed by an immuno-gold labeling study of transgenic tobacco harboring barley cDNA, which showed BADH protein inside peroxisomes. Northern blot analysis revealed that the level of BADH mRNA is salt-inducible.

  9. Fungal isolates and metabolites in locally processed rice from five agro-ecological zones of Nigeria.

    PubMed

    Abdus-Salaam, Rofiat; Atanda, Olusegun; Fanelli, Francesca; Sulyok, Micheal; Cozzi, Giuseppe; Bavaro, Simona; Krska, Rudolf; Logrieco, Antonio F; Ezekiel, Chibundu N; Salami, Waheed A

    2016-12-01

    This study reports the distribution of fungal isolates and fungal metabolites that naturally contaminate locally processed rice from five agro-ecological zones of Nigeria. The fungal species were isolated by the dilution plate technique and identified by appropriate diagnostics, while metabolites were determined by a liquid chromatographic tandem mass spectrometric method. Aspergillus and Penicillium species were the predominant isolates found in the rice samples while Fusarium spp. were not isolated. The mean fungal count differed significantly (p < 0.05) across the zones and ranged from 9.98 × 10(2) cfu g(-1) in the Southern Guinea Savannah to 96.97 × 10(2) cfu g(-1) in the Derived Savannah. For 16 fungal metabolites, selected from 63 positively identified fungal metabolites based on their concentration and spread across the zones, an occurrence map was constructed. The Northern Guinea Savannah recorded the highest contamination of fungal metabolites while the Sudan Savannah zone recorded the least.

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

    PubMed

    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.

  11. Metaproteomic Identification of Diazotrophic Methanotrophs and Their Localization in Root Tissues of Field-Grown Rice Plants

    PubMed Central

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

    2014-01-01

    In a previous study by our group, CH4 oxidation and N2 fixation were simultaneously activated in the roots of wild-type rice plants in a paddy field with no N input; both processes are likely controlled by a rice gene for microbial symbiosis. The present study examined which microorganisms in rice roots were responsible for CH4 oxidation and N2 fixation under the field conditions. Metaproteomic analysis of root-associated bacteria from field-grown rice (Oryza sativa Nipponbare) revealed that nitrogenase complex-containing nitrogenase reductase (NifH) and the alpha subunit (NifD) and beta subunit (NifK) of dinitrogenase were mainly derived from type II methanotrophic bacteria of the family Methylocystaceae, including Methylosinus spp. Minor nitrogenase proteins such as Methylocella, Bradyrhizobium, Rhodopseudomonas, and Anaeromyxobacter were also detected. Methane monooxygenase proteins (PmoCBA and MmoXYZCBG) were detected in the same bacterial group of the Methylocystaceae. Because these results indicated that Methylocystaceae members mediate both CH4 oxidation and N2 fixation, we examined their localization in rice tissues by using catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH). The methanotrophs were localized around the epidermal cells and vascular cylinder in the root tissues of the field-grown rice plants. Our metaproteomics and CARD-FISH results suggest that CH4 oxidation and N2 fixation are performed mainly by type II methanotrophs of the Methylocystaceae, including Methylosinus spp., inhabiting the vascular bundles and epidermal cells of rice roots. PMID:24928870

  12. Prevalence, isolation and characterization of Bacillus cereus strains from rice of local cultivators of Sabah, Sarawak, and Peninsular Malaysia

    NASA Astrophysics Data System (ADS)

    Sawei, Jelin; Sani, Norrakiah Abdullah

    2016-11-01

    Bacillus cereus is a spore-forming, facultative anaerobic, motile microorganism that has been identified as a causative agent of two types of gastrointestinal diseases such as emetic and diarrhea. This foodborne pathogen is found in both vegetative cells and endospores form in foods such as rice either raw or cooked. The aim of this study is to investigate and determine the prevalence, characterize and identify the isolation of vegetative cells and endospores of B. cereus in thirty varieties (n=3) of raw rice from Sabah, Sarawak and Peninsular Malaysia. A total of 90 (n=90) raw rice were examined and 84 (93.33%) samples were positive to vegetative cells of B. cereus. However, only 32 (35.56%) samples were positive for endospore cells that able to germinate after samples were heated at 75°C for 15 mins. The mean log cfu/g for vegetative cells were higher range (0.00 - 4.1533) than visible endospores (0.00 - 3.7533 mean log cfu/g). Sample of raw red rice (UKMRC9) had significantly higher contamination by both vegetative cells and endospores at p<0.05, than the other raw rice samples.

  13. Localization and speciation of arsenic and trace elements in rice tissues

    SciTech Connect

    Smith, Euan; Kempson, Ivan; Juhasz, Albert L.; Weber, John; Skinner, William M.; Gräfe, Markus

    2009-09-14

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

  14. Newly identified CSP41b gene localized in chloroplasts affects leaf color in rice.

    PubMed

    Mei, Jiasong; Li, Feifei; Liu, Xuri; Hu, Guocheng; Fu, Yaping; Liu, Wenzhen

    2017-03-01

    A rice mutant with light-green leaves was discovered from a transgenic line of Oryza sativa. The mutant has reduced chlorophyll content and abnormal chloroplast morphology throughout its life cycle. Genetic analysis revealed that a single nuclear-encoded recessive gene is responsible for the mutation, here designated as lgl1. To isolate the lgl1 gene, a high-resolution physical map of the chromosomal region around the lgl1 gene was made using a mapping population consisting of 1984 mutant individuals. The lgl1 gene was mapped in the 76.5kb region between marker YG4 and marker YG5 on chromosome 12. Sequence analysis revealed that there was a 39bp deletion within the fourth exon of the candidate gene Os12g0420200 (TIGR locus Os12g23180) encoding a chloroplast stem-loop-binding protein of 41kDa b (CSP41b). The lgl1 mutation was rescued by transformation with the wild type CSP41b gene. Accordingly, the CSP41b gene is identified as the LGL1 gene. CSP41b was transcribed in various tissues and was mainly expressed in leaves. Expression of CSP41b-GFP fusion protein indicated that CSP41b is localized in chloroplasts. The expression levels of some key genes involved in chlorophyll biosynthesis and photosynthesis, such as ChlD, ChlI, Hema1, Ygl1, POR, Cab1R, Cab2R, PsaA, and rbcL, was significantly changed in the lgl1 mutant. Our results demonstrate that CSP41b is a novel gene required for normal leaf color and chloroplast morphology in rice.

  15. Stress-Responsive Expression, Subcellular Localization and Protein-Protein Interactions of the Rice Metacaspase Family.

    PubMed

    Huang, Lei; Zhang, Huijuan; Hong, Yongbo; Liu, Shixia; Li, Dayong; Song, Fengming

    2015-07-17

    Metacaspases, a class of cysteine-dependent proteases like caspases in animals, are important regulators of programmed cell death (PCD) during development and stress responses in plants. The present study was focused on comprehensive analyses of expression patterns of the rice metacaspase (OsMC) genes in response to abiotic and biotic stresses and stress-related hormones. Results indicate that members of the OsMC family displayed differential expression patterns in response to abiotic (e.g., drought, salt, cold, and heat) and biotic (e.g., infection by Magnaporthe oryzae, Xanthomonas oryzae pv. oryzae and Rhizoctonia solani) stresses and stress-related hormones such as abscisic acid, salicylic acid, jasmonic acid, and 1-amino cyclopropane-1-carboxylic acid (a precursor of ethylene), although the responsiveness to these stresses or hormones varies to some extent. Subcellular localization analyses revealed that OsMC1 was solely localized and OsMC2 was mainly localized in the nucleus. Whereas OsMC3, OsMC4, and OsMC7 were evenly distributed in the cells, OsMC5, OsMC6, and OsMC8 were localized in cytoplasm. OsMC1 interacted with OsLSD1 and OsLSD3 while OsMC3 only interacted with OsLSD1 and that the zinc finger domain in OsMC1 is responsible for the interaction activity. The systematic expression and biochemical analyses of the OsMC family provide valuable information for further functional studies on the biological roles of OsMCs in PCD that is related to abiotic and biotic stress responses.

  16. Effect of gamma irradiation on physicochemical, functional and pasting properties of some locally-produced rice (Oryza spp) cultivars in Ghana

    NASA Astrophysics Data System (ADS)

    Ocloo, Fidelis C. K.; Owureku-Asare, Mavis; Agyei-Amponsah, Joyce; Agbemavor, Wisdom S. K.; Egblewogbe, Martin N. Y. H.; Apea-Bah, Franklin B.; Sarfo, Adjoa; Apatey, John; Doku, Henry; Ofori-Appiah, Dora; Ayeh, Ernestina

    2017-01-01

    Rice (Oryza sativa L.) is a staple crop in Ghana and much of West Africa, where it serves as an important convenience food for urban consumers. The objective of this study was to determine the effect of gamma irradiation as insect disinfestation technique on some physicochemical, functional and pasting properties of selected locally-produced rice cultivars in Ghana. Four local rice cultivars and an imported (commercial) type were purchased, cleaned and irradiated at doses of 0.0, 0.25, 0.50, 0.75, 1.0 and 1.5 kGy. The irradiated rice cultivars were milled and their physicochemical, functional and pasting properties determined. There were reductions in pH and swelling power, as well as increase in solubility of rice cultivars after gamma irradiation. Gamma irradiation did not change the XRD pattern of the rice cultivars. Gamma irradiation significantly (P<0.05) decreased peak time for BAL and VNT rice cultivars. Gamma irradiation significantly (P<0.05) decreased PV, HPV, BDV, FV and SBV for all the rice cultivars. This study shows that flours from gamma irradiated rice cultivars have potential in food formulations that require low viscosity.

  17. A set of GFP-based organelle marker lines combined with DsRed-based gateway vectors for subcellular localization study in rice (Oryza sativa L.).

    PubMed

    Wu, Tsung-Meng; Lin, Ke-Chun; Liau, Wei-Shiang; Chao, Yun-Yang; Yang, Ling-Hung; Chen, Szu-Yun; Lu, Chung-An; Hong, Chwan-Yang

    2016-01-01

    In the post-genomic era, many useful tools have been developed to accelerate the investigation of gene functions. Fluorescent proteins have been widely used as protein tags for studying the subcellular localization of proteins in plants. Several fluorescent organelle marker lines have been generated in dicot plants; however, useful and reliable fluorescent organelle marker lines are lacking in the monocot model rice. Here, we developed eight different GFP-based organelle markers in transgenic rice and created a set of DsRed-based gateway vectors for combining with the marker lines. Two mitochondrial-localized rice ascorbate peroxidase genes fused to DsRed and successfully co-localized with mitochondrial-targeted marker lines verified the practical use of this system. The co-localization of GFP-fusion marker lines and DsRed-fusion proteins provide a convenient platform for in vivo or in vitro analysis of subcellular localization of rice proteins.

  18. Speciation And Localization Of Arsenic In White And Brown Rice Grains

    EPA Science Inventory

    Synchrotron-based X-ray fluorescence (S-XRF) was utilized to locate arsenic (As) in polished (white) and unpolished (brown) rice grains from the United States, China, and Bangladesh. In white rice As was generally dispersed throughout the grain, the bulk of which constitutes the...

  19. Delivering golden rice to developing countries.

    PubMed

    Mayer, Jorge E

    2007-01-01

    Micronutrient deficiencies create a vicious circle of malnutrition, poverty, and economic dependency that we must strive to break. Golden Rice offers a sustainable solution to reduce the prevalence of vitamin A deficiency-related diseases and mortality, a problem that affects the health of millions of children in all developing countries. The technology is based on the reconstitution of the carotenoid biosynthetic pathway by addition of 2 transgenes. The outcome of this high-tech approach will be provided to end users as nutrient-dense rice varieties that are agronomically identical to their own, locally adapted varieties. This intervention has the potential to reach remote rural populations without access to fortification and supplementation programs. As part of our delivery strategy, we are partnering with government and nongovernment, national and international agricultural institutions to navigate through cumbersome and expensive regulatory regimes that affect the release of genetically modified crops, and to create local demand for the biofortified rice varieties.

  20. Crystal structure of rice importin-α and structural basis of its interaction with plant-specific nuclear localization signals.

    PubMed

    Chang, Chiung-Wen; Couñago, Rafael Lemos Miguez; Williams, Simon J; Bodén, Mikael; Kobe, Boštjan

    2012-12-01

    In the classical nucleocytoplasmic import pathway, nuclear localization signals (NLSs) in cargo proteins are recognized by the import receptor importin-α. Importin-α has two separate NLS binding sites (the major and the minor site), both of which recognize positively charged amino acid clusters in NLSs. Little is known about the molecular basis of the unique features of the classical nuclear import pathway in plants. We determined the crystal structure of rice (Oryza sativa) importin-α1a at 2-Å resolution. The structure reveals that the autoinhibitory mechanism mediated by the importin-β binding domain of importin-α operates in plants, with NLS-mimicking sequences binding to both minor and major NLS binding sites. Consistent with yeast and mammalian proteins, rice importin-α binds the prototypical NLS from simian virus 40 large T-antigen preferentially at the major NLS binding site. We show that two NLSs, previously described as plant specific, bind to and are functional with plant, mammalian, and yeast importin-α proteins but interact with rice importin-α more strongly. The crystal structures of their complexes with rice importin-α show that they bind to the minor NLS binding site. By contrast, the crystal structures of their complexes with mouse (Mus musculus) importin-α show preferential binding to the major NLS binding site. Our results reveal the molecular basis of a number of features of the classical nuclear transport pathway specific to plants.

  1. Detection of Transgenes in Local Maize Varieties of Small-Scale Farmers in Eastern Cape, South Africa

    PubMed Central

    Iversen, Marianne; Grønsberg, Idun M.; van den Berg, Johnnie; Fischer, Klara; Aheto, Denis Worlanyo; Bøhn, Thomas

    2014-01-01

    Small-scale subsistence farmers in South Africa have been introduced to genetically modified (GM) crops for more than a decade. Little is known about i) the extent of transgene introgression into locally recycled seed, ii) what short and long-term ecological and socioeconomic impacts such mixing of seeds might have, iii) how the farmers perceive GM crops, and iv) to what degree approval conditions are followed and controlled. This study conducted in the Eastern Cape, South Africa, aims primarily at addressing the first of these issues. We analysed for transgenes in 796 individual maize plants (leaves) and 20 seed batches collected in a village where GM insect resistant maize was previously promoted and grown as part of an governmental agricultural development program over a seven year period (2001–2008). Additionally, we surveyed the varieties of maize grown and the farmers’ practices of recycling and sharing of seed in the same community (26 farmers were interviewed). Recycling and sharing of seeds were common in the community and may contribute to spread and persistence of transgenes in maize on a local or regional level. By analysing DNA we found that the commonly used transgene promoter p35s occurred in one of the 796 leaf samples (0.0013%) and in five of the 20 seed samples (25%). Three of the 20 seed samples (15%) included herbicide tolerant maize (NK603) intentionally grown by the farmers from seed bought from local seed retailers or acquired through a currently running agricultural development program. The two remaining positive seed samples (10%) included genes for insect resistance (from MON810). In both cases the farmers were unaware of the transgenes present. In conclusion, we demonstrate that transgenes are mixed into seed storages of small-scale farming communities where recycling and sharing of seeds are common, i.e. spread beyond the control of the formal seed system. PMID:25551616

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

    PubMed

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

    2013-12-01

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

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

    PubMed Central

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

    2013-01-01

    Omics research in Oryza sativa (rice) relies on the use of multiple databases to obtain different types of information to define gene function. We present Rice DB, an Oryza information portal that is a functional genomics database, linking gene loci to comprehensive annotations, expression data and the subcellular location of encoded proteins. Rice DB has been designed to integrate the direct comparison of rice with Arabidopsis (Arabidopsis thaliana), based on orthology or ‘expressology’, thus using and combining available information from two pre-eminent plant models. To establish Rice DB, gene identifiers (more than 40 types) and annotations from a variety of sources were compiled, functional information based on large-scale and individual studies was manually collated, hundreds of microarrays were analysed to generate expression annotations, and the occurrences of potential functional regulatory motifs in promoter regions were calculated. A range of computational subcellular localization predictions were also run for all putative proteins encoded in the rice genome, and experimentally confirmed protein localizations have been collated, curated and linked to functional studies in rice. A single search box allows anything from gene identifiers (for rice and/or Arabidopsis), motif sequences, subcellular location, to keyword searches to be entered, with the capability of Boolean searches (such as AND/OR). To demonstrate the utility of Rice DB, several examples are presented including a rice mitochondrial proteome, which draws on a variety of sources for subcellular location data within Rice DB. Comparisons of subcellular location, functional annotations, as well as transcript expression in parallel with Arabidopsis reveals examples of conservation between rice and Arabidopsis, using Rice DB (http://ricedb.plantenergy.uwa.edu.au). PMID:24147765

  4. Assessing Weather-Yield Relationships in Rice at Local Scale Using Data Mining Approaches.

    PubMed

    Delerce, Sylvain; Dorado, Hugo; Grillon, Alexandre; Rebolledo, Maria Camila; Prager, Steven D; Patiño, Victor Hugo; Garcés Varón, Gabriel; Jiménez, Daniel

    2016-01-01

    Seasonal and inter-annual climate variability have become important issues for farmers, and climate change has been shown to increase them. Simultaneously farmers and agricultural organizations are increasingly collecting observational data about in situ crop performance. Agriculture thus needs new tools to cope with changing environmental conditions and to take advantage of these data. Data mining techniques make it possible to extract embedded knowledge associated with farmer experiences from these large observational datasets in order to identify best practices for adapting to climate variability. We introduce new approaches through a case study on irrigated and rainfed rice in Colombia. Preexisting observational datasets of commercial harvest records were combined with in situ daily weather series. Using Conditional Inference Forest and clustering techniques, we assessed the relationships between climatic factors and crop yield variability at the local scale for specific cultivars and growth stages. The analysis showed clear relationships in the various location-cultivar combinations, with climatic factors explaining 6 to 46% of spatiotemporal variability in yield, and with crop responses to weather being non-linear and cultivar-specific. Climatic factors affected cultivars differently during each stage of development. For instance, one cultivar was affected by high nighttime temperatures in the reproductive stage but responded positively to accumulated solar radiation during the ripening stage. Another was affected by high nighttime temperatures during both the vegetative and reproductive stages. Clustering of the weather patterns corresponding to individual cropping events revealed different groups of weather patterns for irrigated and rainfed systems with contrasting yield levels. Best-suited cultivars were identified for some weather patterns, making weather-site-specific recommendations possible. This study illustrates the potential of data mining for

  5. Assessing Weather-Yield Relationships in Rice at Local Scale Using Data Mining Approaches

    PubMed Central

    Delerce, Sylvain; Dorado, Hugo; Grillon, Alexandre; Rebolledo, Maria Camila; Prager, Steven D.; Patiño, Victor Hugo; Garcés Varón, Gabriel; Jiménez, Daniel

    2016-01-01

    Seasonal and inter-annual climate variability have become important issues for farmers, and climate change has been shown to increase them. Simultaneously farmers and agricultural organizations are increasingly collecting observational data about in situ crop performance. Agriculture thus needs new tools to cope with changing environmental conditions and to take advantage of these data. Data mining techniques make it possible to extract embedded knowledge associated with farmer experiences from these large observational datasets in order to identify best practices for adapting to climate variability. We introduce new approaches through a case study on irrigated and rainfed rice in Colombia. Preexisting observational datasets of commercial harvest records were combined with in situ daily weather series. Using Conditional Inference Forest and clustering techniques, we assessed the relationships between climatic factors and crop yield variability at the local scale for specific cultivars and growth stages. The analysis showed clear relationships in the various location-cultivar combinations, with climatic factors explaining 6 to 46% of spatiotemporal variability in yield, and with crop responses to weather being non-linear and cultivar-specific. Climatic factors affected cultivars differently during each stage of development. For instance, one cultivar was affected by high nighttime temperatures in the reproductive stage but responded positively to accumulated solar radiation during the ripening stage. Another was affected by high nighttime temperatures during both the vegetative and reproductive stages. Clustering of the weather patterns corresponding to individual cropping events revealed different groups of weather patterns for irrigated and rainfed systems with contrasting yield levels. Best-suited cultivars were identified for some weather patterns, making weather-site-specific recommendations possible. This study illustrates the potential of data mining for

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed

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

    2014-01-01

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

  8. Genome-Wide Transcriptome Analysis During Anthesis Reveals New Insights into the Molecular Basis of Heat Stress Responses in Tolerant and Sensitive Rice Varieties.

    PubMed

    González-Schain, Nahuel; Dreni, Ludovico; Lawas, Lovely M F; Galbiati, Massimo; Colombo, Lucia; Heuer, Sigrid; Jagadish, Krishna S V; Kater, Martin M

    2016-01-01

    Rice is one of the main food crops in the world. In the near future, yield is expected to be under pressure due to unfavorable climatic conditions, such as increasing temperatures. Therefore, improving rice germplasm in order to guarantee rice production under harsh environmental conditions is of top priority. Although many physiological studies have contributed to understanding heat responses during anthesis, the most heat-sensitive stage, molecular data are still largely lacking. In this study, an RNA-sequencing approach of heat- and control-treated reproductive tissues during anthesis was carried out using N22, one of the most heat-tolerant rice cultivars known to date. This analysis revealed that expression of genes encoding a number of transcription factor families, together with signal transduction and metabolic pathway genes, is repressed. On the other hand, expression of genes encoding heat shock factors and heat shock proteins was highly activated. Many of these genes are predominantly expressed at late stages of anther development. Further physiological experiments using heat-tolerant N22 and two sensitive cultivars suggest that reduced yield in heat-sensitive plants may be associated with poor pollen development or production in anthers prior to anthesis. In parallel, induction levels of a set of heat-responsive genes in these tissues correlated well with heat tolerance. Altogether, these findings suggest that proper expression of protective chaperones in anthers is needed before anthesis to overcome stress damage and to ensure fertilization. Genes putatively controlling this process were identified and are valuable candidates to consider for molecular breeding of highly productive heat-tolerant cultivars.

  9. A map of rice genome variation reveals the origin of cultivated rice.

    PubMed

    Huang, Xuehui; Kurata, Nori; Wei, Xinghua; Wang, Zi-Xuan; Wang, Ahong; Zhao, Qiang; Zhao, Yan; Liu, Kunyan; Lu, Hengyun; Li, Wenjun; Guo, Yunli; Lu, Yiqi; Zhou, Congcong; Fan, Danlin; Weng, Qijun; Zhu, Chuanrang; Huang, Tao; Zhang, Lei; Wang, Yongchun; Feng, Lei; Furuumi, Hiroyasu; Kubo, Takahiko; Miyabayashi, Toshie; Yuan, Xiaoping; Xu, Qun; Dong, Guojun; Zhan, Qilin; Li, Canyang; Fujiyama, Asao; Toyoda, Atsushi; Lu, Tingting; Feng, Qi; Qian, Qian; Li, Jiayang; Han, Bin

    2012-10-25

    Crop domestications are long-term selection experiments that have greatly advanced human civilization. The domestication of cultivated rice (Oryza sativa L.) ranks as one of the most important developments in history. However, its origins and domestication processes are controversial and have long been debated. Here we generate genome sequences from 446 geographically diverse accessions of the wild rice species Oryza rufipogon, the immediate ancestral progenitor of cultivated rice, and from 1,083 cultivated indica and japonica varieties to construct a comprehensive map of rice genome variation. In the search for signatures of selection, we identify 55 selective sweeps that have occurred during domestication. In-depth analyses of the domestication sweeps and genome-wide patterns reveal that Oryza sativa japonica rice was first domesticated from a specific population of O. rufipogon around the middle area of the Pearl River in southern China, and that Oryza sativa indica rice was subsequently developed from crosses between japonica rice and local wild rice as the initial cultivars spread into South East and South Asia. The domestication-associated traits are analysed through high-resolution genetic mapping. This study provides an important resource for rice breeding and an effective genomics approach for crop domestication research.

  10. Rice ( Oryza) hemoglobins

    PubMed Central

    Arredondo-Peter, Raúl; Moran, Jose F.; Sarath, Gautam

    2014-01-01

    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 single copy of the thb gene exist in Oryza sativa var. indica and O. sativa var. japonica, Hb transcripts coexist in rice organs and Hb polypeptides exist in rice embryonic and vegetative organs and in the cytoplasm of differentiating cells. At the structural level, the crystal structure of rice Hb1 has been elucidated, and the structures of the other rice Hbs have been modeled. Kinetic analysis indicated that rice Hb1 and 2, and possibly rice Hb3 and 4, exhibit a very high affinity for O 2, whereas rice Hb5 and tHb possibly exhibit a low to moderate affinity for O 2. Based on the accumulated information on the properties of rice Hbs and data from the analysis of other plant and non-plant Hbs, it is likely that Hbs play a variety of roles in rice organs, including O 2-transport, O 2-sensing, NO-scavenging and redox-signaling. From an evolutionary perspective, an outline for the evolution of rice Hbs is available. Rice nshb and thb genes vertically evolved through different lineages, rice nsHbs evolved into clade I and clade II lineages and rice nshbs and thbs evolved under the effect of neutral selection. This review also reveals lacunae in our ability to completely understand rice Hbs. Primary lacunae are the absence of experimental information about the precise functions of rice Hbs, the properties of modeled rice Hbs and the cis-elements and trans-acting factors that regulate the expression of rice hb genes, and the partial understanding of the evolution of rice Hbs. PMID:25653837

  11. Rice ( Oryza) hemoglobins.

    PubMed

    Arredondo-Peter, Raúl; Moran, Jose F; Sarath, Gautam

    2014-01-01

    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 single copy of the thb gene exist in Oryza sativa var. indica and O. sativa var. japonica, Hb transcripts coexist in rice organs and Hb polypeptides exist in rice embryonic and vegetative organs and in the cytoplasm of differentiating cells. At the structural level, the crystal structure of rice Hb1 has been elucidated, and the structures of the other rice Hbs have been modeled. Kinetic analysis indicated that rice Hb1 and 2, and possibly rice Hb3 and 4, exhibit a very high affinity for O 2, whereas rice Hb5 and tHb possibly exhibit a low to moderate affinity for O 2. Based on the accumulated information on the properties of rice Hbs and data from the analysis of other plant and non-plant Hbs, it is likely that Hbs play a variety of roles in rice organs, including O 2-transport, O 2-sensing, NO-scavenging and redox-signaling. From an evolutionary perspective, an outline for the evolution of rice Hbs is available. Rice nshb and thb genes vertically evolved through different lineages, rice nsHbs evolved into clade I and clade II lineages and rice nshbs and thbs evolved under the effect of neutral selection. This review also reveals lacunae in our ability to completely understand rice Hbs. Primary lacunae are the absence of experimental information about the precise functions of rice Hbs, the properties of modeled rice Hbs and the cis-elements and trans-acting factors that regulate the expression of rice hb genes, and the partial understanding of the evolution of rice Hbs.

  12. Fungal and bacterial metabolites associated with natural contamination of locally processed rice (Oryza sativa L.) in Nigeria.

    PubMed

    Rofiat, Abdus-Salaam; Fanelli, Francesca; Atanda, Olusegun; Sulyok, Michael; Cozzi, Giuseppe; Bavaro, Simona; Krska, Rudolf; Logrieco, Antonio F; Ezekiel, Chibundu N

    2015-01-01

    This study reports the fungal and bacterial metabolites associated with natural contamination of 38 composite samples of locally processed rice from five agro-ecological zones of Nigeria (AEZs). The samples were evaluated for the presence of microbial metabolites by LC-MS/MS. Among the identified metabolites, 63 fungal and 5 bacterial metabolites were measured at varying concentrations and occurrence levels. Fusarium toxins had the highest incidence of 79%, but occurred in low amounts with fumonisin B1 (FB1) having the highest percentage incidence of 39.5% and a mean of 18.5 µg/kg. Among the Aspergillus toxins, aflatoxins (AFs) occurred in 36.9% of the rice samples, with aflatoxin B1 (AFB1) having the highest occurrence level of 18.4% and a mean value of 5 µg/kg. About 12 metabolites had incidence levels > 50%, including beauvericin (BEA) and tryptophol, which had occurrence levels of 100%. Among the emerging toxins under evaluation by international organisations such as the European Food Safety Authority (EFSA) and the Food and Agriculture Organisation of the United Nations (FAO), citrinin, sterigmatocystin (STER) and beauvericin were detected with maximum values of 207, 125 and 131 μg/kg, respectively. This paper also reports the first documented evidence of the contamination of Nigerian rice by bacterial and Alternaria metabolites, nivalenol, kojic acid, STER, moniliformin, fusaric acid, fumonisin B3, citrinin, 3-nitropropionic acid, andrastin A, cytochalasins, emodin and physicon.

  13. Preparation and characterization of lidocaine rice gel for oral application.

    PubMed

    Okonogi, Siriporn; Kaewpinta, Adchareeya; Yotsawimonwat, Songwut; Khongkhunthian, Sakornrat

    2015-12-01

    The objective of the present study was to prepare buccal anesthetic gels using rice as gelling agent. Rice grains of four rice varieties, Jasmine (JM), Saohai (SH), Homnil (HN), and Doisket (DS) were chemically modified. Buccal rice gels, containing lidocaine hydrochloride as local anesthetic drug were formulated using the respective modified rice varieties. The gels were evaluated for outer appearance, pH, color, gel strength, foaming property, adhesion, in vitro drug release and in vivo efficacy. It was found that the developed rice gels possessed good texture. Rice varieties showed influence on gel strength, color, turbidity, adhesive property, release property, and anesthetic efficacy. JM gel showed the lowest turbidity with light transmission of 86.76 ± 1.18% whereas SH gel showed the highest gel strength of 208.78 ± 10.42 g/cm(2). Lidocaine hydrochloride can cause a decrease in pH and adhesive property but an increase in turbidity of the gels. In vitro drug release profile within 60 min of lidocaine SH gel and lidocaine HN gel showed that lidocaine could be better released from SH gel. Evaluation of in vivo anesthetic efficacy in 100 normal volunteers indicates that both lidocaine rice gels have high efficacy but different levels. Lidocaine SH gel possesses faster onset of duration and longer duration of action than lidocaine HN gel.

  14. The perspective effects of various seed coating substances on rice seed variety Khao Dawk Mali 105 storability II: the case study of chemical and biochemical properties.

    PubMed

    Thobunluepop, P; Pan-in, W; Pawelzik, E; Vearasilp, S

    2009-04-01

    The aim of this study was to investigate the effects of seed coating substances; chemical fungicide (CA) and biological fungicide polymers [chitosan-lignosulphonate polymer (CL) and eugenol incorporated into chitosan-lignosulphonate polymer (E+CL)] on chemical and biochemical changes of rice seeds cv. KDML 105, which have been studied during storage for 12 months. CA significantly affected the rice seed chemical properties and the associated seed deterioration. After 12 months storage, protein content decreased accompanied by declined of lipid content, increased free fatty acids and activated lipoxygenase enzyme. In the case of biological fungicide coated seeds, the antioxidative scavenging enzymes were ascorbate peroxidase and superoxide dismutase and a high antioxidant activity protected them. Moreover, the sugar content was positive correlated with seed germination and vigor. The biological coated seeds were found to maintain high sugar contents inside the seeds, which resulted high seed storability significantly. In contrast, under fungicide stress (CA), those compounds were lost that directly affected seed vigor during storage.

  15. "Tinni" rice (Oryza rufipogon Griff.) production: an integrated sociocultural agroecosystem in eastern Uttar Pradesh of India.

    PubMed

    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.

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

    NASA Astrophysics Data System (ADS)

    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.

  17. [Drought-resistance of local wheat varieties in Shanxi Province of China: a comprehensive evaluation by using GGE biplot and subordinate function].

    PubMed

    Yang, Jin-wen; Zhu, Jun-gang; Wang, Shu-guang; Sun, Dai-zhen; ShiI, Yu-gang; Chen, Wei-guo

    2013-04-01

    Taking 7 local wheat varieties in Shanxi Province of China and two other control varieties as test materials, this paper studied their morphological and physiological traits under normal and water stress field conditions. The drought-resistance coefficient of each index of the traits was calculated. On the basis of principal component analysis, the correlations between the drought-resistance indices and their relationships with the drought-resistance of different varieties were analyzed by GGE biplot, and the drought resistance of the wheat varieties was comprehensively evaluated with the combination of subordinate function and drought resistance index analysis. The main morphological and physiological factors affecting the drought-resistance of the wheat varieties were uppermost internode length, plant height, internode length, leaf area, leaf POD and SOD activities, and leaf relative water content and relative electric conductivity. There existed different degrees of correlation between these indices, and each index had different effects on the drought resistance of the varieties, being the main cause for the different drought resistance of the wheat varieties. Based on the drought-resistance, the test varieties could be classified into three groups, i. e. , drought-resistance group, intermediate group, and sensitive group. Two highly drought-resistance cultivars, Baiheshangtou and Zhuganqing, whose drought-resistance was similar to that of drought-resistant Jinmai 47, could be used as the parent materials for breeding drought-resistance wheat.

  18. Localized Flux Maxima of Arsenic, Lead, and Iron around Root Apices in Flooded Lowland Rice

    PubMed Central

    2014-01-01

    In wetland-adapted plants, such as rice, it is typically root apexes, sites of rapid entry for water/nutrients, where radial oxygen losses (ROLs) are highest. Nutrient/toxic metal uptake therefore largely occurs through oxidized zones and pH microgradients. However, the processes controlling the acquisition of trace elements in rice have been difficult to explore experimentally because of a lack of techniques for simultaneously measuring labile trace elements and O2/pH. Here, we use new diffusive gradients in thin films (DGT)/planar optode sandwich sensors deployed in situ on rice roots to demonstrate a new geochemical niche of greatly enhanced As, Pb, and Fe(II) mobilization into solution immediately adjacent to the root tips characterized by O2 enrichment and low pH. Fe(II) mobilization was congruent to that of the peripheral edge of the aerobic root zone, demonstrating that the Fe(II) mobilization maximum only developed in a narrow O2 range as the oxidation front penetrates the reducing soil. The Fe flux to the DGT resin at the root apexes was 3-fold higher than the anaerobic bulk soil and 27 times greater than the aerobic rooting zone. These results provide new evidence for the importance of coupled diffusion and oxidation of Fe in modulating trace metal solubilization, dispersion, and plant uptake. PMID:24967508

  19. Genetic structure and isolation by distance in a landrace of Thai rice

    PubMed Central

    Pusadee, Tonapha; Jamjod, Sansanee; Chiang, Yu-Chung; Rerkasem, Benjavan; Schaal, Barbara A.

    2009-01-01

    Rice is among the 3 most important crops worldwide. While much of the world's rice harvest is based on modern high-yield varieties, traditional varieties of rice grown by indigenous groups have great importance as a resource for future crop improvement. These local landraces represent an intermediate stage of domestication between a wild ancestor and modern varieties and they serve as reservoirs of genetic variation. Such genetic variation is influenced both by natural processes such as selection and drift, and by the agriculture practices of local farmers. How these processes interact to shape and change the population genetics of landrace rice is unknown. Here, we determine the population genetic structure of a single variety of landrace rice, Bue Chomee, cultivated by Karen people of Thailand. Microsatellite markers reveal high level of genetic variation despite predominant inbreeding in the crop. Bue Chomee rice shows slight but significant genetic differentiation among Karen villages. Moreover, genetically determined traits such as flowering time can vary significantly among villages. An unanticipated result was the overall pattern of genetic differentiation across villages which conforms to an isolation by distance model of differentiation. Isolation by distance is observed in natural plant species where the likelihood of gene flow is inversely related to distance. In Karen rice, gene flow is the result of farmers' seed sharing networks. Taken together, these data suggest that landrace rice is a dynamic genetic system that responds to evolutionary forces, both natural and those imposed by humans. PMID:19651617

  20. Structural determination of elicitors in Sogatella furcifera (Horváth) that induce Japonica rice plant varieties (Oryza sativa L.) to produce an ovicidal substance against S. furcifera eggs.

    PubMed

    Yang, Jeong-Oh; Nakayama, Naoya; Toda, Kyohei; Tebayashi, Shinichi; Kim, Chul-Sa

    2014-01-01

    Certain Japonica rice plant varieties (Oryza sativa L.) show resistance to the eggs of the white backed planthopper (Sogatella furcifera Horváth) by the formation of watery lesions and production of benzyl benzoate, an active ovicidal compound. Benzyl benzoate results in high ovicidal activity of S. furcifera eggs and reduces egg hatchability. The production of benzyl benzoate by the rice plants is only induced by an unknown elicitor(s) from the female S. furcifera. Therefore, we tried to isolate and identify these elicitors. An active 80% MeOH extract of S. furcifera was separated on a reverse-phase ODS MPLC, and the elicitor(s) was eluted in 100% MeOH and 100% EtOH fractions. Further separation of the active 100% MeOH fraction using a HPLC led to the isolation of four active compounds. The structures of each compound were determined by using NMR, LC-MS, and GC-MS spectra. The compounds were 1,2-dilinoleoyl-sn-glycero-3-phosphocholine, 1,2-dipalmitoyl-sn-glycero-3-phosphoethanolamine, 1-palmitoyl-2-oleoyl-X-glycero-3-phosphoethanolamine, and 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine.

  1. The perspective effects of various seed coating substances on rice seed variety Khao DAWK Mali 105 storability I: the case study of physiological properties.

    PubMed

    Thobunluepop, P; Pawelzik, E; Vearasilp, S

    2008-10-01

    This study aimed to evaluate the perspective changes of several physiological performances of rice seeds cv. KDML 105 which were coated with various seed coating substances [chemical fungicide, captan (CA) and biological coating polymers; chitosan-lignosulphonate polymer (CL) and eugenol incorporated into chitosan-lignosulphonate polymer (E + CL)] during storage (12 months). CA significantly increased seed moisture content and seed water activity through out the storage period. The qualities and viability of the seeds were seriously declined by this treatment. Moreover, CA inhibited the shoot and root development, seedling dry weight accumulation, delayed the seed germination and seedling growth rate. CA treated seeds were susceptible to stress conditions that declined the seed germination potential under cold, high moisture and temperature stress conditions. Nevertheless, CL and E + CL coating polymer could maintain seed storability, which significantly improved seed germination and seedling performances. These improvements were attributed to maintain the nutritive reserve and dehydrogenase activity in seeds. Moreover, the biological seed treatment stimulated the embryo growth and so speeding up the seedling emergence when compared untreated seeds.

  2. Localized surface plasmon behavior of Ag-Cu alloy nanoparticles stabilized by rice-starch and gelatin

    SciTech Connect

    Singh, Manish Kumar; Mandal, R. K.; Manda, Premkumar; Singh, A. K.

    2015-10-15

    The purpose of this communication was to understand localized surface plasmon behavior of a series of Ag-Cu alloy nanoparticles capped by rice-starch and gelatin. The structures of dried powders were investigated with the help of X-ray diffraction. The analysis revealed Ag-rich and Cu-rich phases with maximum solid solubility of Cu ∼9 atom per cent; 8 atom per cent and Ag ∼ 16 atom per cent; 14 atom per cent in rice-starch and gelatin capped samples respectively. Transmission electron microscope was used for knowing the particle size as well as to supplement FCC phase formations of Ag-rich and Cu-rich solid phases arrived at based on X-ray diffraction studies. The UV-Vis spectra of sols were examined for the formation and stability of alloy nanoparticles. The temporal evolution of LSPR curves gave us to assert that the sol is stable for more than two months. Small angle X-ray scattering in the sol state was extensively utilized to understand nature of suspensions in terms of fractals. Such a study is important for having a correlation between LSPR behaviors with those of nanoparticle dispersion in aqueous media. It is believed that this work will be a contribution to the emerging field of plasmonics that include applications in the area of photophysical processes and photochemical reactions.

  3. Transcripts of two ent-copalyl diphosphate synthase genes differentially localize in rice plants according to their distinct biological roles

    PubMed Central

    Toyomasu, Tomonobu; Usui, Masami; Sugawara, Chizu; Kanno, Yuri; Sakai, Arisa; Takahashi, Hirokazu; Nakazono, Mikio; Kuroda, Masaharu; Miyamoto, Koji; Morimoto, Yu; Mitsuhashi, Wataru; Okada, Kazunori; Yamaguchi, Shinjiro; Yamane, Hisakazu

    2015-01-01

    Gibberellins (GAs) are diterpenoid phytohormones that regulate various aspects of plant growth. Tetracyclic hydrocarbon ent-kaurene is a biosynthetic intermediate of GAs, and is converted from geranylgeranyl diphosphate, a common precursor of diterpenoids, via ent-copalyl diphosphate (ent-CDP) through successive cyclization reactions catalysed by two distinct diterpene synthases, ent-CDP synthase and ent-kaurene synthase. Rice (Oryza sativa L.) has two ent-CDP synthase genes, OsCPS1 and OsCPS2. It has been thought that OsCPS1 participates in GA biosynthesis, while OsCPS2 participates in the biosynthesis of phytoalexins, phytocassanes A–E, and oryzalexins A–F. It has been shown previously that loss-of-function OsCPS1 mutants display a severe dwarf phenotype caused by GA deficiency despite possessing another ent-CDP synthase gene, OsCPS2. Here, experiments were performed to account for the non-redundant biological function of OsCPS1 and OsCPS2. Quantitative reverse transcription–PCR (qRT–PCR) analysis showed that OsCPS2 transcript levels were drastically lower than those of OsCPS1 in the basal parts, including the meristem of the second-leaf sheaths of rice seedlings. qRT–PCR results using tissue samples prepared by laser microdissection suggested that OsCPS1 transcripts mainly localized in vascular bundle tissues, similar to Arabidopsis CPS, which is responsible for GA biosynthesis, whereas OsCPS2 transcripts mainly localized in epidermal cells that address environmental stressors such as pathogen attack. Furthermore, the OsCPS2 transgene under regulation of the OsCPS1 promoter complemented the dwarf phenotype of an OsCPS1 mutant, oscps1-1. The results indicate that transcripts of the two ent-CDP synthase genes differentially localize in rice plants according to their distinct biological roles, OsCPS1 for growth and OsCPS2 for defence. PMID:25336684

  4. Transcripts of two ent-copalyl diphosphate synthase genes differentially localize in rice plants according to their distinct biological roles.

    PubMed

    Toyomasu, Tomonobu; Usui, Masami; Sugawara, Chizu; Kanno, Yuri; Sakai, Arisa; Takahashi, Hirokazu; Nakazono, Mikio; Kuroda, Masaharu; Miyamoto, Koji; Morimoto, Yu; Mitsuhashi, Wataru; Okada, Kazunori; Yamaguchi, Shinjiro; Yamane, Hisakazu

    2015-01-01

    Gibberellins (GAs) are diterpenoid phytohormones that regulate various aspects of plant growth. Tetracyclic hydrocarbon ent-kaurene is a biosynthetic intermediate of GAs, and is converted from geranylgeranyl diphosphate, a common precursor of diterpenoids, via ent-copalyl diphosphate (ent-CDP) through successive cyclization reactions catalysed by two distinct diterpene synthases, ent-CDP synthase and ent-kaurene synthase. Rice (Oryza sativa L.) has two ent-CDP synthase genes, OsCPS1 and OsCPS2. It has been thought that OsCPS1 participates in GA biosynthesis, while OsCPS2 participates in the biosynthesis of phytoalexins, phytocassanes A-E, and oryzalexins A-F. It has been shown previously that loss-of-function OsCPS1 mutants display a severe dwarf phenotype caused by GA deficiency despite possessing another ent-CDP synthase gene, OsCPS2. Here, experiments were performed to account for the non-redundant biological function of OsCPS1 and OsCPS2. Quantitative reverse transcription-PCR (qRT-PCR) analysis showed that OsCPS2 transcript levels were drastically lower than those of OsCPS1 in the basal parts, including the meristem of the second-leaf sheaths of rice seedlings. qRT-PCR results using tissue samples prepared by laser microdissection suggested that OsCPS1 transcripts mainly localized in vascular bundle tissues, similar to Arabidopsis CPS, which is responsible for GA biosynthesis, whereas OsCPS2 transcripts mainly localized in epidermal cells that address environmental stressors such as pathogen attack. Furthermore, the OsCPS2 transgene under regulation of the OsCPS1 promoter complemented the dwarf phenotype of an OsCPS1 mutant, oscps1-1. The results indicate that transcripts of the two ent-CDP synthase genes differentially localize in rice plants according to their distinct biological roles, OsCPS1 for growth and OsCPS2 for defence.

  5. Genetic Structure and Molecular Diversity of Cacao Plants Established as Local Varieties for More than Two Centuries: The Genetic History of Cacao Plantations in Bahia, Brazil.

    PubMed

    Santos, Elisa S L; Cerqueira-Silva, Carlos Bernard M; Mori, Gustavo M; Ahnert, Dário; Mello, Durval L N; Pires, José Luis; Corrêa, Ronan X; de Souza, Anete P

    2015-01-01

    Bahia is the most important cacao-producing state in Brazil, which is currently the sixth-largest country worldwide to produce cacao seeds. In the eighteenth century, the Comum, Pará and Maranhão varieties of cacao were introduced into southern Bahia, and their descendants, which are called 'Bahian cacao' or local Bahian varieties, have been cultivated for over 200 years. Comum plants have been used to start plantations in African countries and extended as far as countries in South Asia and Oceania. In Brazil, two sets of clones selected from Bahian varieties and their mutants, the Agronomic Institute of East (SIAL) and Bahian Cacao Institute (SIC) series, represent the diversity of Bahian cacao in germplasm banks. Because the genetic diversity of Bahian varieties, which is essential for breeding programs, remains unknown, the objective of this work was to assess the genetic structure and diversity of local Bahian varieties collected from farms and germplasm banks. To this end, 30 simple sequence repeat (SSR) markers were used to genotype 279 cacao plants from germplasm and local farms. The results facilitated the identification of 219 cacao plants of Bahian origin, and 51 of these were SIAL or SIC clones. Bahian cacao showed low genetic diversity. It could be verified that SIC and SIAL clones do not represent the true diversity of Bahian cacao, with the greatest amount of diversity found in cacao trees on the farms. Thus, a core collection to aid in prioritizing the plants to be sampled for Bahian cacao diversity is suggested. These results provide information that can be used to conserve Bahian cacao plants and applied in breeding programs to obtain more productive Bahian cacao with superior quality and tolerance to major diseases in tropical cacao plantations worldwide.

  6. Genetic Structure and Molecular Diversity of Cacao Plants Established as Local Varieties for More than Two Centuries: The Genetic History of Cacao Plantations in Bahia, Brazil

    PubMed Central

    Santos, Elisa S. L.; Cerqueira-Silva, Carlos Bernard M.; Mori, Gustavo M.; Ahnert, Dário; Mello, Durval L. N.; Pires, José Luis; Corrêa, Ronan X.; de Souza, Anete P.

    2015-01-01

    Bahia is the most important cacao-producing state in Brazil, which is currently the sixth-largest country worldwide to produce cacao seeds. In the eighteenth century, the Comum, Pará and Maranhão varieties of cacao were introduced into southern Bahia, and their descendants, which are called ‘Bahian cacao’ or local Bahian varieties, have been cultivated for over 200 years. Comum plants have been used to start plantations in African countries and extended as far as countries in South Asia and Oceania. In Brazil, two sets of clones selected from Bahian varieties and their mutants, the Agronomic Institute of East (SIAL) and Bahian Cacao Institute (SIC) series, represent the diversity of Bahian cacao in germplasm banks. Because the genetic diversity of Bahian varieties, which is essential for breeding programs, remains unknown, the objective of this work was to assess the genetic structure and diversity of local Bahian varieties collected from farms and germplasm banks. To this end, 30 simple sequence repeat (SSR) markers were used to genotype 279 cacao plants from germplasm and local farms. The results facilitated the identification of 219 cacao plants of Bahian origin, and 51 of these were SIAL or SIC clones. Bahian cacao showed low genetic diversity. It could be verified that SIC and SIAL clones do not represent the true diversity of Bahian cacao, with the greatest amount of diversity found in cacao trees on the farms. Thus, a core collection to aid in prioritizing the plants to be sampled for Bahian cacao diversity is suggested. These results provide information that can be used to conserve Bahian cacao plants and applied in breeding programs to obtain more productive Bahian cacao with superior quality and tolerance to major diseases in tropical cacao plantations worldwide. PMID:26675449

  7. Developing and delivering biofortified Rice to the consumer

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Biofortified rice varieties include those that have been enhanced for protein, vitamins, minerals, or other nutritional compounds. Delivering biofortified rice varieties carries with it extra challenges as compared to conventional varieties. Nutritional compounds must be present at significantly hig...

  8. Differential Gene Expression Reflects Morphological Characteristics and Physiological Processes in Rice Immunity against Blast Pathogen Magnaporthe oryzae

    PubMed Central

    Mahmood, Maziah; Abdullah, Siti N. A.; Hanafi, Mohamed M.; Nejat, Naghmeh; Latif, Muhammad A.

    2015-01-01

    The rice blast fungus Magnaporthe oryzae is a serious pathogen that jeopardises the world’s most important food-security crop. Ten common Malaysian rice varieties were examined for their morphological, physiological and genomic responses to this rice blast pathogen. qPCR quantification was used to assess the growth of the pathogen population in resistant and susceptible rice varieties. The chlorophyll content and photosynthesis were also measured to further understand the disruptive effects that M. oryzae has on infected plants of these varieties. Real-time PCR was used to explore the differential expression of eight blast resistance genes among the ten local varieties. Blast disease has destructive effects on the growth of rice, and the findings of our study provide evidence that the Pikh, Pi9, Pi21, and Osw45 genes are involved in defence responses in the leaves of Malaysian rice at 31 h after inoculation with M. oryzae pathotype P7.2. Both the chlorophyll content and photosynthesis were reduced, but the levels of Pikh gene expression remained constant in susceptible varieties, with a developed pathogen population and mild or severe symptoms. The Pi9, Pi21, and Osw45 genes, however, were simultaneously upregulated in infected rice plants. Therefore, the presence of the Pikh, Pi9, Pi21, and Osw45 genes in the germplasm is useful for improving the resistance of rice varieties. PMID:26001124

  9. Differential Gene Expression Reflects Morphological Characteristics and Physiological Processes in Rice Immunity against Blast Pathogen Magnaporthe oryzae.

    PubMed

    Azizi, Parisa; Rafii, Mohd Y; Mahmood, Maziah; Abdullah, Siti N A; Hanafi, Mohamed M; Nejat, Naghmeh; Latif, Muhammad A; Sahebi, Mahbod

    2015-01-01

    The rice blast fungus Magnaporthe oryzae is a serious pathogen that jeopardises the world's most important food-security crop. Ten common Malaysian rice varieties were examined for their morphological, physiological and genomic responses to this rice blast pathogen. qPCR quantification was used to assess the growth of the pathogen population in resistant and susceptible rice varieties. The chlorophyll content and photosynthesis were also measured to further understand the disruptive effects that M. oryzae has on infected plants of these varieties. Real-time PCR was used to explore the differential expression of eight blast resistance genes among the ten local varieties. Blast disease has destructive effects on the growth of rice, and the findings of our study provide evidence that the Pikh, Pi9, Pi21, and Osw45 genes are involved in defence responses in the leaves of Malaysian rice at 31 h after inoculation with M. oryzae pathotype P7.2. Both the chlorophyll content and photosynthesis were reduced, but the levels of Pikh gene expression remained constant in susceptible varieties, with a developed pathogen population and mild or severe symptoms. The Pi9, Pi21, and Osw45 genes, however, were simultaneously upregulated in infected rice plants. Therefore, the presence of the Pikh, Pi9, Pi21, and Osw45 genes in the germplasm is useful for improving the resistance of rice varieties.

  10. Analysis of Recombinant Proteins in Transgenic Rice Seeds: Identity, Localization, Tolerance to Digestion, and Plant Stress Response.

    PubMed

    Wakasa, Yuhya; Takaiwa, Fumio

    2016-01-01

    Rice seeds are an ideal production platform for high-value recombinant proteins in terms of economy, scalability, safety, and stability. Strategies for the expression of large amounts of recombinant proteins in rice seeds have been established in the past decade and transgenic rice seeds that accumulate recombinant products such as bioactive peptides and proteins, which promote the health and quality of life of humans, have been generated in many laboratories worldwide. One of the most important advantages is the potential for direct oral delivery of transgenic rice seeds without the need for recombinant protein purification (downstream processing), which has been attributed to the high expression levels of recombinant products. Transgenic rice will be beneficial as a delivery system for pharmaceuticals and nutraceuticals in the future. This chapter introduces the strategy for producing recombinant protein in the edible part (endosperm) of the rice grain and describes methods for the analysis of transgenic rice seeds in detail.

  11. PANMIN: sequential and parallel global optimization procedures with a variety of options for the local search strategy

    NASA Astrophysics Data System (ADS)

    Theos, F. V.; Lagaris, I. E.; Papageorgiou, D. G.

    2004-05-01

    We present two sequential and one parallel global optimization codes, that belong to the stochastic class, and an interface routine that enables the use of the Merlin/MCL environment as a non-interactive local optimizer. This interface proved extremely important, since it provides flexibility, effectiveness and robustness to the local search task that is in turn employed by the global procedures. We demonstrate the use of the parallel code to a molecular conformation problem. Program summaryTitle of program: PANMIN Catalogue identifier: ADSU Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADSU Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Computer for which the program is designed and others on which it has been tested: PANMIN is designed for UNIX machines. The parallel code runs on either shared memory architectures or on a distributed system. The code has been tested on a SUN Microsystems ENTERPRISE 450 with four CPUs, and on a 48-node cluster under Linux, with both the GNU g77 and the Portland group compilers. The parallel implementation is based on MPI and has been tested with LAM MPI and MPICH Installation: University of Ioannina, Greece Programming language used: Fortran-77 Memory required to execute with typical data: Approximately O( n2) words, where n is the number of variables No. of bits in a word: 64 No. of processors used: 1 or many Has the code been vectorised or parallelized?: Parallelized using MPI No. of bytes in distributed program, including test data, etc.: 147163 No. of lines in distributed program, including the test data, etc.: 14366 Distribution format: gzipped tar file Nature of physical problem: A multitude of problems in science and engineering are often reduced to minimizing a function of many variables. There are instances that a local optimum does not correspond to the desired physical solution and hence the search for a better solution is required. Local optimization techniques can be

  12. Processing and intracellular localization of rice stripe virus Pc2 protein in insect cells

    SciTech Connect

    Zhao, Shuling; Zhang, Gaozhan; Dai, Xuejuan; Hou, Yanling; Li, Min; Liang, Jiansheng; Liang, Changyong

    2012-08-01

    Rice stripe virus (RSV) belongs to the genus Tenuivirus and its genome consists of four single-stranded RNAs encoding seven proteins. Here, we have analyzed the processing and membrane association of Pc2 encoded by vcRNA2 in insect cells. The enhanced green fluorescent protein (eGFP) was fused to the Pc2 and used for the detection of Pc2 fusion proteins. The results showed that Pc2 was cleaved to produce two proteins named Pc2-N and Pc2-C. When expressed alone, either Pc2-N or Pc2-C could transport to the Endoplasmic reticulum (ER) membranes independently. Further mutagenesis studies revealed that Pc2 contained three ER-targeting domains. The results led us to propose a model for the topology of the Pc2 in which an internal signal peptide immediately followed a cleavage site, and two transmembrane regions are contained.

  13. Pathogen effectors and plant immunity determine specialization of the blast fungus to rice subspecies

    PubMed Central

    Liao, Jingjing; Huang, Huichuan; Meusnier, Isabelle; Adreit, Henri; Ducasse, Aurélie; Bonnot, François; Pan, Lei; He, Xiahong; Kroj, Thomas; Fournier, Elisabeth; Tharreau, Didier; Gladieux, Pierre; Morel, Jean-Benoit

    2016-01-01

    Understanding how fungi specialize on their plant host is crucial for developing sustainable disease control. A traditional, centuries-old rice agro-system of the Yuanyang terraces was used as a model to show that virulence effectors of the rice blast fungus Magnaporthe oryzaeh play a key role in its specialization on locally grown indica or japonica local rice subspecies. Our results have indicated that major differences in several components of basal immunity and effector-triggered immunity of the japonica and indica rice varieties are associated with specialization of M. oryzae. These differences thus play a key role in determining M. oryzae host specificity and may limit the spread of the pathogen within the Yuanyang agro-system. Specifically, the AVR-Pia effector has been identified as a possible determinant of the specialization of M. oryzae to local japonica rice. DOI: http://dx.doi.org/10.7554/eLife.19377.001 PMID:28008850

  14. Knock-Down of a Tonoplast Localized Low-Affinity Nitrate Transporter OsNPF7.2 Affects Rice Growth under High Nitrate Supply

    PubMed Central

    Hu, Rui; Qiu, Diyang; Chen, Yi; Miller, Anthony J.; Fan, Xiaorong; Pan, Xiaoping; Zhang, Mingyong

    2016-01-01

    The large nitrate transporter 1/peptide transporter family (NPF) has been shown to transport diverse substrates, including nitrate, amino acids, peptides, phytohormones, and glucosinolates. However, the rice (Oryza sativa) root-specific family member OsNPF7.2 has not been functionally characterized. Here, our data show that OsNPF7.2 is a tonoplast localized low-affinity nitrate transporter, that affects rice growth under high nitrate supply. Expression analysis showed that OsNPF7.2 was mainly expressed in the elongation and maturation zones of roots, especially in the root sclerenchyma, cortex and stele. It was also induced by high concentrations of nitrate. Subcellular localization analysis showed that OsNPF7.2 was localized on the tonoplast of large and small vacuoles. Heterologous expression in Xenopus laevis oocytes suggested that OsNPF7.2 was a low-affinity nitrate transporter. Knock-down of OsNPF7.2 retarded rice growth under high concentrations of nitrate. Therefore, we deduce that OsNPF7.2 plays a role in intracellular allocation of nitrate in roots, and thus influences rice growth under high nitrate supply. PMID:27826301

  15. Short-Term Local Adaptation of Historical Common Bean (Phaseolus vulgaris L.) Varieties and Implications for In Situ Management of Bean Diversity

    PubMed Central

    Klaedtke, Stephanie M.; Caproni, Leonardo; Klauck, Julia; de la Grandville, Paul; Dutartre, Martin; Stassart, Pierre M.; Chable, Véronique; Negri, Valeria; Raggi, Lorenzo

    2017-01-01

    Recognizing both the stakes of traditional European common bean diversity and the role farmers’ and gardeners’ networks play in maintaining this diversity, the present study examines the role that local adaptation plays for the management of common bean diversity in situ. To the purpose, four historical bean varieties and one modern control were multiplied on two organic farms for three growing seasons. The fifteen resulting populations, the initial ones and two populations of each variety obtained after the three years of multiplication, were then grown in a common garden. Twenty-two Simple Sequence Repeat (SSR) markers and 13 phenotypic traits were assessed. In total, 68.2% of tested markers were polymorphic and a total of 66 different alleles were identified. FST analysis showed that the genetic composition of two varieties multiplied in different environments changed. At the phenotypic level, differences were observed in flowering date and leaf length. Results indicate that three years of multiplication suffice for local adaptation to occur. The spatial dynamics of genetic and phenotypic bean diversity imply that the maintenance of diversity should be considered at the scale of the network, rather than individual farms and gardens. The microevolution of bean populations within networks of gardens and farms emerges as a research perspective. PMID:28264476

  16. Short-Term Local Adaptation of Historical Common Bean (Phaseolus vulgaris L.) Varieties and Implications for In Situ Management of Bean Diversity.

    PubMed

    Klaedtke, Stephanie M; Caproni, Leonardo; Klauck, Julia; de la Grandville, Paul; Dutartre, Martin; Stassart, Pierre M; Chable, Véronique; Negri, Valeria; Raggi, Lorenzo

    2017-02-28

    Recognizing both the stakes of traditional European common bean diversity and the role farmers' and gardeners' networks play in maintaining this diversity, the present study examines the role that local adaptation plays for the management of common bean diversity in situ. To the purpose, four historical bean varieties and one modern control were multiplied on two organic farms for three growing seasons. The fifteen resulting populations, the initial ones and two populations of each variety obtained after the three years of multiplication, were then grown in a common garden. Twenty-two Simple Sequence Repeat (SSR) markers and 13 phenotypic traits were assessed. In total, 68.2% of tested markers were polymorphic and a total of 66 different alleles were identified. FST analysis showed that the genetic composition of two varieties multiplied in different environments changed. At the phenotypic level, differences were observed in flowering date and leaf length. Results indicate that three years of multiplication suffice for local adaptation to occur. The spatial dynamics of genetic and phenotypic bean diversity imply that the maintenance of diversity should be considered at the scale of the network, rather than individual farms and gardens. The microevolution of bean populations within networks of gardens and farms emerges as a research perspective.

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

    PubMed Central

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

    2016-01-01

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

  18. Phloem-exudate proteome analysis of response to insect brown plant-hopper in rice.

    PubMed

    Du, Ba; Wei, Zhe; Wang, Zhanqi; Wang, Xiaoxiao; Peng, Xinxin; Du, Bo; Chen, Rongzhi; Zhu, Lili; He, Guangcun

    2015-07-01

    Brown plant-hopper (Nilaparvata lugens Stål, BPH), one of the most devastating agricultural insect pests of rice throughout Asia, ingests nutrients from rice sieve tubes and causes a dramatic yield loss. Planting resistant variety is an efficient and economical way to control this pest. Understanding the mechanisms of host resistance is extremely valuable for molecular design of resistant rice variety. Here, we used an iTRAQ-based quantitative proteomics approach to perform analysis of protein expression profiles in the phloem exudates of BPH-resistant and susceptible rice plants following BPH infestation. A total of 238 proteins were identified, most of which were previously described to be present in the phloem of rice and other plants. The expression of genes for selected proteins was confirmed using a laser capture micro-dissection method and RT-PCR. The mRNAs for three proteins, RGAP, TCTP, and TRXH, were further analyzed by using in situ mRNA hybridization and localized in the phloem cells. Our results showed that BPH feeding induced significant changes in the abundance of proteins in phloem sap of rice involved in multiple pathways, including defense signal transduction, redox regulation, and carbohydrate and protein metabolism, as well as cell structural proteins. The results presented provide new insights into rice resistance mechanisms and should facilitate the breeding of novel elite BPH-resistant rice varieties.

  19. Are habitat fragmentation, local adaptation and isolation-by-distance driving population divergence in wild rice Oryza rufipogon?

    PubMed

    Zhao, Yao; Vrieling, Klaas; Liao, Hui; Xiao, Manqiu; Zhu, Yongqing; Rong, Jun; Zhang, Wenju; Wang, Yuguo; Yang, Ji; Chen, Jiakuan; Song, Zhiping

    2013-11-01

    Habitat fragmentation weakens the connection between populations and is accompanied with isolation by distance (IBD) and local adaptation (isolation by adaptation, IBA), both leading to genetic divergence between populations. To understand the evolutionary potential of a population and to formulate proper conservation strategies, information on the roles of IBD and IBA in driving population divergence is critical. The putative ancestor of Asian cultivated rice (Oryza sativa) is endangered in China due to habitat loss and fragmentation. We investigated the genetic variation in 11 Chinese Oryza rufipogon populations using 79 microsatellite loci to infer the effects of habitat fragmentation, IBD and IBA on genetic structure. Historical and current gene flows were found to be rare (mh  = 0.0002-0.0013, mc  = 0.007-0.029), indicating IBD and resulting in a high level of population divergence (FST  = 0.343). High within-population genetic variation (HE  = 0.377-0.515), relatively large effective population sizes (Ne  = 96-158), absence of bottlenecks and limited gene flow were found, demonstrating little impact of recent habitat fragmentation on these populations. Eleven gene-linked microsatellite loci were identified as outliers, indicating local adaptation. Hierarchical AMOVA and partial Mantel tests indicated that population divergence of Chinese O. rufipogon was significantly correlated with environmental factors, especially habitat temperature. Common garden trials detected a significant adaptive population divergence associated with latitude. Collectively, these findings imply that IBD due to historical rather than recent fragmentation, followed by local adaptation, has driven population divergence in O. rufipogon.

  20. The maintenance of regional dialects: a matter of gender? Boys, but not girls, use local varieties in relation to their friends' nativeness and local identity

    PubMed Central

    Barbu, Stéphanie; Martin, Nathael; Chevrot, Jean-Pierre

    2014-01-01

    The linguistic diversity enduring beyond institutional pressures and social prejudices against non-standard dialects questions the social forces influencing language maintenance across generations and how children contribute to this process. Children encounter multi-dialectal interactions in their early environment, and increasing evidence shows that the acquisition of sociolinguistic variation is not a side issue but an inherent part of the general acquisition process. Despite these recent advances in sociolinguistic acquisition, children's sociolinguistic uses remain under-studied in relation to peer social networks and the ability to use dialect for identity purposes. Our study focused on a grammatical sociolinguistic variable consisting of the alternation between a regional and a standard variant of the third person object pronoun in French. The regional variant is a remnant of the Francoprovençal language and its usage by adults is strongly associated with local identity in the French Alps. We described, using questionnaires, the social networks of 117 10–11 year-old girls and boys living in the same restricted rural area. Thirteen native target children (7 girls and 6 boys) were selected from the sample, as well as 39 same-sex friends chosen according to their place of birth (native vs. non-native) and the duration of their friendship with the targets (number of years they have known each other). The target children were recorded during spontaneous dyadic conversations during free play at school with each category of friends. Target boys, but not girls, used the regional variant significantly more frequently with their long-term native friends than with their non-native friends. This adjustment mirrored their partners' uses. Moreover, with long-term native friends, boys used the regional variant twice as frequently as girls. Boys appeared thus as key actors in the maintenance and the diffusion of regional cues in local social networks. PMID:25400617

  1. Volatiles induction in rice stink bug host grasses and rice plants

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Rice stink bug (RSB), Oebalus pugnax F., is an important pest of heading rice in the United States. Little is known about plant volatiles production following herbivory by the rice stink bug. RSB feeding induced volatiles production in different RSB host grasses and rice varieties, and may help expl...

  2. The Chloroplast-Localized Phospholipases D α4 and α5 Regulate Herbivore-Induced Direct and Indirect Defenses in Rice1[C][W

    PubMed Central

    Qi, Jinfeng; Zhou, Guoxin; Yang, Lijuan; Erb, Matthias; Lu, Yanhua; Sun, Xiaoling; Cheng, Jiaan; Lou, Yonggen

    2011-01-01

    The oxylipin pathway is of central importance for plant defensive responses. Yet, the first step of the pathway, the liberation of linolenic acid following induction, is poorly understood. Phospholipases D (PLDs) have been hypothesized to mediate this process, but data from Arabidopsis (Arabidopsis thaliana) regarding the role of PLDs in plant resistance have remained controversial. Here, we cloned two chloroplast-localized PLD genes from rice (Oryza sativa), OsPLDα4 and OsPLDα5, both of which were up-regulated in response to feeding by the rice striped stem borer (SSB) Chilo suppressalis, mechanical wounding, and treatment with jasmonic acid (JA). Antisense expression of OsPLDα4 and -α5 (as-pld), which resulted in a 50% reduction of the expression of the two genes, reduced elicited levels of linolenic acid, JA, green leaf volatiles, and ethylene and attenuated the SSB-induced expression of a mitogen-activated protein kinase (OsMPK3), a lipoxygenase (OsHI-LOX), a hydroperoxide lyase (OsHPL3), as well as a 1-aminocyclopropane-1-carboxylic acid synthase (OsACS2). The impaired oxylipin and ethylene signaling in as-pld plants decreased the levels of herbivore-induced trypsin protease inhibitors and volatiles, improved the performance of SSB and the rice brown planthopper Nilaparvata lugens, and reduced the attractiveness of plants to a larval parasitoid of SSB, Apanteles chilonis. The production of trypsin protease inhibitors in as-pld plants could be partially restored by JA, while the resistance to rice brown planthopper and SSB was restored by green leaf volatile application. Our results show that phospholipases function as important components of herbivore-induced direct and indirect defenses in rice. PMID:21984727

  3. Arsenic localization, speciation, and co-occurrence with iron on rice (Oryza sativa L.) roots having variable Fe coatings.

    PubMed

    Seyfferth, Angelia L; Webb, Samuel M; Andrews, Joy C; Fendorf, Scott

    2010-11-01

    Arsenic contamination of rice is widespread, but the rhizosphere processes influencing arsenic attenuation remain unresolved. In particular, the formation of Fe plaque around rice roots is thought to be an important barrier to As uptake, but the relative importance of this mechanism is not well characterized. Here we elucidate the colocalization of As species and Fe on rice roots with variable Fe coatings; we used a combination of techniques--X-ray fluorescence imaging, μXANES, transmission X-ray microscopy, and tomography--for this purpose. Two dominant As species were observed in fine roots-inorganic As(V) and As(III) -with minor amounts of dimethylarsinic acid (DMA) and arsenic trisglutathione (AsGlu(3)). Our investigation shows that variable Fe plaque formation affects As entry into rice roots. In roots with Fe plaque, As and Fe were strongly colocated around the root; however, maximal As and Fe were dissociated and did not encapsulate roots that had minimal Fe plaque. Moreover, As was not exclusively associated with Fe plaque in the rice root system; Fe plaque does not coat many of the young roots or the younger portion of mature roots. Young, fine roots, important for solute uptake, have little to no iron plaque. Thus, Fe plaque does not directly intercept (and hence restrict) As supply to and uptake by rice roots but rather serves as a bulk scavenger of As predominantly near the root base.

  4. Cellular localization and detergent dependent oligomerization of rice allene oxide synthase-1.

    PubMed

    Yoeun, Sereyvath; Kim, Jeong-Il; Han, Oksoo

    2015-01-01

    Allene oxide synthase-1 from Oryza sativa (OsAOS1) localizes to the chloroplast, but lacks a putative chloroplast targeting sequence typically found in dicot AOS. Here, kinetic parameters and the oligomerization state/subunit composition of OsAOS1 were characterized in vitro in the absence or presence of detergent micelles. The catalytic efficiency (k(cat)/K(m)) of OsAOS1 reached a maximum near the critical micelle concentration for polyoxyethylene 10 tridecyl ether. Native gel analysis showed that OsAOS1 exists as a multimer in the absence of detergent micelles. The multimeric form of OsAOS1 was stably cross-linked in the absence of detergents, while only monomeric OsAOS1 was detected in the presence of detergent micelles. Gel filtration analysis indicated that the oligomeric state of OsAOS1 depends strongly on the detergents and that the monomer becomes the predominant form in the presence of detergent micelles. These data suggest that the detergent-dependent oligomeric state of OsAOS1 is an important factor for the regulation of its catalytic efficiency.

  5. Molecular characterization of two small heat shock protein genes in rice: their expression patterns, localizations, networks, and heterogeneous overexpressions.

    PubMed

    Ham, Deok-Jae; Moon, Jun-Chul; Hwang, Sun-Goo; Jang, Cheol Seong

    2013-09-28

    Heat stress is an example of a severe abiotic stress that plants can suffer in the field, causing a significant detrimental effect on their growth and productivity. Understanding the mechanism of plant response to heat stress is important for improving the productivity of crop plants under global warming. We used a microarray dataset that is deposited in the public database to evaluate plant responses to heat stress, and we selected the top 10 genes that are highly expressed under heat stress in rice. Two genes, OsSHSP1 (Os03g16030) and OsSHSP2 (Os01g04380), were selected for further study. These genes were highly induced in response to salt and drought but not in response to cold. In addition, OsSHSP1 and OsSHSP2 gene transcripts were induced under abscisic acid and salicylic acid but not under jasmonic acid and ethylene. Subcellular localization of proteins of 35S::OsSHSP1 were associated with the cytosol, whereas those of and 35S::OsSHSP2 were associated with the cytosol and nucleus. Heterogeneous overexpression of both genes exhibited higher germination rates than those of wild-type plants under the salt treatment, but not under heat or drought stress, supporting a hypothesis regarding functional specialization of members of small heat-shock protein family over evolutionary time. The network of both genes harboring nine sHSPs as well as at least 13 other chaperone genes might support the idea of a role for sHSPs in the chaperone network. Our findings might provide clues to shed light on the molecular functions of OsSHSP1 and OsSHSP2 in response to abiotic stresses, especially heat stress.

  6. Expression of cytochrome P450 CYP81A6 in rice: tissue specificity, protein subcellular localization, and response to herbicide application*

    PubMed Central

    Lu, Hai-ping; Edwards, Martin; Wang, Qi-zhao; Zhao, Hai-jun; Fu, Hao-wei; Huang, Jian-zhong; Gatehouse, Angharad; Shu, Qing-yao

    2015-01-01

    The cytochrome P450 gene CYP81A6 confers tolerance to bentazon and metsulfuron-methyl, two selective herbicides widely used for weed control in rice and wheat fields. Knockout mutants of CYP81A6 are highly susceptible to both herbicides. The present study aimed to characterize the CYP81A6 expression in rice. Quantitative real-time polymerase chain reaction (PCR) analyses demonstrated that foliar treatment of bentazon (500 mg/L) greatly induced expression of CYP81A6 in both wild-type (Jiazhe B) and its knockout mutant (Jiazhe mB): a 10-fold increase at 9 h before returning to basal levels at 24 h in Jiazhe B, while in the mutant the expression level rose to >20-fold at 12 h and maintained at such high level up to 24 h post exposure. In contrast, metsulfuron-methyl (500 mg/L) treatment did not affect the expression of CYP81A6 in Jiazhe B within 80 h; thereafter the expression peaked at 120 h and returned gradually to basal levels by Day 6. We suggest that a metabolite of metsulfuron-methyl, 1H-2,3-benzothiazin-4-(3H)-one-2,2-dioxide, is likely to be responsible for inducing CYP81A6 expression, rather than the metsulfuron-methyl itself. Use of a promoter-GUS reporter construct (CYP81A6Pro::GUS) demonstrated that CYP81A6 was constitutively expressed throughout the plant, with the highest expression in the upper surfaces of leaves. Subcellular localization studies in rice protoplasts showed that CYP81A6 was localized in the endoplasmic reticulum. These observations advance our understanding of CYP81A6 expression in rice, particularly its response to the two herbicides. PMID:25644466

  7. 7 CFR 201.10 - Variety.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ..., striate; Millet, foxtail; Millet, pearl; Oat; Pea, field; Peanut; Rice; Rye; Safflower; Sorghum; Sorghum... seed,” shall apply only to seed of the variety named, except for the labeling of hybrids as provided in § 201.11a. If separate percentages for the kind and the variety or hybrid are shown, the name of...

  8. 7 CFR 201.10 - Variety.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ..., striate; Millet, foxtail; Millet, pearl; Oat; Pea, field; Peanut; Rice; Rye; Safflower; Sorghum; Sorghum... seed,” shall apply only to seed of the variety named, except for the labeling of hybrids as provided in § 201.11a. If separate percentages for the kind and the variety or hybrid are shown, the name of...

  9. 7 CFR 201.10 - Variety.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ..., striate; Millet, foxtail; Millet, pearl; Oat; Pea, field; Peanut; Rice; Rye; Safflower; Sorghum; Sorghum... seed,” shall apply only to seed of the variety named, except for the labeling of hybrids as provided in § 201.11a. If separate percentages for the kind and the variety or hybrid are shown, the name of...

  10. 7 CFR 201.10 - Variety.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ..., striate; Millet, foxtail; Millet, pearl; Oat; Pea, field; Peanut; Rice; Rye; Safflower; Sorghum; Sorghum... seed,” shall apply only to seed of the variety named, except for the labeling of hybrids as provided in § 201.11a. If separate percentages for the kind and the variety or hybrid are shown, the name of...

  11. 7 CFR 201.10 - Variety.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ..., striate; Millet, foxtail; Millet, pearl; Oat; Pea, field; Peanut; Rice; Rye; Safflower; Sorghum; Sorghum... seed,” shall apply only to seed of the variety named, except for the labeling of hybrids as provided in § 201.11a. If separate percentages for the kind and the variety or hybrid are shown, the name of...

  12. Contractions of affine spherical varieties

    SciTech Connect

    Arzhantsev, I V

    1999-08-31

    The language of filtrations and contractions is used to describe the class of G-varieties obtainable as the total spaces of the construction of contraction applied to affine spherical varieties, which is well-known in invariant theory. These varieties are local models for arbitrary affine G-varieties of complexity 1 with a one-dimensional categorical quotient. As examples, reductive algebraic semigroups and three-dimensional SL{sub 2}-varieties are considered.

  13. Arsenic Intake through Consumed Rice in Iran: Markets Role or Government Responsibility

    PubMed Central

    Nemati, Sepideh; Mosaferi, Mohammad; Ostadrahimi, Alireza; Mohammadi, Amir

    2014-01-01

    Background: the present study investigated arsenic content in Iranian, imported rice on sale in Tabriz (fourth most populous city of Iran) market, and assesses daily arsenic intake from rice. Methods: A total of 33 locally available rice samples from different brands were collected and then wet and dry ashing digestion procedures were compared for decomposition of them before analyzing by graphite furnace atomic absorption spectrometry (GFAAS). Results: The mean arsenic concentration in Iranian rice was 0.065 mg/kg versus 0.082 mg/kg in imported samples. There was no significant difference between arsenic concentrations between two groups of samples (P=0.061). The average daily ingestion rate of total arsenic was 0.11 and 0.15 μg/kg body weight from consumption of 110g of Iranian and imported rice respectively. Conclusion: Based on our estimation, daily dietary intake of arsenic from Iranian and imported rice was approximately 7 and 9 μg/day for local population, respectively.All of the rice grains that were sampled from Tabriz market were low in total arsenic compared to the standard. Nonetheless regular monitoring of all rice varieties should be continued. PMID:25648387

  14. Utilization of weedy rice for development of japonica hybrid rice (Oryza sativa L.).

    PubMed

    Tang, Liang; Ma, Dian Rong; Xu, Zheng Jin; Deng, Hua Feng; Chen, Wen Fu; Yuan, Long Ping

    2011-05-01

    Two representative weedy rice lines, three typical japonica varieties and three typical indica varieties were used for 6 pairs of reciprocal crosses. The morphological traits of twelve F(1) hybrid lines, their parents and four elite cultivars were investigated for heterosis over mid-parent (HM), over parent (HP) and competitive heterosis (CH) analysis. Traits detected in weedy rice lines seemed larger than those in cultivars and excellent heterosis was produced in weedy rice crossing with japonica rice. Although weedy rice kept closer relationships with japonica rice compared to indica rice. But the heterosis of reciprocal crosses between weedy rice and japonica was closed to those of crosses between indica rice and japonica rice. In six of one hundred and eighteen weedy rice lines, the fertility restore gene for BT type cytoplasmic male sterility (BT-CMS) were detected. Weedy rice was very valuable germplasm resources with the abundant polymorphism. Meanwhile, the disadvantage, lodging, shattering and incompact plant type, should be modified by hybridization, backcross and multiple cross with japonica rice. Although it is difficult to use weedy rice directly, weedy rice may be available to breed both male sterile line and restorer line through improvement, developing japonica hybrid rice.

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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 ...

  16. Changes in CH4 emission from rice fields from 1960 to 1990s: 1. Impacts of modern rice technology

    NASA Astrophysics Data System (ADS)

    Gon, Hugo Denier

    2000-03-01

    Four countries (Indonesia, Philippines, Thailand, and Nepal) were taken as an example to assess the impact of changes in rice cultivation on methane emissions from rice fields since the 1960s. The change of rice area by type of culture from 1960-1990s is estimated, and its relative contribution to national harvested rice area is calculated and multiplied with an emission factor, to derive the relative methane emission per unit rice land. Relative methane emission per ha rice land has increased since 1960 for all four countries, largely due to an increase in irrigated rice area and partly due to a decrease in upland rice area. Patterns of rice area changes and related emission changes differ considerably among countries. On the basis of the rice area increases between 1960 and the 1990s, significant increases in methane emissions from rice fields due to increases in total rice cultivated area are not to be expected in the future. The impact of modern rice variety adoption is assessed by relating methane emissions to rice production. The organic matter returned to the paddy soil is largely determined by rice biomass production which, given a certain yield, is different for traditional and modern rice varieties. By calculating total organic matter returned to rice paddy soils and assuming a constant fraction to be emitted as methane, rice production and methane emission can be related. The analysis indicates that (1) up to now, rice yield increases in countries with high modern rice variety adoption have not resulted in increased methane emissions per unit of harvested area and, (2) global annual emission from rice fields may be considerably lower than generally assumed. The introduction of modern rice varieties can be regarded as a historical methane emission mitigation strategy because higher rice yields resulted in lower or equal methane emissions.

  17. Changes in CH4 emission from rice fields from 1960 to 1990s. 1. Impacts of modern rice technology

    NASA Astrophysics Data System (ADS)

    van der Gon, Hugo Denier

    2000-03-01

    Four countries (Indonesia, Philippines, Thailand, and Nepal) were taken as an example to assess the impact of changes in rice cultivation on methane emissions from rice fields since the 1960s. The change of rice area by type of culture from 1960-1990s is estimated, and its relative contribution to national harvested rice area is calculated and multiplied with an emission factor, to derive the relative methane emission per unit rice land. Relative methane emission per ha rice land has increased since 1960 for all four countries, largely due to an increase in irrigated rice area and partly due to a decrease in upland rice area. Patterns of rice area changes and related emission changes differ considerably among countries. On the basis of the rice area increases between 1960 and the 1990s, significant increases in methane emissions from rice fields due to increases in total rice cultivated area are not to be expected in the future. The impact of modern rice variety adoption is assessed by relating methane emissions to rice production. The organic matter returned to the paddy soil is largely determined by rice biomass production which, given a certain yield, is different for traditional and modern rice varieties. By calculating total organic matter returned to rice paddy soils and assuming a constant fraction to be emitted as methane, rice production and methane emission can be related. The analysis indicates that (1) up to now, rice yield increases in countries with high modern rice variety adoption have not resulted in increased methane emissions per unit of harvested area and, (2) global annual emission from rice fields may be considerably lower than generally assumed. The introduction of modern rice varieties can be regarded as a historical methane emission mitigation strategy because higher rice yields resulted in lower or equal methane emissions.

  18. Basmati Rice Fraud under the Magnifying Glass of DNA Analysis.

    PubMed

    Fridez, Françoise

    2016-01-01

    Basmati rice is a perfumed rice of high commercial value which is easily adulterated. A list of rice varieties accepted as true Basmati is the subject of an agreement between Europe, Pakistan and India. Each rice variety can be characterized by DNA profiling, thus offering to the control authorities a powerful tool to detect fraud. Mixtures of authentic Basmati and non-Basmati varieties can be quantified. During the last six years, about one third of the analysed samples proved to be fraudulent.

  19. A Positive Feedback Loop between HEAT SHOCK PROTEIN101 and HEAT STRESS-ASSOCIATED 32-KD PROTEIN Modulates Long-Term Acquired Thermotolerance Illustrating Diverse Heat Stress Responses in Rice Varieties1[W][OPEN

    PubMed Central

    Lin, Meng-yi; Chai, Kuo-hsing; Ko, Swee-suak; Kuang, Lin-yun; Lur, Huu-Sheng; Charng, Yee-yung

    2014-01-01

    Heat stress is an important factor that has a negative impact on rice (Oryza sativa) production. To alleviate this problem, it is necessary to extensively understand the genetic basis of heat tolerance and adaptability to heat stress in rice. Here, we report the molecular mechanism underlying heat acclimation memory that confers long-term acquired thermotolerance (LAT) in this monocot plant. Our results showed that a positive feedback loop formed by two heat-inducible genes, HEAT SHOCK PROTEIN101 (HSP101) and HEAT STRESS-ASSOCIATED 32-KD PROTEIN (HSA32), at the posttranscriptional level prolongs the effect of heat acclimation in rice seedlings. The interplay between HSP101 and HSA32 also affects basal thermotolerance of rice seeds. These findings are similar to those reported for the dicot plant Arabidopsis (Arabidopsis thaliana), suggesting a conserved function in plant heat stress response. Comparison between two rice cultivars, japonica Nipponbare and indica N22 showed opposite performance in basal thermotolerance and LAT assays. ‘N22’ seedlings have a higher basal thermotolerance level than cv Nipponbare and vice versa at the LAT level, indicating that these two types of thermotolerance can be decoupled. The HSP101 and HSA32 protein levels were substantially higher in cv Nipponbare than in cv N22 after a long recovery following heat acclimation treatment, at least partly explaining the difference in the LAT phenotype. Our results point out the complexity of thermotolerance diversity in rice cultivars, which may need to be taken into consideration when breeding for heat tolerance for different climate scenarios. PMID:24520156

  20. Detection algorithm for multiple rice seeds images

    NASA Astrophysics Data System (ADS)

    Cheng, F.; Ying, Y. B.

    2006-10-01

    The objective of this research is to develop a digital image analysis algorithm for detection of multiple rice seeds images. The rice seeds used for this study involved a hybrid rice seed variety. Images of multiple rice seeds were acquired with a machine vision system for quality inspection of bulk rice seeds, which is designed to inspect rice seeds on a rotating disk with a CCD camera. Combining morphological operations and parallel processing gave improvements in accuracy, and a reduction in computation time. Using image features selected based on classification ability; a highly acceptable defects classification was achieved when the algorithm was implemented for all the samples to test the adaptability.

  1. Identification and characterization of a novel chloroplast/mitochondria co-localized glutathione reductase 3 involved in salt stress response in rice.

    PubMed

    Wu, Tsung-Meng; Lin, Wan-Rong; Kao, Yun-Ting; Hsu, Yi-Ting; Yeh, Ching-Hui; Hong, Chwan-Yang; Kao, Ching Huei

    2013-11-01

    Glutathione reductases (GRs) are important components of the antioxidant machinery that plants use to respond against abiotic stresses. In rice, one cytosolic and two chloroplastic GR isoforms have been identified. In this work, we describe the cloning and characterization of the full-length cDNA encoding OsGR3, a chloroplast-localized GR that up to now was considered as a non-functional enzyme because of assumed lack of N-terminal conserved domains. The expression of OsGR3 in E. coli validated that it can be translated as a protein with GR activity. OsGR3 shows 76 and 53 % identity with OsGR1 (chloroplastic) and OsGR2 (cytosolic), respectively. Phylogenetic analysis revealed 2 chloroplastic GRs in Poaceae species, including rice, sorghum and brachypodium, but only one chloroplastic GR in dicots. A plastid transit peptide is located at the N terminus of OsGR3, and genetic transformation of rice with a GR3-GFP fusion construct further confirmed its localization in chloroplasts. Furthermore, OsGR1 and OsGR3 are also targeted to mitochondria, which suggest a combined antioxidant mechanism in both chloroplasts and mitochondria. However, both isoforms showed a distinct response to salinity: the expression of OsGR3 but not OsGR1 was induced by salt stress. In addition, the transcript level of OsGR3 was greatly increased with salicylic acid treatment but was not significantly affected by methyl jasmonate, dehydration or heat shock stress. Our results provide new clues about the possible roles of functional OsGR3 in salt stress and biotic stress tolerance.

  2. PDH45 overexpressing transgenic tobacco and rice plants provide salinity stress tolerance via less sodium accumulation.

    PubMed

    Nath, Manoj; Garg, Bharti; Sahoo, Ranjan Kumar; Tuteja, Narendra

    2015-01-01

    Salinity stress negatively affects the crop productivity worldwide, including that of rice. Coping with these losses is a major concern for all countries. The pea DNA helicase, PDH45 is a unique member of helicase family involved in the salinity stress tolerance. However, the exact mechanism of the PDH45 in salinity stress tolerance is yet to be established. Therefore, the present study was conducted to investigate the mechanism of PDH45-mediated salinity stress tolerance in transgenic tobacco and rice lines along with wild type (WT) plants using CoroNa Green dye based sodium localization in root and shoot sections. The results showed that under salinity stress root and shoot of PDH45 overexpressing transgenic tobacco and rice accumulated less sodium (Na(+)) as compared to their respective WT. The present study also reports salinity tolerant (FL478) and salinity susceptible (Pusa-44) varieties of rice accumulated lowest and highest Na(+) level, respectively. All the varieties and transgenic lines of rice accumulate differential Na(+) ions in root and shoot. However, roots accumulate high Na(+) as compared to the shoots in both tobacco and rice transgenic lines suggesting that the Na(+) transport in shoot is somehow inhibited. It is proposed that the PDH45 is probably involved in the deposition of apoplastic hydrophobic barriers and consequently inhibit Na(+) transport to shoot and therefore confers salinity stress tolerance to PDH45 overexpressing transgenic lines. This study concludes that tobacco (dicot) and rice (monocot) transgenic plants probably share common salinity tolerance mechanism mediated by PDH45 gene.

  3. Plasma membrane localization is essential for Oryza sativa Pto-interacting protein 1a-mediated negative regulation of immune signaling in rice.

    PubMed

    Matsui, Hidenori; Fujiwara, Masayuki; Hamada, Satoshi; Shimamoto, Ko; Nomura, Yuko; Nakagami, Hirofumi; Takahashi, Akira; Hirochika, Hirohiko

    2014-09-01

    Oryza sativa Pto-interacting protein 1a (OsPti1a), an ortholog of tomato (Solanum lycopersicum) SlPti1, functions as a negative regulator of innate immunity in rice (Oryza sativa). In ospti1a mutants, the activation of immune responses, including hypersensitive response-like cell death, is caused by loss of the OsPti1a protein; however, it is as yet unclear how OsPti1a suppresses immune responses. Here, we report that OsPti1a localizes to detergent-resistant membrane fractions of the plasma membrane through lipid modification of the protein's amino terminus, which is highly conserved among Pti1 orthologs in several plant species. Importantly, mislocalization of OsPti1a after deletion of its amino terminus reduced its ability to complement the mutant phenotypes, including hypersensitive response-like cell death. Furthermore, complex formation of OsPti1a depends on its amino terminus-mediated membrane localization. Liquid chromatography-tandem mass spectrometry analysis of OsPti1a complex-interacting proteins identified several defense-related proteins. Collectively, these findings indicate that appropriate complex formation by OsPti1a at the plasma membrane is required for the negative regulation of plant immune responses in rice.

  4. Blast resistance in rice: a review of conventional breeding to molecular approaches.

    PubMed

    Miah, G; Rafii, M Y; Ismail, M R; Puteh, A B; Rahim, H A; Asfaliza, R; Latif, M A

    2013-03-01

    Blast disease caused by the fungal pathogen Magnaporthe oryzae is the most severe diseases of rice. Using classical plant breeding techniques, breeders have developed a number of blast resistant cultivars adapted to different rice growing regions worldwide. However, the rice industry remains threatened by blast disease due to the instability of blast fungus. Recent advances in rice genomics provide additional tools for plant breeders to improve rice production systems that would be environmentally friendly. This article outlines the application of conventional breeding, tissue culture and DNA-based markers that are used for accelerating the development of blast resistant rice cultivars. The best way for controlling the disease is to incorporate both qualitative and quantitative genes in resistant variety. Through conventional and molecular breeding many blast-resistant varieties have been developed. Conventional breeding for disease resistance is tedious, time consuming and mostly dependent on environment as compare to molecular breeding particularly marker assisted selection, which is easier, highly efficient and precise. For effective management of blast disease, breeding work should be focused on utilizing the broad spectrum of resistance genes and pyramiding genes and quantitative trait loci. Marker assisted selection provides potential solution to some of the problems that conventional breeding cannot resolve. In recent years, blast resistant genes have introgressed into Luhui 17, G46B, Zhenshan 97B, Jin 23B, CO39, IR50, Pusa1602 and Pusa1603 lines through marker assisted selection. Introduction of exotic genes for resistance induced the occurrence of new races of blast fungus, therefore breeding work should be concentrated in local resistance genes. This review focuses on the conventional breeding to the latest molecular progress in blast disease resistance in rice. This update information will be helpful guidance for rice breeders to develop durable blast

  5. Maize Varieties Released in Different Eras Have Similar Root Length Density Distributions in the Soil, Which Are Negatively Correlated with Local Concentrations of Soil Mineral Nitrogen

    PubMed Central

    Ning, Peng; Li, Sa; White, Philip J.; Li, Chunjian

    2015-01-01

    Larger, and deeper, root systems of new maize varieties, compared to older varieties, are thought to have enabled improved acquisition of soil resources and, consequently, greater grain yields. To compare the spatial distributions of the root systems of new and old maize varieties and their relationships with spatial variations in soil concentrations of available nitrogen (N), phosphorus (P) and potassium (K), two years of field experiments were performed using six Chinese maize varieties released in different eras. Vertical distributions of roots, and available N, P and K in the 0–60 cm soil profile were determined in excavated soil monoliths at silking and maturity. The results demonstrated that new maize varieties had larger root dry weight, higher grain yield and greater nutrient accumulation than older varieties. All varieties had similar total root length and vertical root distribution at silking, but newer varieties maintained greater total root length and had more roots in the 30–60 cm soil layers at maturity. The spatial variation of soil mineral N (Nmin) in each soil horizon was larger than that of Olsen-P and ammonium-acetate-extractable K, and was inversely correlated with root length density (RLD), especially in the 0–20 cm soil layer. It was concluded that greater acquisition of mineral nutrients and higher yields of newer varieties were associated with greater total root length at maturity. The negative relationship between RLD and soil Nmin at harvest for all varieties suggests the importance of the spatial distribution of the root system for N uptake by maize. PMID:25799291

  6. Isolation, in silico characterization, localization and expression analysis of abiotic stress-responsive rice G-protein β subunit (RGB1).

    PubMed

    Yadav, Dinesh K; Shukla, Devesh; Tuteja, Narendra

    2014-01-01

    Heterotrimeric G-proteins constitute the classical signaling paradigm along with their cognate G-protein coupled receptors (GPCRs) and appropriate downstream effectors. G-protein complex is composed of highly conserved Gα, Gβ, and Gγ subunits. In the present study, we have characterized the cis-regulatory elements of the promoter, signature motifs, transcript profile in response to abiotic stresses, and sub-cellular localization of G-protein β subunit RGB1(I) from Indica rice. The RGB1(I) promoter sequence has various stress-related cis-regulatory elements suggesting its role in abiotic stress signaling. Presence of six WD-40 repeat signature motifs in RGB1(I) suggest its role in exchange of GDP by GTP in Gα subunit and receptor recognition. Presence of multiple N-myristoylation consensus sites in RGB1(I) protein sequence, which is necessary for membrane localization of protein, confirms the association of RGB1(I) in plasma membrane. Extrinsic association of RGB1(I) with plasma membrane seems essential for its role in regulation of signaling pathways and adaptation to high salt stress. We report the sub-cellular localization of RGB1(I) in plasma membrane, cytosol and nucleus. The localization of RGB1(I) in nucleus supports its possible interaction with transcription factors regulating the expression of salt stress responsive genes. The RGB1(I) transcript was upregulated under KCl, cold, dehydration and micronutrient (Mn (2+) and Zn (2+)) stress. However, transcript variation under elevated temperature, ABA, NaCl, and toxic heavy metals (viz. arsenite, arsenate, cadmium and lead) was not encouraging. These evidences indicate an active and significant role of RGB1(I) in the regulation of abiotic stresses in rice and propound its possible exploitation in the development of abiotic stress tolerance in crops.

  7. Potential health risk of total arsenic from consumption of farm rice (Oryza sativa) from the southern Caspian Sea littoral and from imported rice in Iran.

    PubMed

    Rezaitabar, Soheila; Esmaili-Sari, Abbas; Bahramifar, Nader

    2012-04-01

    In this study, Arsenic (As) was measured in several varieties of imported and local cultivated rice. Soil samples collected from rice farms situated in south Caspian Sea (Iran) were also studied. The mean concentration of As in imported rice, local farmed rice and soil, were determined as 0.28, 0.39 and 3.80 μg g(-1) dry weight, respectively. Estimated daily intake of As through human consumption of imported and local produced rice was 0.77 and 1.074 μg day(-1) kg(-1) B.W., respectively. These values are much lower than the tolerable daily intakes estimated by JECFA. The As concentration in the soil (3.80 μg g(-1) dry) was below acceptable limit for agricultural soil of 20.0 mg kg(-1) as recommended by the European Community (EC). No correlation between the As concentrations in rice and soil samples was found (p > 0.05).

  8. Rice: a high or low glycemic index food?

    PubMed

    Miller, J B; Pang, E; Bramall, L

    1992-12-01

    We determined the glycemic (GI) and insulin-index (II) values for 12 rice products, using eight healthy subjects. The products were brown and white versions of three commercial varieties of rice [two varieties with normal amylose content (20%) and the other with 28% amylose], a waxy rice (0-2% amylose), a converted rice, a quick-cooking brown rice, puffed rice cakes, rice pasta, and rice bran. The GI of the rices ranged from 64 +/- 9 to 93 +/- 11, where glucose = 100. The high amylose rice gave a lower GI and II (P < 0.01) than did the normal-amylose and waxy-rice varieties. The converted rice and most other rice products gave a high GI. Insulin indices correlated positively with GI (r = 0.75, P < 0.05), although they were lower than expected. These results indicate that many varieties of rice, whether white, brown, or parboiled, should be classified as high GI foods. Only high-amylose varieties are potentially useful in low-GI diets.

  9. Increasing rice plant growth by Trichoderma sp.

    NASA Astrophysics Data System (ADS)

    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.

  10. Rice epigenomics and epigenetics: challenges and opportunities.

    PubMed

    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.

  11. Mapping QTLs for traits related to salinity tolerance at seedling stage of rice (Oryza sativa L.): an agrigenomics study of an Iranian rice population.

    PubMed

    Ghomi, Khadijeh; Rabiei, Babak; Sabouri, Hossein; Sabouri, Atefeh

    2013-05-01

    Rice (Oryza sativa L.) is one of the most important food crops in the world, especially in Asian countries, and salinity is a major constraint to the sustainability and expansion of rice cultivation. Genetically improving salt tolerance of rice is a highly important objective of rice breeding programs. Traits such as salt tolerance are quantitatively inherited. Hence, mapping quantitative trait loci (QTL) with molecular markers can be very helpful to plant breeders in the field of agricultural genomics (AgriGenomics). In this investigation, QTL analysis of physiological traits related to salt tolerance was carried out using F2:4 population of rice derived from a cross between a salt-tolerant variety, Gharib (indica), and a salt-sensitive variety, Sepidroud (indica). A linkage map based on 148 F2 individuals was constructed with 131 SSR markers and 105 AFLP markers, covering 2475.7 cM of rice genome with an average distance of 10.48 cM between flanking markers. A total of 41 QTLs for twelve physiological traits under salinity stress were detected distributed on all rice chromosomes, some of them being reported for the first time. Also, overlapping of QTLs related to salt tolerance were observed in this study. Some of the identified QTLs on specific chromosomal regions explaining high phenotypic variance could be used for marker-assisted selection (MAS) programs. New QTLs retrieved in this study play an important role in growth of rice at seedling stage in an Iranian local population under high salinity conditions.

  12. Evaluation of weather-based rice yield models in India

    NASA Astrophysics Data System (ADS)

    Sudharsan, D.; Adinarayana, J.; Reddy, D. Raji; Sreenivas, G.; Ninomiya, S.; Hirafuji, M.; Kiura, T.; Tanaka, K.; Desai, U. B.; Merchant, S. N.

    2013-01-01

    The objective of this study was to compare two different rice simulation models—standalone (Decision Support System for Agrotechnology Transfer [DSSAT]) and web based (SImulation Model for RIce-Weather relations [SIMRIW])—with agrometeorological data and agronomic parameters for estimation of rice crop production in southern semi-arid tropics of India. Studies were carried out on the BPT5204 rice variety to evaluate two crop simulation models. Long-term experiments were conducted in a research farm of Acharya N G Ranga Agricultural University (ANGRAU), Hyderabad, India. Initially, the results were obtained using 4 years (1994-1997) of data with weather parameters from a local weather station to evaluate DSSAT simulated results with observed values. Linear regression models used for the purpose showed a close relationship between DSSAT and observed yield. Subsequently, yield comparisons were also carried out with SIMRIW and DSSAT, and validated with actual observed values. Realizing the correlation coefficient values of SIMRIW simulation values in acceptable limits, further rice experiments in monsoon (Kharif) and post-monsoon (Rabi) agricultural seasons (2009, 2010 and 2011) were carried out with a location-specific distributed sensor network system. These proximal systems help to simulate dry weight, leaf area index and potential yield by the Java based SIMRIW on a daily/weekly/monthly/seasonal basis. These dynamic parameters are useful to the farming community for necessary decision making in a ubiquitous manner. However, SIMRIW requires fine tuning for better results/decision making.

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

    PubMed

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

    2016-12-07

    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.

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

    PubMed Central

    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

  15. Effects of rice harvest moisture on kernel damage and milled rice surface free fatty acid levels.

    PubMed

    Parker, Amanda M; Proctor, Andrew; Eason, Robert L; Jain, Vishal

    2007-01-01

    Surface free fatty acid (FFA) on milled rice is a key factor in determining rice quality and acceptability to the brewing industry. Rice FFA oxidizes, causing off-flavors and odors to develop, compromising the brewing quality of milled rice. The effect of harvest moisture (13%, 16%, and 20%), harvester type (1688 Case and 9500 John Deere), and rice variety (Cocodrie and Bengal) on harvest damaged rough rice and milled rice surface FFA after drying to 12% moisture and 6 mo rough rice storage was examined. The Case harvester produced more damaged kernels than the John Deere harvester, but this was not reflected in surface FFA development. There were no significant FFA differences in variety or harvester type. Rice harvested at a higher moisture content (20%) produced significantly greater FFA values, with a peak near 0.1%, than rice harvested at lower moisture contents (13% and 16%), which had FFA values near 0.08%. Retention of bran by damaged kernels at high harvest moisture probably was responsible for promoting surface FFA development, but if bran was lost at lower harvest moistures, surface FFA, development was limited. Harvest moisture affected milled rice FFA, although rough rice was dried to 12% immediately after harvesting.

  16. The 3,000 rice genomes project: new opportunities and challenges for future rice research.

    PubMed

    Li, Jia-Yang; Wang, Jun; Zeigler, Robert S

    2014-01-01

    Rice is the world's most important staple grown by millions of small-holder farmers. Sustaining rice production relies on the intelligent use of rice diversity. The 3,000 Rice Genomes Project is a giga-dataset of publically available genome sequences (averaging 14× depth of coverage) derived from 3,000 accessions of rice with global representation of genetic and functional diversity. The seed of these accessions is available from the International Rice Genebank Collection. Together, they are an unprecedented resource for advancing rice science and breeding technology. Our immediate challenge now is to comprehensively and systematically mine this dataset to link genotypic variation to functional variation with the ultimate goal of creating new and sustainable rice varieties that can support a future world population that will approach 9.6 billion by 2050.

  17. Processes Underpinning Development and Maintenance of Diversity in Rice in West Africa: Evidence from Combining Morphological and Molecular Markers

    PubMed Central

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

    2014-01-01

    We assessed the interplay of artificial and natural selection in rice adaptation in low-input farming systems in West Africa. Using 20 morphological traits and 176 molecular markers, 182 farmer varieties of rice (Oryza spp.) from 6 West African countries were characterized. Principal component analysis showed that the four botanical groups (Oryza sativa ssp. indica, O. sativa ssp. japonica, O. glaberrima, and interspecific farmer hybrids) exhibited different patterns of morphological diversity. Regarding O. glaberrima, morphological and molecular data were in greater conformity than for the other botanical groups. A clear difference in morphological features was observed between O. glaberrima rices from the Togo hills and those from the Upper Guinea Coast, and among O. glaberrima rices from the Upper Guinea Coast. For the other three groups such clear patterns were not observed. We argue that this is because genetic diversity is shaped by different environmental and socio-cultural selection pressures. For O. glaberrima, recent socio-cultural selection pressures seemed to restrict genetic diversity while this was not observed for the other botanical groups. We also show that O. glaberrima still plays an important role in the selection practices of farmers and resulting variety development pathways. This is particularly apparent in the case of interspecific farmer hybrids where a relationship was found between pericarp colour, panicle attitude and genetic diversity. Farmer varieties are the product of long and complex trajectories of selection governed by local human agency. In effect, rice varieties have emerged that are adapted to West African farming conditions through genotype × environment × society interactions. The diversity farmers maintain in their rice varieties is understood to be part of a risk-spreading strategy that also facilitates successful and often serendipitous variety innovations. We advocate, therefore, that farmers and farmer varieties should

  18. (/sup 3/H)Batrachotoxinin A 20 alpha-benzoate binding to voltage-sensitive sodium channels: a rapid and quantitative assay for local anesthetic activity in a variety of drugs

    SciTech Connect

    McNeal, E.T.; Lewandowski, G.A.; Daly, J.W.; Creveling, C.R.

    1985-03-01

    (/sup 3/H)Batrachotoxinin A benzoate ((/sup 3/H)BTX-B) binds with high affinity to sites on voltage-dependent sodium channels in a vesicular preparation from guinea pig cerebral cortex. In this preparation, local anesthetics competitively antagonize the binding of (/sup 3/H)BTX-B. The potencies of some 40 classical local anesthetics and a variety of catecholamine, histamine, serotonin, adenosine, GABA, glycine, acetylcholine, and calcium antagonists, tranquilizers, antidepressants, barbiturates, anticonvulsants, steroids, vasodilators, antiinflammatories, anticoagulants, analgesics, and other agents have been determined. An excellent correlation with the known local anesthetic activity of many of these agents indicate that antagonism of binding of (/sup 3/H)BTX-B binding provides a rapid, quantitative, and facile method for the screening and investigation of local anesthetic activity.

  19. Determination of sockage for accurate rough rice quality assessment

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Determination of dockage of freshly harvested rice is crucial for precise development of a universal rice shrinking chart. The objectives of this research were to determine the effect of different factors, including rice variety, farm location, harvest moisture and time, drying, dropping, weather ev...

  20. Correlation analysis of simulated MODIS vegetation indices and the red edge and rice agricultural parameter

    NASA Astrophysics Data System (ADS)

    Cheng, Qian; Wu, Xiuju

    2007-10-01

    In this study, Hyperspectral data of two variety of rice (common rice and hybrid rice) in whole growing stage during 2002 and 2003 was measured using the ASD FieldSpec UV/VNIR Spectroradiometer with resolution of 3 nm, and the LAI and leaf chlorophyll content of rice agricultural parameter were obtained. Analyses of the correlation between rice agricultural parameter, and hyperspectal data, normalized difference vegetation index (NDVI), enhanced vegetation index (EVI) and the red-edge position (REP) were studied. Results showed that a strong non-linear correlation was found between the rice LAI of two varieties and REP. The REP, EVI and NDVI were well related with LAI for the common rice, but the REP and EVI were more sensitive than the NDVI to rice LAI for the hybrid rice because of different body for two variety rice.

  1. Effects of simulated acid rain on the morphology, phenology and dry biomass of a local variety of maize (Suwan-1) in Southwestern Nigeria.

    PubMed

    Macaulay, Babajide Milton; Enahoro, Gloria Ebarunosen

    2015-10-01

    Effects of acid rain on the morphology, phenology and dry biomass of maize (Suwan-1 variety) were investigated. The maize seedlings were subjected to different pH treatments (1.0, 2.0, 3.0, 4.0, 5.0 and 6.0) of simulated acid rain (SAR) with pH 7.0 as the control for a period of 90 days. The common morphological defects due to SAR application were necrosis and chlorosis. It was observed that necrosis increased in severity as the acidity increased whilst chlorosis was dominant as the acidity decreased. SAR encouraged rapid floral and cob growth but with the consequence of poor floral and cob development in pH 1.0 to 3.0 treatments. The result for the dry biomass indicates that pH treatments 2.0 to 7.0 for total plant biomass were not significantly different (P > 0.05) from one another, but were all significantly higher (P < 0.05) than pH 1.0. Therefore, it may be deduced that Suwan-1 has the potential to withstand acid rain but with pronounced morphological and phenological defects which, however, have the capacity to reduce drastically the market value of the crop. Therefore, it may be concluded that Suwan-1 tolerated acid rain in terms of the parameters studied at pH 4.0 to 7.0 which makes it a suitable crop in acid rain-stricken climes. This research could also serve as a good reference for further SAR studies on maize or other important cereals.

  2. Energy use pattern in rice milling industries-a critical appraisal.

    PubMed

    Goyal, S K; Jogdand, S V; Agrawal, A K

    2014-11-01

    Rice milling industry is one of the most energy consuming industries. Like capital, labour and material, energy is one of the production factors which used to produce final product. In economical term, energy is demand-derived goods and can be regarded as intermediate good whose demand depends on the demand of final product. This paper deals with various types of energy pattern used in rice milling industries viz., thermal energy, mechanical energy, electrical energy and human energy. The important utilities in a rice mill are water, air, steam, electricity and labour. In a rice mill some of the operations are done manually namely, cleaning, sun drying, feeding paddy to the bucket elevators, weighing and packaging, etc. So the man-hours are also included in energy accounting. Water is used for soaking and steam generation. Electricity is the main energy source for these rice mills and is imported form the state electricity board grids. Electricity is used to run motors, pumps, blowers, conveyors, fans, lights, etc. The variations in the consumption rate of energy through the use of utilities during processing must also accounted for final cost of the finished product. The paddy milling consumes significant quantity of fuels and electricity. The major energy consuming equipments in the rice milling units are; boilers and steam distribution, blowers, pumps, conveyers, elevators, motors, transmission systems, weighing, etc. Though, wide variety of technologies has been evolved for efficient use of energy for various equipments of rice mills, so far, only a few have improved their energy efficiency levels. Most of the rice mills use old and locally available technologies and are also completely dependent on locally available technical personnel.

  3. Association mapping of stigma and spikelet characteristics in rice (Oryza sativa L.)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Hybrid rice exhibits a yield advantage of 15 to 20 percent (or more than one ton of paddy rice per hectare) over the best traditional varieties. Because rice plants are self-pollinating, commercial production of hybrid seed plays a key role in successful implementation of hybrid rice. Stigma exserti...

  4. Coat proteins of Rice tungro bacilliform virus and Mungbean yellow mosaic virus contain multiple nuclear-localization signals and interact with importin alpha.

    PubMed

    Guerra-Peraza, O; Kirk, D; Seltzer, V; Veluthambi, K; Schmit, A C; Hohn, T; Herzog, E

    2005-06-01

    Transport of the viral genome into the nucleus is an obligatory step in the replication cycle of plant pararetro- and geminiviruses. In both these virus types, the multifunctional coat protein (CP) is thought to be involved in this process. Here, a green fluorescent protein tagging approach was used to demonstrate nuclear import of the CPs of Rice tungro bacilliform virus (RTBV) and Mungbean yellow mosaic virus--Vigna (MYMV) in Nicotiana plumbaginifolia protoplasts. In both cases, at least two nuclear localization signals (NLSs) were identified and characterized. The NLSs of RTBV CP are located within both N- and C-terminal regions (residues 479KRPK/497KRK and 744KRK/758RRK), and those of MYMV CP within the N-terminal part (residues 3KR and 41KRRR). The MYMV and RTBV CP NLSs resemble classic mono- and bipartite NLSs, respectively. However, the N-terminal MYMV CP NLS and both RTBV CP NLSs show peculiarities in the number and position of basic residues. In vitro pull-down assays revealed interaction of RTBV and MYMV CPs with the nuclear import factor importin alpha, suggesting that both CPs are imported into the nucleus via an importin alpha-dependent pathway. The possibility that this pathway could serve for docking of virions to the nucleus is discussed.

  5. Arsenic in rice: a cause for concern.

    PubMed

    Hojsak, Iva; Braegger, Christian; Bronsky, Jiri; Campoy, Cristina; Colomb, Virginie; Decsi, Tamas; Domellöf, Magnus; Fewtrell, Mary; Mis, Nataša Fidler; Mihatsch, Walter; Molgaard, Christian; van Goudoever, Johannes

    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 of the rice products, strict regulation should be enforced regarding arsenic content. Moreover, infants and young children should consume a balanced diet including a variety of grains as carbohydrate sources. Although rice protein-based infant formulas are an option for infants with cows' milk protein allergy, the inorganic arsenic content should be declared and the potential risks should be considered when using these products.

  6. Origin, dispersal, cultivation and variation of rice.

    PubMed

    Khush, G S

    1997-09-01

    There are two cultivated and twenty-one wild species of genus Oryza. O. sativa, the Asian cultivated rice is grown all over the world. The African cultivated rice, O. glaberrima is grown on a small scale in West Africa. The genus Oryza probably originated about 130 million years ago in Gondwanaland and different species got distributed into different continents with the breakup of Gondwanaland. The cultivated species originated from a common ancestor with AA genome. Perennial and annual ancestors of O. sativa are O. rufipogon and O. nivara and those of O. glaberrima are O. longistaminata, O. breviligulata and O. glaberrima probably domesticated in Niger river delta. Varieties of O. sativa are classified into six groups on the basis of genetic affinity. Widely known indica rices correspond to group I and japonicas to group VI. The so called javanica rices also belong to group VI and are designated as tropical japonicas in contrast to temperate japonicas grown in temperate climate. Indica and japonica rices had a polyphyletic origin. Indicas were probably domesticated in the foothills of Himalayas in Eastern India and japonicas somewhere in South China. The indica rices dispersed throughout the tropics and subtropics from India. The japonica rices moved northward from South China and became the temperate ecotype. They also moved southward to Southeast Asia and from there to West Africa and Brazil and became tropical ecotype. Rice is now grown between 55 degrees N and 36 degrees S latitudes. It is grown under diverse growing conditions such as irrigated, rainfed lowland, rainfed upland and floodprone ecosystems. Human selection and adaptation to diverse environments has resulted in numerous cultivars. It is estimated that about 120,000 varieties of rice exist in the world. After the establishment of International Rice Research Institute in 1960, rice varietal improvement was intensified and high yielding varieties were developed. These varieties are now planted to 70

  7. Simulating rice response to climate change

    SciTech Connect

    Singh, U.; Padilla, J.L. |

    1995-12-31

    The response of rice (Oryza sativa L.) to elevated CO{sub 2} concentration and temperature increase was simulated using the CERES-rice model. CERES-rice belongs to the International Benchmark Sites Network for Agrotechnology Transfer (IBSNAT) family of crop and nutrient dynamics models. Long-term historical data from the International Rice Research Institute (IRRI) wetland site was used to quantify the climatic change effects. The model simulated such beneficial effects of CO{sub 2} enrichment as increased grain yields, reduced transpiration, increased water use efficiency, improved use of intercepted radiation, reduced N losses, and higher N use efficiency. The trends were reversed for all of the above parameters with increase in temperature. CERES-rice simulated these negative trends in low input rice production as well. Based on the model`s prediction, some of the negative effects of temperature increase in warmer regions of the world could be offset by use of rice varieties that are tolerant to high temperature-induced spikelet sterility, and planting varieties with longer growth duration, particularly, longer grain filling duration. With improved varieties and good management future impact of climate change could be capitalized to have positive effects on rice production. Although the model has been extensively tested, it is critical to validate it with field data from extreme temperature and CO{sub 2} level studies. 33 refs., 13 figs., 3 tabs.

  8. Rayada specialty: the forgotten resource of elite features of rice

    PubMed Central

    2013-01-01

    Crop domestication and thereafter gradual selection or directional breeding have narrowed the genetic diversity of elite varieties and even promoted gathering of deleterious mutations in their stress response mechanisms, whereas local ecotypes, landraces and wild relatives still growing on native environment and preferences keep the genetic diversities for features like stress tolerance. Rayada is such an exceptional ecotype, variant of typical deepwater rice, completely endemic to certain areas of Madhumati river tracts of Bangladesh and still shares some features of wild rices. Multiple physiological features of Rayadas are distinctly different from typical deepwater rice. Tolerance to prolonged flood, submergence and cold are special features along with strong photoperiod sensitivity and lack of dormancy. Moreover, longer root system and prompt recovery capacity make it as an elite resource of stress tolerance. However, it has long been neglected because of mainly its long life cycle and poor yield. This review examines the specialty of Rayada rice and the potential use of its unique traits. PMID:24359642

  9. The local impact of a coal-fired power plant on inorganic mercury and methyl-mercury distribution in rice (Oryza sativa L.).

    PubMed

    Xu, Xiaohang; Meng, Bo; Zhang, Chao; Feng, Xinbin; Gu, Chunhao; Guo, Jianyang; Bishop, Kevin; Xu, Zhidong; Zhang, Sensen; Qiu, Guangle

    2017-04-01

    Emission from coal-fired power plants is one of the major anthropogenic sources of mercury (Hg) in the environment, because emitted Hg can be quickly deposited nearby the source, attention is paid to the effects of coal-burning facilities on levels of toxic methyl-mercury (MeHg) in biota near such sources. Since rice is an agricultural crop that can bio-accumulate MeHg, the potential effects of a large Hg-emitting coal-fired power plant in Hunan Province, China on both inorganic Hg (Hg(II)) and MeHg distributions in rice was investigated. Relatively high MeHg (up to 3.8 μg kg(-1)) and Hg(II) (up to 22 μg kg(-1)) concentrations were observed in rice samples collected adjacent to the plant, suggesting a potential impact of Hg emission from the coal fired power plant on the accumulation of Hg in rice in the area. Concentrations of MeHg in rice were positively correlated with soil MeHg, soil S, and gaseous elemental Hg (GEM) in ambient air. Soil MeHg was the most important factor controlling MeHg concentrations in rice. The methylation of Hg in soils may be controlled by factors such as the chemical speciation of inorganic Hg, soil S, and ambient GEM.

  10. Oryzabase. An integrated biological and genome information database for rice.

    PubMed

    Kurata, Nori; Yamazaki, Yukiko

    2006-01-01

    The aim of Oryzabase is to create a comprehensive view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information (http://www.shigen.nig.ac.jp/rice/oryzabase/top/top.jsp). The database contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. The anatomical description of rice development is unique and is the first known representation for rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. The systematic presentation of a large number of rice mutant and mutant trait genes is indispensable, as is description of research in wild strains, core collections, and their detailed characterization. Several genetic, physical, and expression maps with full genome and cDNA sequences are also combined with biological data in Oryzabase. These datasets, when pooled together, could provide a useful tool for gaining greater knowledge about the life cycle of rice, the relationship between phenotype and gene function, and rice genetic diversity. For exchanging community information, Oryzabase publishes the Rice Genetics Newsletter organized by the Rice Genetics Cooperative and provides a mailing service, rice-e-net/rice-net.

  11. Iron biofortification of myanmar rice.

    PubMed

    Aung, May Sann; Masuda, Hiroshi; Kobayashi, Takanori; Nakanishi, Hiromi; Yamakawa, Takashi; Nishizawa, Naoko K

    2013-01-01

    Iron (Fe) deficiency 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 or high-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.

  12. Golden Indica and Japonica rice lines amenable to deregulation.

    PubMed

    Hoa, Tran Thi Cuc; Al-Babili, Salim; Schaub, Patrick; Potrykus, Ingo; Beyer, Peter

    2003-09-01

    As an important step toward free access and, thus, impact of GoldenRice, a freedom-to-operate situation has been achieved for developing countries for the technology involved. Specifically, to carry the invention beyond its initial "proof-of-concept" status in a Japonica rice (Oryza sativa) cultivar, we report here on two transformed elite Indica varieties (IR64 and MTL250) plus one Japonica variety Taipei 309. Indica varieties are predominantly consumed in the areas with vitamin A deficiency. To conform with regulatory constraints, we changed the vector backbone, investigated the absence of beyond-border transfer, and relied on Agrobacterium tumefaciens-mediated transformation to obtain defined integration patterns. To avoid an antibiotic selection system, we now rely exclusively on phosphomannose isomerase as the selectable marker. Single integrations were given a preference to minimize potential epigenetic effects in subsequent generations. These novel lines, now in the T(3) generation, are highly valuable because they are expected to more readily receive approval for follow-up studies such as nutritional and risk assessments and for breeding approaches leading to locally adapted variety development.

  13. [Comparison on submergence tolerance of different type rice at tillering stage in lower reaches of Yangtze River].

    PubMed

    Ming, Liu; Yan, Li; Gui-hua, Guo; Hai-yan, Liu; Gang-hua, Li; Shao-hua, Wang; Zheng-hui, Liu; Yan-feng, Ding

    2015-05-01

    The agronomic traits, physiological characteristics and yield traits of 9 rice varieties popularized in lower reaches of Yangtze River were investigated under submergence stress at the tillering stage. The differences of environmental adaptability to submergence stress for conventional japonica rice, indica hybrid rice and hybrid japonica rice, were also analyzed and compared. The results showed that the stem and the upper three leaves under submergence stress were elongated compared with the control. And the elongation of the different varieties was shown as, hybrid japonica rice > indica hybrid rice > conventional japonica rice. As to the numbers of tillers and green leaves, and the aboveground dry mass, the reduction of indica hybrid rice was all between hybrid japonica rice and conventional japonica rice. The damage of hybrid japonica was the lightest. The content of MDA in the leaves of conventional japonica rice increased, while the activities of SOD and CAT decreased. However, the performances of hybrid japonica rice and indica hybrid rice were opposite with conventional japonica rice. The yield loss of conventional japonica rice was significantly higher than those of the other types of rice. These results suggested that the submergence tolerance ability of hybrid japonica rice is superior to indica hybrid rice, and the submergence tolerance ability of conventional japonica rice is the weakest.

  14. Identification of rice blast resistance genes using international monogenic differentials

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Rice blast disease, caused by the fungal pathogen Magnaporthe oryzae, is one of the most devastating diseases of rice that severely affects crop production in Jilin Province, Northeast China, where temperate japonica rice is primarily grown. In the present study, 44 representative local blast isolat...

  15. Fine mapping and identification of candidate rice genes associated with qSTV11(SG), a major QTL for rice stripe disease resistance.

    PubMed

    Kwon, Tackmin; Lee, Jong-Hee; Park, Soo-Kwon; Hwang, Un-Ha; Cho, Jun-Hyun; Kwak, Do-Yeon; Youn, Yeong-Nam; Yeo, Un-Sang; Song, You-Chun; Nam, Jaesung; Kang, Hang-Won; Nam, Min-Hee; Park, Dong-Soo

    2012-09-01

    Rice stripe disease, caused by rice stripe virus (RSV) is a serious constraint to rice production in subtropical regions of East Asia. We performed fine mapping of a RSV resistance QTL on chromosome 11, qSTV11 ( SG ), using near-isogenic lines (NILs, BC(6)F(4)) derived from a cross between the highly resistant variety, Shingwang, and the highly susceptible variety, Ilpum, using 11 insertion and deletion (InDel) markers. qSTV11 ( SG ) was localized to a 150-kb region between InDel 11 (17.86 Mbp) and InDel 5 (18.01 Mbp). Among the two markers in this region, InDel 7 is diagnostic of RSV resistance in 55 Korean japonica and indica rice varieties. InDel 7 could also distinguish the allele type of Nagdong, Shingwang, Mudgo, and Pe-bi-hun from Zenith harboring the Stv-b ( i ) allele. As a result, qSTV11 ( SG ) is likely to be the Stv-b ( i ) allele. There were 21 genes in the 150-kb region harboring the qSTV11 ( SG ) locus. Three of these genes, LOC_Os11g31430, LOC_Os11g31450, and LOC_Os11g31470, were exclusively expressed in the susceptible variety. These expression profiles were consistent with the quantitative nature along with incomplete dominance of RSV resistance. Sequencing of these genes showed that there were several amino acid substitutions between susceptible and resistant varieties. Putative functions of these candidate genes for qSTV11 (SG) are discussed.

  16. Evaluation of the potential role of glufosinate-tolerant rice in integrated pest management programs for rice water weevil (Coleoptera: Curculionidae).

    PubMed

    Tindall, K V; Stout, M J; Williams, B J

    2004-12-01

    The impact of a herbicide-tolerant rice, Oryza sativa L., variety was assessed for its resistance to rice water weevil, Lissorhoptrus oryzophilus Kuschel (Coleoptera: Curculionidae), and its place in current integrated pest management (IPM) programs. Greenhouse experiments were conducted to evaluate the resistance of a glufosinate-tolerant rice variety and its glufosinate-susceptible parent line Bengal to the rice water weevil in the presence and absence of glufosinate applications. The LC50 dose-response and behavioral effects of glufosinate on adult rice water weevils also were studied. Field studies investigated the impacts of glufosinate-tolerant rice on rice water weevil management in the presence and absence of glufosinate under early and delayed flood conditions. Greenhouse studies demonstrated that in the absence of glufosinate, oviposition was 30% higher on the glufosinate-tolerant rice line than on Bengal rice or on glufosinate-tolerant line treated with recommended rates of commercially formulated glufosinate. Applications of glufosinate to glufosinate-tolerant rice resulted in a 20% reduction in rice water weevil larval densities compared with nontreated glufosinate-tolerant rice. The LC50 of glufosinate against adult rice water weevil was nearly 2 times the concentration recommended for application to glufosinate-tolerant rice. There was no difference in the amount of leaf area consumed by adult rice water weevils on glufosinate-treated and nontreated foliage. The absence of direct toxicity of glufosinate to rice water weevil at recommended glufosinate use rates and lack of behavioral effects suggest that the reduction in rice water weevil densities observed after glufosinate applications resulted from herbicide-induced plant resistance. Field experiments showed that neither rice variety nor herbicide use affected larval densities; however, delaying flood and applying insecticide effectively reduced numbers of rice water weevil larvae.

  17. QTLs analysis for resistance to blast disease in US weedy rice

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Understanding the genetic architecture of adaptation is of great importance in evolutionary biology. US weedy rice is well-adapted to the local conditions in US rice fields. Rice blast disease is one of the most destructive diseases of cultivated rice worldwide. However, information about resistance...

  18. Phylogeography of Asian wild rice, Oryza rufipogon, reveals multiple independent domestications of cultivated rice, Oryza sativa.

    PubMed

    Londo, Jason P; Chiang, Yu-Chung; Hung, Kuo-Hsiang; Chiang, Tzen-Yuh; Schaal, Barbara A

    2006-06-20

    Cultivated rice, Oryza sativa L., represents the world's most important staple food crop, feeding more than half of the human population. Despite this essential role in world agriculture, the history of cultivated rice's domestication from its wild ancestor, Oryza rufipogon, remains unclear. In this study, DNA sequence variation in three gene regions is examined in a phylogeographic approach to investigate the domestication of cultivated rice. Results indicate that India and Indochina may represent the ancestral center of diversity for O. rufipogon. Additionally, the data suggest that cultivated rice was domesticated at least twice from different O. rufipogon populations and that the products of these two independent domestication events are the two major rice varieties, Oryza sativa indica and Oryza sativa japonica. Based on this geographical analysis, O. sativa indica was domesticated within a region south of the Himalaya mountain range, likely eastern India, Myanmar, and Thailand, whereas O. sativa japonica was domesticated from wild rice in southern China.

  19. Varieties of English.

    ERIC Educational Resources Information Center

    Brook, G. L.

    The English language is not a monolithic entity but an amalgam of many different varieties that can be associated respectively with groups of speakers, with individuals, and with the occasion. Among such varieties are slang, regional and class dialects, the language of children, and the language used by public speakers, journalists, lawyers,…

  20. Peanut variety tests

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Managed peanut variety trials located in various state-wide regions are an essential part of peanut variety development and release. In this study, trials were conducted in Caddo, Beckham, and Custer counties of Oklahoma. Trial entries included 9 runner types, 4 Spanish types, and 7 Virginia types...

  1. Peanut variety tests

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Managed peanut variety trials located in various state-wide regions are an essential part of peanut variety development and release. In this study, trials were conducted in Caddo, Beckham, and Custer counties of Oklahoma. Trial entries included 10 runner types, 4 Spanish types, and 6 Virginia type...

  2. Peanut Variety Tests

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Managed peanut variety trials located in various state-wide regions are an essential part of peanut variety development and release. In this study, trials were conducted in Caddo, Custer, and Tillman counties of Oklahoma. Trial entries included 8 runner types, 4 Spanish types, and 4 Virginia types...

  3. Peanut variety tests

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Managed peanut variety trials located in various state-wide regions are an essential part of peanut variety development and release. In this study, trials were conducted in Caddo, Custer, and Tillman counties of Oklahoma. Trial entries included 12 runner types, 4 Spanish types and 8 Virginia types...

  4. Varieties of Musical Experience

    ERIC Educational Resources Information Center

    Bharucha, J. Jamshed; Curtis, Meagan; Paroo, Kaivon

    2006-01-01

    In this paper, we argue that music cognition involves the use of acoustic and auditory codes to evoke a variety of conscious experiences. The variety of domains that are encompassed by music is so diverse that it is unclear whether a single domain of structure or experience is defining. Music is best understood as a form of communication in which…

  5. Own Variety Bias

    PubMed Central

    García, Andrea Ariza

    2015-01-01

    In a language identification task, native Belgian French and native Swiss French speakers identified French from France as their own variety. However, Canadian French was not subject to this bias. Canadian and French listeners didn’t claim a different variety as their own. PMID:27648211

  6. Gene flow from transgenic rice to red rice (Oryza sativa L.) in the field.

    PubMed

    Busconi, M; Baldi, G; Lorenzoni, C; Fogher, C

    2014-01-01

    In this study, we simulate a transgenic rice crop highly infested with red rice to examine transgene transfer from a transgenic line (A2504) resistant to glufosinate ammonium to cohabitant red rice. The red rice was sown along with the transgenic line at the highest density found in naturally infested crops in the region. Agricultural practices similar to those used to control red rice infestation in northern Italy rice fields were used to reproduce the local rice production system. During the first 2 years, the field was treated with herbicide at the appropriate time; in the first year the dosage of herbicide was three times the recommended amount. In this first year, detectable red rice plants that escaped herbicide treatment were manually removed. Nevertheless, two herbicide-resistant hybrid plants (named 101 and 104) were identified in the experimental field during the second year of cultivation. Phenotypic and molecular characterisation suggests the hybrid nature of these two plants, deriving from crossing events involving A2504, respectively, with red rice (plant 101) and the buffer cultivar Gladio (plant 104). The progeny of two subsequent generations of the two plants were examined and the presence of the transgene detected, indicating stable transfer of the transgene across generations. In conclusion, despite control methods, red rice progeny tolerant to the herbicide can be expected following use of transgenic rice and, consequently, difficulties in controlling this weed with chemicals will emerge in a relatively short time.

  7. Induction of antioxidant enzyme activity and lipid peroxidation level in ion-beam-bombarded rice seeds

    NASA Astrophysics Data System (ADS)

    Semsang, Nuananong; Yu, LiangDeng

    2013-07-01

    Low-energy ion beam bombardment has been used to mutate a wide variety of plant species. To explore the indirect effects of low-energy ion beam on biological damage due to the free radical production in plant cells, the increase in antioxidant enzyme activities and lipid peroxidation level was investigated in ion-bombarded rice seeds. Local rice seeds were bombarded with nitrogen or argon ion beams at energies of 29-60 keV and ion fluences of 1 × 1016 ions cm-2. The activities of the antioxidant enzymes; superoxide dismutase (SOD), catalase (CAT), ascorbate peroxidase (APX), dehydroascorbate reductase (DHAR), glutathione reductase (GR), glutathione S-transferase (GST) and lipid peroxidation level were assayed in the germinated rice seeds after ion bombardment. The results showed most of the enzyme activities and lipid peroxidation levels in both the argon and nitrogen bombarded samples were higher than those in the natural control. N-ion bombardment could induce higher levels of antioxidant enzyme activities in the rice samples than the Ar-ion bombardment. Additional effects due to the vacuum condition were found to affect activities of some antioxidant enzymes and lipid peroxidation level. This study demonstrates that ion beam bombardment and vacuum condition could induce the antioxidant enzyme activity and lipid peroxidation level which might be due to free radical production in the bombarded rice seeds.

  8. Classification of Malaysia aromatic rice using multivariate statistical analysis

    NASA Astrophysics Data System (ADS)

    Abdullah, A. H.; Adom, A. H.; Shakaff, A. Y. Md; Masnan, M. J.; Zakaria, A.; Rahim, N. A.; Omar, O.

    2015-05-01

    Aromatic rice (Oryza sativa L.) is considered as the best quality premium rice. The varieties are preferred by consumers because of its preference criteria such as shape, colour, distinctive aroma and flavour. The price of aromatic rice is higher than ordinary rice due to its special needed growth condition for instance specific climate and soil. Presently, the aromatic rice quality is identified by using its key elements and isotopic variables. The rice can also be classified via Gas Chromatography Mass Spectrometry (GC-MS) or human sensory panels. However, the uses of human sensory panels have significant drawbacks such as lengthy training time, and prone to fatigue as the number of sample increased and inconsistent. The GC-MS analysis techniques on the other hand, require detailed procedures, lengthy analysis and quite costly. This paper presents the application of in-house developed Electronic Nose (e-nose) to classify new aromatic rice varieties. The e-nose is used to classify the variety of aromatic rice based on the samples odour. The samples were taken from the variety of rice. The instrument utilizes multivariate statistical data analysis, including Principal Component Analysis (PCA), Linear Discriminant Analysis (LDA) and K-Nearest Neighbours (KNN) to classify the unknown rice samples. The Leave-One-Out (LOO) validation approach is applied to evaluate the ability of KNN to perform recognition and classification of the unspecified samples. The visual observation of the PCA and LDA plots of the rice proves that the instrument was able to separate the samples into different clusters accordingly. The results of LDA and KNN with low misclassification error support the above findings and we may conclude that the e-nose is successfully applied to the classification of the aromatic rice varieties.

  9. Classification of Malaysia aromatic rice using multivariate statistical analysis

    SciTech Connect

    Abdullah, A. H.; Adom, A. H.; Shakaff, A. Y. Md; Masnan, M. J.; Zakaria, A.; Rahim, N. A.; Omar, O.

    2015-05-15

    Aromatic rice (Oryza sativa L.) is considered as the best quality premium rice. The varieties are preferred by consumers because of its preference criteria such as shape, colour, distinctive aroma and flavour. The price of aromatic rice is higher than ordinary rice due to its special needed growth condition for instance specific climate and soil. Presently, the aromatic rice quality is identified by using its key elements and isotopic variables. The rice can also be classified via Gas Chromatography Mass Spectrometry (GC-MS) or human sensory panels. However, the uses of human sensory panels have significant drawbacks such as lengthy training time, and prone to fatigue as the number of sample increased and inconsistent. The GC–MS analysis techniques on the other hand, require detailed procedures, lengthy analysis and quite costly. This paper presents the application of in-house developed Electronic Nose (e-nose) to classify new aromatic rice varieties. The e-nose is used to classify the variety of aromatic rice based on the samples odour. The samples were taken from the variety of rice. The instrument utilizes multivariate statistical data analysis, including Principal Component Analysis (PCA), Linear Discriminant Analysis (LDA) and K-Nearest Neighbours (KNN) to classify the unknown rice samples. The Leave-One-Out (LOO) validation approach is applied to evaluate the ability of KNN to perform recognition and classification of the unspecified samples. The visual observation of the PCA and LDA plots of the rice proves that the instrument was able to separate the samples into different clusters accordingly. The results of LDA and KNN with low misclassification error support the above findings and we may conclude that the e-nose is successfully applied to the classification of the aromatic rice varieties.

  10. Rice antioxidants: phenolic acids, flavonoids, anthocyanins, proanthocyanidins, tocopherols, tocotrienols, γ-oryzanol, and phytic acid.

    PubMed

    Goufo, Piebiep; Trindade, Henrique

    2014-03-01

    Epidemiological studies suggested that the low incidence of certain chronic diseases in rice-consuming regions of the world might be associated with the antioxidant compound contents of rice. The molecules with antioxidant activity contained in rice include phenolic acids, flavonoids, anthocyanins, proanthocyanidins, tocopherols, tocotrienols, γ-oryzanol, and phytic acid. This review provides information on the contents of these compounds in rice using a food composition database built from compiling data from 316 papers. The database provides access to information that would have otherwise remained hidden in the literature. For example, among the four types of rice ranked by color, black rice varieties emerged as those exhibiting the highest antioxidant activities, followed by purple, red, and brown rice varieties. Furthermore, insoluble compounds appear to constitute the major fraction of phenolic acids and proanthocyanidins in rice, but not of flavonoids and anthocyanins. It is clear that to maximize the intake of antioxidant compounds, rice should be preferentially consumed in the form of bran or as whole grain. With respect to breeding, japonica rice varieties were found to be richer in antioxidant compounds compared with indica rice varieties. Overall, rice grain fractions appear to be rich sources of antioxidant compounds. However, on a whole grain basis and with the exception of γ-oryzanol and anthocyanins, the contents of antioxidants in other cereals appear to be higher than those in rice.

  11. Mitigation options for methane emissions from rice fields in the Philippines

    SciTech Connect

    Lantin, R.S.; Buendia, L.V.; Wassmann, R.

    1996-12-31

    The contribution of Philippine rice production to global methane emission and breakthroughs in methane emission studies conducted in the country are presented in this paper. A significant impact in the reduction of GHG emissions from agriculture can be achieved if methane emissions from ricefields can be abated. This study presents the contribution of Philippine rice cultivation to global methane emission and breakthroughs in methane emission studies in the country which address the issue of mitigation. Using the derived emission factors from local measurements, rice cultivation contributes 566.6 Gg of methane emission in the Philippines. This value is 62% of the total methane emitted from the agriculture sector. The emission factors employed which are 78% of the IPCC value for irrigated rice and 95% for rainfed rice were derived from measurements with an automatic system taken during the growth duration in the respective ecosystems. Plots drained for 2 weeks at midtillering and before harvest gave a significant reduction in methane emission as opposed to continuously flooded plots and plots drained before harvest. The cultivar Magat reduced methane emission by 50% as compared to the check variety IR72. The application of ammonium sulfate instead of urea reduced methane emission by 10% to 34%. Addition of 6 t ha{sup {minus}1} phosphogypsum in combination with urea reduced emission by 74% as opposed to plots applied with urea alone. It is also from the results of such measurements that abatement strategies are based as regards to modifying treatments such as water management, fertilization, and choice of rice variety. It is not easy to identify and recommend mitigation strategies that will fit a particular cropping system. However, the identified mitigation options provide focus for the abatement of methane emission from ricefields.

  12. Rice, indica (Oryza sativa L.).

    PubMed

    Hiei, Yukoh; Ishida, Yuji; Komari, Toshihiko

    2015-01-01

    Indica varieties, which are generally recalcitrant to tissue culture and transformation, occupy 80 % of rice cultivation area in the world. Therefore, transformation method for indica rice must be improved greatly so that global rice production would take full advantage of cutting-edge biotechnology. An efficient protocol for indica transformation mediated by Agrobacterium tumefaciens is hereby described. Immature embryos collected from plants in a greenhouse are cocultivated with A. tumefaciens after pretreatment with heat and centrifuging. The protocol was successfully tested in many elite indica cultivars such as IR8, IR24, IR58025B, IR64, IR72, Suweon 258, and Nanjing 11, yielding between 5 and 15 of independent transgenic plants per immature embryo. The use of immature embryos is recommended because gene transfer to them could be much more efficient and much less genotype dependent than gene transfer to callus.

  13. Application of imaging mass spectrometry for the analysis of Oryza sativa rice.

    PubMed

    Zaima, Nobuhiro; Goto-Inoue, Naoko; Hayasaka, Takahiro; Setou, Mitsutoshi

    2010-09-01

    Rice is one of the most important food crops in the world and new varieties have been bred for specific purposes, such as the development of drought-resistance, or the enrichment of functional food factors. The localization and composition of metabolites in such new varieties must be investigated because all artificial interventions are expected to change the metabolites of rice. Imaging mass spectrometry using matrix-assisted laser desorption/ionization (MALDI-IMS) is a suitable tool for investigating the localization and composition of metabolites; however, suitable methodologies for the MALDI-IMS analysis of rice have not yet been established. In this study, we optimized the methods for analyzing rice grains by MALDI-IMS using adhesive film and found the characteristic distribution of metabolites in rice. Lysophosphatidylcholine (LPC) was localized in the endosperm. Phosphatidylcholine (PC), gamma-oryzanol and phytic acid were localized in the bran (germ and seed coat), and alpha-tocopherol was distributed in the germ (especially in the scutellum). In addition, MALDI-IMS revealed the LPC and PC composition of the rice samples. The LPC composition, LPC (1-acyl 16:0), LPC (1-acyl 18:2), LPC (1-acyl 18:1) and LPC (1-acyl 18:0), was 59.4 +/- 4.5%, 19.6 +/- 2.5%, 14.2 +/- 4.5% and 6.8 +/- 1.4%. The PC composition, PC (diacyl 16:0/18:2), PC (diacyl 16:0/18:1), PC (diacyl 18:1/18:3), PC (diacyl 18:1/18:2) and PC (diacyl 18:1/18:2), was 19.6 +/- 1.0%, 21.0 +/- 1.0%, 15.0 +/- 1.4%, 26.7 +/- 0.7% and 17.8 +/- 1.9%. This approach can be applied to the assessment of metabolites not only in rice, but also in other foods for which the preparation of sections is a challenging task.

  14. Ontogenetic changes in vitamin C in selected rice varieties

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Vitamin C (L-ascorbic acid, AsA) is a key antioxidant for both plants and animals. In plants, AsA is involved in several key physiological processes including photosynthesis, cell expansion, cell division, growth, flowering, and senescence. In addition, AsA is an enzyme cofactor and a regulator of...

  15. In vitro digestibility and physicochemical properties of milled rice.

    PubMed

    Dhital, Sushil; Dabit, Laura; Zhang, Bin; Flanagan, Bernadine; Shrestha, Ashok K

    2015-04-01

    Rice is a staple diet as well as a major ingredient in many processed foods. The physicochemical and supra-molecular structure of eight rice varieties with amylose content from 9% to 19% were studied to elucidate the factors responsible for variation in enzymatic digestibility of raw and cooked rice. Parboiled rice had a digestion rate coefficient almost 4.5 times higher than the least digestible Low GI rice. The rate coefficient was found to be independent of helical structure and long range molecular order, possibly attributed to the effect of rice flour architecture. Strong swelling and pasting behaviour and lower gelatinisation temperature were linked with apparently higher in vitro digestibility but the relationship was statistically insignificant. It is concluded that the enzymatic susceptibility of rice flours are independent of supra-molecular structure and are most likely controlled by external factors not limited to particle size, presence of intact cell wall and other non-starch polymers.

  16. Molecular mapping of the new blast resistance genes Pi47 and Pi48 in the durably resistant local rice cultivar Xiangzi 3150.

    PubMed

    Huang, Hongmei; Huang, Ling; Feng, Guangping; Wang, Suhua; Wang, Yue; Liu, Jinling; Jiang, Nan; Yan, Weiting; Xu, Lingchao; Sun, Pingyong; Li, Zhiqiang; Pan, Sujun; Liu, Xionglun; Xiao, Yinghui; Liu, Erming; Dai, Liangying; Wang, Guo-Liang

    2011-05-01

    The indica rice cultivar Xiangzi 3150 (XZ3150) confers a high level of resistance to 95% of the isolates of Magnaporthe oryzae (the agent of rice blast disease) collected in Hunan Province, China. To identify the resistance (R) gene(s) controlling the high level of resistance in this cultivar, we developed 286 F(9) recombinant inbred lines (RILs) from a cross between XZ3150 and the highly susceptible cultivar CO39. Inoculation of the RILs and an F(2) population from a cross between the two cultivars with the avirulent isolate 193-1-1 in the growth chamber indicated the presence of two dominant R genes in XZ3150. A linkage map with 134 polymorphic simple sequence repeat and single feature polymorphism markers was constructed with the genotype data of the 286 RILs. Composite interval mapping (CIM) using the results of 193-1-1 inoculation showed that two major R genes, designated Pi47 and Pi48, were located between RM206 and RM224 on chromosome 11, and between RM5364 and RM7102 on chromosome 12, respectively. Interestingly, the CIM analysis of the four resistant components of the RILs to the field blast population revealed that Pi47 and Pi48 were also the major genetic factors responsible for the field resistance in XZ3150. The DNA markers linked to the new R genes identified in this study should be useful for further fine mapping, gene cloning, and marker-aided breeding of blast-resistant rice cultivars.

  17. Spread of herbicide-resistant weedy rice (red rice, Oryza sativa L.) after 5 years of Clearfield rice cultivation in Italy.

    PubMed

    Busconi, M; Rossi, D; Lorenzoni, C; Baldi, G; Fogher, C

    2012-09-01

    The weedy relative of cultivated rice, red rice, can invade and severely infest rice fields, as reported by rice farmers throughout the world. Because of its close genetic relationship to commercial rice, red rice has proven difficult to control. Clearfield (Cl) varieties, which are resistant to the inhibiting herbicides in the chemical group AHAS (acetohydroxyacid synthase), provide a highly efficient opportunity to control red rice infestations. In order to reduce the risk of herbicide resistance spreading from cultivated rice to red rice, stewardship guidelines are regularly released. In Italy, the cultivation of Cl cultivars started in 2006. In 2010, surveillance of the possible escape of herbicide resistance was carried out; 168 red rice plants were sampled in 16 fields from six locations containing Cl and traditional cultivars. A first subsample of 119 plants was analysed after herbicide treatment and the resistance was found in 62 plants. Of these 119 plants, 78 plants were randomly selected and analysed at the level of the AHAS gene to search for the Cl mutation determining the resistant genotype: the Cl mutation was present in all the resistant plants. Nuclear and chloroplast microsatellite markers revealed a high correlation between genetic similarity and herbicide resistance. The results clearly show that Cl herbicide-resistant red rice plants are present in the field, having genetic relationships with the Cl variety. Finding plants homozygous for the mutation suggests that the crossing event occurred relatively recently and that these plants are in the F2 or later generations. These observations raise the possibility that Cl red rice is already within the cultivated rice seed supply.

  18. Rice CONSTITUTIVE TRIPLE-RESPONSE2 is involved in the ethylene-receptor signalling and regulation of various aspects of rice growth and development.

    PubMed

    Wang, Qin; Zhang, Wei; Yin, Zhongming; Wen, Chi-Kuang

    2013-11-01

    In Arabidopsis, the ethylene-receptor signal output occurs at the endoplasmic reticulum and is mediated by the Raf-like protein CONSTITUTIVE TRIPLE RESPONSE1 (CTR1) but is prevented by overexpression of the CTR1 N terminus. A phylogenic analysis suggested that rice OsCTR2 is closely related to CTR1, and ectopic expression of CTR1p:OsCTR2 complemented Arabidopsis ctr1-1. Arabidopsis ethylene receptors ETHYLENE RESPONSE1 and ETHYLENE RESPONSE SENSOR1 physically interacted with OsCTR2 on yeast two-hybrid assay, and green fluorescence protein-tagged OsCTR2 was localized at the endoplasmic reticulum. The osctr2 loss-of-function mutation and expression of the 35S:OsCTR2 (1-513) transgene that encodes the OsCTR2 N terminus (residues 1-513) revealed several and many aspects, respectively, of ethylene-induced growth alteration in rice. Because the osctr2 allele did not produce all aspects of ethylene-induced growth alteration, the ethylene-receptor signal output might be mediated in part by OsCTR2 and by other components in rice. Yield-related agronomic traits, including flowering time and effective tiller number, were altered in osctr2 and 35S:OsCTR2 (1-513) transgenic lines. Applying prolonged ethylene treatment to evaluate ethylene effects on rice without compromising rice growth is technically challenging. Our understanding of roles of ethylene in various aspects of growth and development in japonica rice varieties could be advanced with the use of the osctr2 and 35S:OsCTR2 (1-513) transgenic lines.

  19. Rice varietal differences in bioactive bran components for inhibition of colorectal cancer cell growth

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Studies support that the bran fraction of rice contains bioactive compounds capable of inhibiting the formation of colonic tumors. Screening bran extracts from diverse rice varieties represents a novel approach to assessing the colon cancer chemopreventive properties of rice bran. We analyzed a pane...

  20. N-Glycomic and Microscopic Subcellular Localization Analyses of NPP1, 2 and 6 Strongly Indicate that trans-Golgi Compartments Participate in the Golgi to Plastid Traffic of Nucleotide Pyrophosphatase/Phosphodiesterases in Rice

    PubMed Central

    Kaneko, Kentaro; Takamatsu, Takeshi; Inomata, Takuya; Oikawa, Kazusato; Itoh, Kimiko; Hirose, Kazuko; Amano, Maho; Nishimura, Shin-Ichiro; Toyooka, Kiminori; Matsuoka, Ken; Pozueta-Romero, Javier; Mitsui, Toshiaki

    2016-01-01

    Nucleotide pyrophosphatase/phosphodiesterases (NPPs) are widely distributed N-glycosylated enzymes that catalyze the hydrolytic breakdown of numerous nucleotides and nucleotide sugars. In many plant species, NPPs are encoded by a small multigene family, which in rice are referred to NPP1–NPP6. Although recent investigations showed that N-glycosylated NPP1 is transported from the endoplasmic reticulum (ER)–Golgi system to the chloroplast through the secretory pathway in rice cells, information on N-glycan composition and subcellular localization of other NPPs is still lacking. Computer-assisted analyses of the amino acid sequences deduced from different Oryza sativa NPP-encoding cDNAs predicted all NPPs to be secretory glycoproteins. Confocal fluorescence microscopy observation of cells expressing NPP2 and NPP6 fused with green fluorescent protein (GFP) revealed that NPP2 and NPP6 are plastidial proteins. Plastid targeting of NPP2–GFP and NPP6–GFP was prevented by brefeldin A and by the expression of ARF1(Q71L), a dominant negative mutant of ADP-ribosylation factor 1 that arrests the ER to Golgi traffic, indicating that NPP2 and NPP6 are transported from the ER–Golgi to the plastidial compartment. Confocal laser scanning microscopy and high-pressure frozen/freeze-substituted electron microscopy analyses of transgenic rice cells ectopically expressing the trans-Golgi marker sialyltransferase fused with GFP showed the occurrence of contact of Golgi-derived membrane vesicles with cargo and subsequent absorption into plastids. Sensitive and high-throughput glycoblotting/mass spectrometric analyses showed that complex-type and paucimannosidic-type glycans with fucose and xylose residues occupy approximately 80% of total glycans of NPP1, NPP2 and NPP6. The overall data strongly indicate that the trans-Golgi compartments participate in the Golgi to plastid trafficking and targeting mechanism of NPPs. PMID:27335351

  1. Moisture diffusivity in rice components during absorption and desorption

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Moisture diffusivity values of different rice kernel components namely, endosperm, bran and husks are required to solve mathematical models describing absorption and desorption processes. In addition to the rice variety and temperature, the moisture diffusivity also depends on its instantaneous mois...

  2. Avian foods, foraging and habitat conservation in world rice fields

    USGS Publications Warehouse

    Stafford, J.D.; Kaminski, R.M.; Reinecke, K.J.

    2010-01-01

    Worldwide, rice (Oryza sativa) agriculture typically involves seasonal flooding and soil tillage, which provides a variety of microhabitats and potential food for birds. Water management in rice fields creates conditions ranging from saturated mud flats to shallow (<30 cm) water, thereby attracting different guilds of birds. Grain not collected during harvest (i.e. waste rice) is typically the most abundant potential food of birds in rice fields, with estimates of seed mass from North America ranging from 66672 kg/ha. Although initially abundant after harvest, waste rice availability can be temporally limited. Few abundance estimates for other foods, such as vertebrate prey or forage vegetation, exist for rice fields. Outside North America, Europe and Japan, little is known about abundance and importance of any avian food in rice fields. Currently, flooding rice fields after harvest is the best known management practice to attract and benefit birds. Studies from North America indicate specific agricultural practices (e.g. burning stubble) may increase use and improve access to food resources. Evaluating and implementing management practices that are ecologically sustainable, increase food for birds and are agronomically beneficial should be global priorities to integrate rice production and avian conservation. Finally, land area devoted to rice agriculture appears to be stable in the USA, declining in China, and largely unquantified in many regions. Monitoring trends in riceland area may provide information to guide avian conservation planning in rice-agriculture ecosystems.

  3. Study on creep properties of Japonica cooked rice and its relationship with rice chemical compositions and sensory evaluation

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Creep properties of four varieties japonica cooked rice were tested using a Dynamic Mechanical Analyser (DMA Q800). The creep curve was described by Burgers model. The creep process of japonica cooked rice mainly consisted of retarded elastic deformation, epsilonR and viscous flow deformation, epsil...

  4. Accumulation of arsenic in tissues of rice plant (Oryza sativa L.) and its distribution in fractions of rice grain.

    PubMed

    Rahman, M Azizur; Hasegawa, H; Rahman, M Mahfuzur; Rahman, M Arifur; Miah, M A M

    2007-10-01

    A study was conducted to investigate the accumulation and distribution of arsenic in different fractions of rice grain (Oryza sativa L.) collected from arsenic affected area of Bangladesh. The agricultural soil of study area has become highly contaminated with arsenic due to the excessive use of arsenic-rich underground water (0.070+/-0.006 mg l(-1), n=6) for irrigation. Arsenic content in tissues of rice plant and in fractions of rice grain of two widely cultivated rice varieties, namely BRRI dhan28 and BRRI hybrid dhan1, were determined. Regardless of rice varieties, arsenic content was about 28- and 75-folds higher in root than that of shoot and raw rice grain, respectively. In fractions of parboiled and non-parboiled rice grain of both varieties, the order of arsenic concentrations was; rice hull>bran-polish>brown rice>raw rice>polish rice. Arsenic content was higher in non-parboiled rice grain than that of parboiled rice. Arsenic concentrations in parboiled and non-parboiled brown rice of BRRI dhan28 were 0.8+/-0.1 and 0.5+/-0.0 mg kg(-1) dry weight, respectively while those of BRRI hybrid dhan1 were 0.8+/-0.2 and 0.6+/-0.2 mg kg(-1) dry weight, respectively. However, parboiled and non-parboiled polish rice grain of BRRI dhan28 contained 0.4+/-0.0 and 0.3+/-0.1 mg kg(-1) dry weight of arsenic, respectively while those of BRRI hybrid dhan1 contained 0.43+/-0.01 and 0.5+/-0.0 mg kg(-1) dry weight, respectively. Both polish and brown rice are readily cooked for human consumption. The concentration of arsenic found in the present study is much lower than the permissible limit in rice (1.0 mg kg(-1)) according to WHO recommendation. Thus, rice grown in soils of Bangladesh contaminated with arsenic of 14.5+/-0.1 mg kg(-1) could be considered safe for human consumption.

  5. VARIETIES OF VIOLENT BEHAVOR*

    PubMed Central

    WIDOM, CATHY SPATZ

    2014-01-01

    There is an implicit assumption of homogeneity across violent behaviors and offenders in the criminology literature. Arguing against this assumption, I draw on three distinct literatures [child abuse and neglect (CAN) and violence, violence and post-traumatic stress disorder (PTSD), and CAN and PTSD] to provide a rationale for an examination of varieties of violent behaviors. I use data from my prospective cohort design study of the long-term consequences of CAN to define three varieties of violent offenders using age of documented cases of CAN, onset of PTSD, and first violent arrest in a temporally correct manner [CAN → to violence, CAN → PTSD → violence (PTSD first), and CAN → violence → PTSD (violence first)], and a fourth variety, violence only. The results illustrate meaningful heterogeneity in violent behavior and different developmental patterns and characteristics. There are three major implications: First, programs and policies that target violence need to recognize the heterogeneity and move away from a “one-size-fits-all” approach. Second, violence prevention policies and programs that target abused and neglected children are warranted, given the prominent role of CAN in the backgrounds of these violent offenders. Third, criminologists and others interested in violence need to attend to the role of PTSD, which is present in about one fifth (21 percent) of these violent offenders, and not relegate the study of these offenders to the psychiatric and psychological literatures. PMID:25505799

  6. VARIETIES OF VIOLENT BEHAVOR.

    PubMed

    Widom, Cathy Spatz

    2014-08-01

    There is an implicit assumption of homogeneity across violent behaviors and offenders in the criminology literature. Arguing against this assumption, I draw on three distinct literatures [child abuse and neglect (CAN) and violence, violence and post-traumatic stress disorder (PTSD), and CAN and PTSD] to provide a rationale for an examination of varieties of violent behaviors. I use data from my prospective cohort design study of the long-term consequences of CAN to define three varieties of violent offenders using age of documented cases of CAN, onset of PTSD, and first violent arrest in a temporally correct manner [CAN → to violence, CAN → PTSD → violence (PTSD first), and CAN → violence → PTSD (violence first)], and a fourth variety, violence only. The results illustrate meaningful heterogeneity in violent behavior and different developmental patterns and characteristics. There are three major implications: First, programs and policies that target violence need to recognize the heterogeneity and move away from a "one-size-fits-all" approach. Second, violence prevention policies and programs that target abused and neglected children are warranted, given the prominent role of CAN in the backgrounds of these violent offenders. Third, criminologists and others interested in violence need to attend to the role of PTSD, which is present in about one fifth (21 percent) of these violent offenders, and not relegate the study of these offenders to the psychiatric and psychological literatures.

  7. HapRice, an SNP haplotype database and a web tool for rice.

    PubMed

    Yonemaru, Jun-ichi; Ebana, Kaworu; Yano, Masahiro

    2014-01-01

    Genome-wide single nucleotide polymorphism (SNP) analysis is a promising tool to examine the genetic diversity of rice populations and genetic traits of scientific and economic importance. Next-generation sequencing technology has accelerated the re-sequencing of diverse rice varieties and the discovery of genome-wide SNPs. Notably, validation of these SNPs by a high-throughput genotyping system, such as an SNP array, could provide a manageable and highly accurate SNP set. To enhance the potential utility of genome-wide SNPs for geneticists and breeders, analysis tools need to be developed. Here, we constructed an SNP haplotype database, which allows visualization of the allele frequency of all SNPs in the genome browser. We calculated the allele frequencies of 3,334 SNPs in 76 accessions from the world rice collection and 3,252 SNPs in 177 Japanese rice accessions; all these SNPs have been validated in our previous studies. The SNP haplotypes were defined by the allele frequency in each cultivar group (aus, indica, tropical japonica and temperate japonica) for the world rice accessions, and in non-irrigated and three irrigated groups (three variety registration periods) for Japanese rice accessions. We also developed web tools for finding polymorphic SNPs between any two rice accessions and for the primer design to develop cleaved amplified polymorphic sequence markers at any SNP. The 'HapRice' database and the web tools can be accessed at http://qtaro.abr.affrc.go.jp/index.html. In addition, we established a core SNP set consisting of 768 SNPs uniformly distributed in the rice genome; this set is of a practically appropriate size for use in rice genetic analysis.

  8. Heavy metals in Australian grown and imported rice and vegetables on sale in Australia: health hazard.

    PubMed

    Rahman, M Azizur; Rahman, Mohammad Mahmudur; Reichman, Suzie M; Lim, Richard P; Naidu, Ravi

    2014-02-01

    Dietary exposure to heavy metals is a matter of concern for human health risk through the consumption of rice, vegetables and other major foodstuffs. In the present study, we investigated concentrations of cadmium (Cd), cobalt (Co), chromium (Cr), copper (Cu), manganese (Mn), nickel (Ni), lead (Pb), and zinc (Zn) in Australian grown and imported rice and vegetables on sale in Australia. The mean concentrations of Cd, Co, Cr, Cu, Mn, Ni, Pb, and Zn in Australian grown rice were 7.5 µg kg(-1), 21 µg kg(-1), 144 µg kg(-1), 2.9 mg kg(-1), 24.4 mg kg(-1), 166 µg kg(-1), 375 µg kg(-1), and 17.1 mg kg(-1) dry weight (d. wt.), respectively. Except Cd, heavy metal concentrations in Australian grown rice were higher than Bangladeshi rice on sale in Australia. However, the concentrations of Cd, Cr, Cu, and Ni in Indian rice on sale in Australia were higher than Australian grown rice. The concentrations of Cu and Ni in Vietnamese rice, and that of Cd, Cr, Cu, Ni, and Pb in Thai rice on sale in Australia were also higher than Australian grown rice. Heavy metal concentrations in Pakistani rice on sale in Australia were substantially lower than that in Australian grown rice. In Australian grown rice varieties, the concentrations of heavy metals were considerably higher in brown rice varieties than white rice varieties, indicating Australian brown rice as a potential source of dietary heavy metals for Australian consumers. The mean concentrations of heavy metals in Australian grown and Bangladeshi vegetables on sale in Australia were also determined. Some of the Australian grown and Bangladeshi vegetables contained heavy metals higher than Australian standard maximum limits indicating them as potential sources of dietary heavy metals for Australian consumers. Further investigation is required to estimate health risks of heavy metals from rice and vegetables consumption for Australian consumers.

  9. An Integrative Genetic Study of Rice Metabolism, Growth and Stochastic Variation Reveals Potential C/N Partitioning Loci

    NASA Astrophysics Data System (ADS)

    Li, Baohua; Zhang, Yuanyuan; Mohammadi, Seyed Abolghasem; Huai, Dongxin; Zhou, Yongming; Kliebenstein, Daniel J.

    2016-07-01

    Studying the genetic basis of variation in plant metabolism has been greatly facilitated by genomic and metabolic profiling advances. In this study, we use metabolomics and growth measurements to map QTL in rice, a major staple crop. Previous rice metabolism studies have largely focused on identifying genes controlling major effect loci. To complement these studies, we conducted a replicated metabolomics analysis on a japonica (Lemont) by indica (Teqing) rice recombinant inbred line population and focused on the genetic variation for primary metabolism. Using independent replicated studies, we show that in contrast to other rice studies, the heritability of primary metabolism is similar to Arabidopsis. The vast majority of metabolic QTLs had small to moderate effects with significant polygenic epistasis. Two metabolomics QTL hotspots had opposing effects on carbon and nitrogen rich metabolites suggesting that they may influence carbon and nitrogen partitioning, with one locus co-localizing with SUSIBA2 (WRKY78). Comparing QTLs for metabolomic and a variety of growth related traits identified few overlaps. Interestingly, the rice population displayed fewer loci controlling stochastic variation for metabolism than was found in Arabidopsis. Thus, it is possible that domestication has differentially impacted stochastic metabolite variation more than average metabolite variation.

  10. An Integrative Genetic Study of Rice Metabolism, Growth and Stochastic Variation Reveals Potential C/N Partitioning Loci

    PubMed Central

    Li, Baohua; Zhang, Yuanyuan; Mohammadi, Seyed Abolghasem; Huai, Dongxin; Zhou, Yongming; Kliebenstein, Daniel J.

    2016-01-01

    Studying the genetic basis of variation in plant metabolism has been greatly facilitated by genomic and metabolic profiling advances. In this study, we use metabolomics and growth measurements to map QTL in rice, a major staple crop. Previous rice metabolism studies have largely focused on identifying genes controlling major effect loci. To complement these studies, we conducted a replicated metabolomics analysis on a japonica (Lemont) by indica (Teqing) rice recombinant inbred line population and focused on the genetic variation for primary metabolism. Using independent replicated studies, we show that in contrast to other rice studies, the heritability of primary metabolism is similar to Arabidopsis. The vast majority of metabolic QTLs had small to moderate effects with significant polygenic epistasis. Two metabolomics QTL hotspots had opposing effects on carbon and nitrogen rich metabolites suggesting that they may influence carbon and nitrogen partitioning, with one locus co-localizing with SUSIBA2 (WRKY78). Comparing QTLs for metabolomic and a variety of growth related traits identified few overlaps. Interestingly, the rice population displayed fewer loci controlling stochastic variation for metabolism than was found in Arabidopsis. Thus, it is possible that domestication has differentially impacted stochastic metabolite variation more than average metabolite variation. PMID:27440503

  11. Head rice yield response to low and high drying and tempering conditions

    NASA Astrophysics Data System (ADS)

    Sadeghi, M.; Nasrnia, E.; Masoumi, A. A.; Hemmat, A.

    2013-03-01

    The influence of drying and tempering conditions on head rice yield of long- and medium-grain rough rice varieties was investigated. The head rice yield values for the medium-grain variety at high drying conditions and 1.5 and 3% points moisture content removal were even significantly higher than the corresponding values for the long-grain variety at low drying conditions. 1.5% points moisture content removal yielded the least damage to the rough rice. Under low drying conditions, tempering had no meaningful effect on head rice yield for all drying durations. For both varieties, using high drying conditions with 6% points moisture content removal at first drying stage associated with 120 min tempering duration could be suggested as a rapid and energysaving operation to achieve high head rice yield values.

  12. Brewers' Rice: A By-Product from Rice Processing Provides Natural Hepatorenal Protection in Azoxymethane-Induced Oxidative Stress in Rats

    PubMed Central

    Tan, Bee Ling; Norhaizan, Mohd Esa; Hairuszah, Ithnin; Hazilawati, Hamzah; Roselina, Karim

    2015-01-01

    Brewers' rice, which is known locally as temukut, is a mixture of broken rice, rice bran, and rice germ. Our present study was designed to identify the effect of brewers' rice on the attenuation of liver and kidney damage induced by azoxymethane (AOM). Alanine transaminase (ALT), alkaline phosphatase (ALP), aspartate transaminase (AST), creatinine, and urea were evaluated to understand potential hepatoprotective effects and the ability of brewers' rice to attenuate kidney pathology induced by AOM treatment. Liver and kidney tissues were evaluated by hematoxylin and eosin (H&E) staining. Overall analyses revealed that brewers' rice improved the levels of serum markers in a manner associated with better histopathological outcomes, which indicated that brewers' rice could enhance recovery from hepatocyte and kidney damage. Taken together, these results suggest that brewers' rice could be used in future applications to combat liver and kidney disease. PMID:26257841

  13. Physical and thermochemical properties of rice husk

    SciTech Connect

    Mansaray, K.G.; Ghaly, A.E.

    1997-11-01

    Rice husk a major by-product of the rice milling industry, is one of the most commonly available lignocellulosic materials that can be converted to different types of fuels and chemical feedstocks through a variety of thermochemical conversion processes. Proper understanding of the physical and thermochemical properties of rice husk is necessary for the design of thermochemical conversion systems. This study provides information on moisture content, bulk density, particle size, heating values, proximate analysis, ultimate analysis, ash composition, and ash fusibility characteristics for six rice husk varieties. The moisture content ranged from 8.68 to 10.44%, and the bulk density ranged from 86 to 114 kg/m{sup 3}. The results showed excessive volatile release of over 60%, high ash content ranging from 15.30 to 24.60% (dry weight basis), and high silica content of the ash ranging from 90 to 97%. The lower heating values ranged from 13.24 to 16.20 MJ/kg (dry weight basis). The ash fusion temperatures of all the varieties were found to be over 1,600 C. The differences in varietal characteristics have significant effects on the chemical properties of rice husk.

  14. A nuclear-localized histone-gene binding protein from rice (OsHBP1b) functions in salinity and drought stress tolerance by maintaining chlorophyll content and improving the antioxidant machinery.

    PubMed

    Lakra, Nita; Nutan, Kamlesh K; Das, Priyanka; Anwar, Khalid; Singla-Pareek, Sneh L; Pareek, Ashwani

    2015-03-15

    Plants have evolved a number of molecular strategies and regulatory mechanisms to cope with abiotic stresses. Among the various key factors/regulators, transcription factors (TFs) play critical role(s) towards regulating the gene expression patterns in response to stress conditions. Altering the expression of the key TFs can greatly influence plant stress tolerance. OsHBP1b (accession no. KM096571) is one such TF belonging to bZIP family, localized within the Saltol QTL, whose expression is induced upon salinity treatment in the rice seedlings. qRT-PCR based expression studies for OsHBP1b in seedlings of contrasting genotypes of rice showed its differential regulation in response to salinity stress. A GFP based in vivo study showed that the OsHBP1b protein is nuclear localized and possesses the trans-activation activity. As compared to the WT tobacco plants, the transgenic plants ectopically expressing OsHBP1b showed better survival and favourable osmotic parameters (such as germination and survival rate, membrane stability, K(+)/Na(+) ratio, lipid peroxidation, electrolyte leakage and proline contents) under salinity and drought stress. Under salinity conditions, the transgenic plants accumulated lower levels of reactive oxygen species as compared to the WT. It was also accompanied by higher activities of antioxidant enzymes (such as ascorbate peroxidase and superoxide dismutase), thereby demonstrating that transgenic plants are physiologically better adapted towards the oxidative damage. Taken together, our findings suggest that OsHBP1b contributes to abiotic stress tolerance through multiple physiological pathways and thus, may serve as a useful 'candidate gene' for improving multiple stress tolerance in crop plants.

  15. Linkage Mapping of Stem Saccharification Digestibility in Rice

    PubMed Central

    Hua, Cangmei; Sun, Lili; Ali, Imran; Huang, Linli; Yu, Chunyan; Simister, Rachael; Steele-King, Clare; Gan, Yinbo; McQueen-Mason, Simon J.

    2016-01-01

    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. PMID:27415441

  16. Fermentation and quality of yellow pigments from golden brown rice solid culture by a selected Monascus mutant.

    PubMed

    Yongsmith, Busaba; Thongpradis, Panida; Klinsupa, Worawan; Chantrapornchai, Withida; Haruthaithanasan, Vichai

    2013-10-01

    A single peak (λmax 370) yellow pigment-producing mutant derived from Monascus sp. TISTR 3179 was used for the pigment production in solid rice culture. Various factors affecting yellow tones were investigated. Hom-mali rice variety was the best amongst five Thai local varieties used for fungus culture. It was also better than corn, mungbean, soybean, potato, sweet potato, or cassava tubers. The moisture content and temperature were the key environmental factors affecting the color tones of creamy, tangerine, and golden brown rice solid cultures. The golden brown rice culture gave the highest yellow pigment concentration. Under an optimum room temperature of 28-32 °C, an initial moisture content of 42 %, and 7-day-old inoculum size of 2 % (v/w) the maximum yield at 2,224.63 A370U/gdw of yellow pigment was produced. A mellow yellow powder at 550 A370U/gdw could be obtained using spray-drying techniques. The powder had a moisture content of 5.15 %, a water activity value of 0.398, a hue angle of 73.70 ° (yellowish orange), high lightness (L) of 74.63, color saturation (C) of 28.97, a neutral pH of 7.42, 0.12 % acidity and solubility of 0.211 g/10 ml. It was noteworthy that the Chinese fresh noodle with spray-dried yellow powder showed no discoloration during 8-day storage.

  17. Mycotoxin production on rice, pulses and oilseeds

    NASA Astrophysics Data System (ADS)

    Begum, Fouzia; Samajpati, N.

    Mycotoxin-producing fungi were isolated from contaminated grains of rice, pulses and oilseeds sold in the local markets of Calcutta for human consumption. It was found that aflatoxin B1 was produced by Aspergillus flavus and Aspergillus parasiticus, aflatoxin G1 by A. flavus, ochratoxin by Aspergillus ochraceous, sterigmatocystin by Aspergillus japonicus and citrinin by Penicillium citrinum. Aflatoxin B1 (333-10416μg/kg) was produced by Aspergillus spp. in rice, pulses and oilseeds.

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

    PubMed

    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.

  19. Rice domestication: histories and mysteries.

    PubMed

    Gross, Briana L

    2012-09-01

    Domesticated rice (Oryza sativa) is one of the world's most important food crops, culturally, nutritionally and economically (Khush 1997). Thus, it is no surprise that there is intense curiosity about its genetic and geographical origins, its response to selection under domestication, and the genetic structure of its wild relative, Oryza rufipogon. Studies of Oryza attempting to answer these questions have accompanied each stage of the development of molecular markers, starting with allozymes and continuing to genome sequencing. While many of these studies have been restricted to small sample sizes, in terms of either the number of markers used or the number and distribution of the accessions, costs are now low enough that researchers are including large numbers of molecular markers and accessions. How will these studies relate to previous findings and long-held assumptions about rice domestication and evolution? If the paper in this issue of Molecular Ecology (Huang et al. 2012) is any indication, there will be some considerable surprises in store. In this study, a geographically and genomically thorough sampling of O. rufipogon and O. sativa revealed two genetically distinct groups of wild rice and also indicated that only one of these groups appears to be related to domesticated rice. While this fits well with previous studies indicating that there are genetic subdivisions within O. rufipogon, it stands in contrast to previous findings that the two major varieties of O. sativa (indica and japonica) were domesticated from two (or more) subpopulations of wild rice.

  20. Evaluation of methane emissions of some rice cultivars of Sri Lanka

    SciTech Connect

    Namaratne, S.Y.; Alwis, H.P.W. de

    1996-12-31

    A field experiment on three local rice cultivars, namely BG 300, BG 304 and AT 303, showed no statistically significant difference (p<0.05) among them with-respect to the methane flux emitted. The methane flux profiles of all three varieties indicated a more or less constant emission during the vegetative and reproductive periods, a peak emission during late flowering/early ripening stage and a dramatic increase in the flux during the late ripening period. The seasonal methane flux of BG 300, BG 304 and AT 303 were 200 {+-} 48, 156 {+-} 52 and 129 {+-} 40 g m{sup {minus}2}, respectively for a 92 day cropping period.

  1. Crop management strategies and disease resistance control the severity of false smut and kernel smut of rice

    Technology Transfer Automated Retrieval System (TEKTRAN)

    False smut and kernel smut are common diseases of rice capable of severe epidemics with dramatic yield losses. The importance of rice smuts is often overlooked in the US, and highly susceptible varieties are now being grown on the majority of production acres in the southern rice producing states. O...

  2. A mathematical model of transmission of rice tungro disease by Nephotettix Virescens

    NASA Astrophysics Data System (ADS)

    Blas, Nikki T.; Addawe, Joel M.; David, Guido

    2016-11-01

    One of the major threats in rice agriculture is the Tungro virus, which is transmitted semi-persistently to rice plants via green rice leafhoppers called Nephotettix Virescens. Tungro is polycyclic and complex disease of rice associated by dual infection with Rice Tungro Bacilliform Virus (RTBV) and Rice Tungro Spherical Virus (RTSV). Interaction of the two viruses results in the degeneration of the host. In this paper, we used a plant-vector system of ordinary differential equations to model the spread of the disease in a model rice field. Parameter values were obtained from studies on the entomology of Nephotettix Virescens and infection rates of RTSV and RTBV. The system was analyzed for equilibrium solutions, and solved numerically for susceptible rice varieties (Taichung Native 1).

  3. Effects of cooking methods and starch structures on starch hydrolysis rates of rice.

    PubMed

    Reed, Michael O; Ai, Yongfeng; Leutcher, Josh L; Jane, Jay-lin

    2013-07-01

    This study aimed to understand effects of different cooking methods, including steamed, pilaf, and traditional stir-fried, on starch hydrolysis rates of rice. Rice grains of 3 varieties, japonica, indica, and waxy, were used for the study. Rice starch was isolated from the grain and characterized. Amylose contents of starches from japonica, indica, and waxy rice were 13.5%, 18.0%, and 0.9%, respectively. The onset gelatinization temperature of indica starch (71.6 °C) was higher than that of the japonica and waxy starch (56.0 and 56.8 °C, respectively). The difference was attributed to longer amylopectin branch chains of the indica starch. Starch hydrolysis rates and resistant starch (RS) contents of the rice varieties differed after they were cooked using different methods. Stir-fried rice displayed the least starch hydrolysis rate followed by pilaf rice and steamed rice for each rice variety. RS contents of freshly steamed japonica, indica, and waxy rice were 0.7%, 6.6%, and 1.3%, respectively; those of rice pilaf were 12.1%, 13.2%, and 3.4%, respectively; and the stir-fried rice displayed the largest RS contents of 15.8%, 16.6%, and 12.1%, respectively. Mechanisms of the large RS contents of the stir-fried rice were studied. With the least starch hydrolysis rate and the largest RS content, stir-fried rice would be a desirable way of preparing rice for food to reduce postprandial blood glucose and insulin responses and to improve colon health of humans.

  4. Health-Promoting Compounds in Pigmented Thai and Wild Rice

    PubMed Central

    Melini, Valentina; Acquistucci, Rita

    2017-01-01

    Organic pigmented Thai rice and wild rice are commonly available in specialized Italian markets and food shops, and they are gaining popularity among consumers demanding healthy foods. Indeed, the typical colour of kernels, which is the unique characteristic of pigmented cereals, is due to the accumulation of pigments that are also responsible for a number of healthy effects. The aim of this study was to provide a portrait of two organic pigmented Thai rice varieties from Thailand and one wild rice variety from Canada, imported into Italy and at Italian consumers’ disposal. To this end, the proximate composition and the content of health-promoting compounds, such as carotenoids, anthocyanins and phenolic compounds, were determined in Thai and wild rice. Moreover, the effect of cooking on phytochemicals was assessed, in order to provide reliable data on the dietary intake of bioactive compounds by samples under investigation. Results show that studied samples have a content of phytochemicals higher than white rice and comparable to other cereals. The cooking process determined a decrease of bioactive compounds in all varieties under investigation. However, some samples were found more resistant to cooking stress, and some phytochemicals were little affected by this process. Therefore, pigmented Thai and wild rice may represent a valuable source of healthy compounds and an alternative to other wholesome foods required by consumers. PMID:28231088

  5. Cytoprotective and Cytotoxic Effects of Rice Bran Extracts in Rat H9c2(2-1) Cardiomyocytes

    PubMed Central

    Tan, Xian Wen; Bhave, Mrinal; Fong, Alan Yean Yip; Matsuura, Eiji; Kobayashi, Kazuko; Shen, Lian Hua; Hwang, Siaw San

    2016-01-01

    This study was aimed at preliminarily assessing the cytoprotective and antioxidative effects of rice bran extracts (RBEs) from a Sarawak local rice variety (local name: “BJLN”) and a commercial rice variety, “MR219,” on oxidative stress in rat H9c2(2-1) cardiomyocytes. The cardiomyocytes were incubated with different concentrations of RBE and hydrogen peroxide (H2O2), respectively, to identify their respective IC50 values and safe dose ranges. Two nonlethal and close-to-IC50 doses of RBE were selected to evaluate their respective effects on H2O2 induced oxidative stress in cardiomyocytes. Both RBEs showed dose-dependent cytotoxicity effects on cardiomyocytes. H2O2 induction of cardiomyocytes pretreated with RBE further revealed the dose-dependent cytoprotective and antioxidative effects of RBE via an increase in IC50 values of H2O2. Preliminary analyses of induction effects of RBE and H2O2 on cellular antioxidant enzyme, catalase (CAT), also revealed their potential in regulating these activities and expression profile of related gene on oxidative stress in cardiomyocytes. Pretreated cardiomyocytes significantly upregulated the enzymatic activity and expression level of CAT under the exposure of H2O2 induced oxidative stress. This preliminary study has demonstrated the potential antioxidant effects of RBE in alleviating H2O2-mediated oxidative injuries via upregulation in enzymatic activities and expression levels of CAT. PMID:27239253

  6. Thermal degradation of rice husks in an oxygen atmosphere

    SciTech Connect

    Mansaray, K.G.; Ghaly, A.E.

    1999-06-01

    Of the various energy conversion options of rice husk, thermochemical conversion processes such as pyrolysis, combustion, and gasification offer the most efficient way to use rice husk. However, a knowledge of the thermal characteristics of rice husks is essential for the optimal design of these systems and for ensuring stringent emissions as well as high conversion efficiency. Thermogravimetric analysis is used to profile weight loss due to physical and chemical phenomena taking place in the sample while being subjected to high temperatures. This technique presents an ideal system to study thermal properties of carbonaceous materials. Evaluation of the thermogravimetric behavior of four rice husk varieties (Lemont, ROK 14, CP 4, and Pa Potho) at three heating rates (10, 20, and 50 C/min) in an oxygen atmosphere is described. The thermal degradation rates, the initial degradation temperature, and the residual weight at 700 C were determined. These thermal degradation indices of rice husks are a function of temperature, heating rate, and the composition of the rice husks. The initial degradation temperature decreased while both the thermal degradation rate and the residual weight at 700 C increased when the heating rate was increased. The higher the cellulosic content of the rice husk, the higher the thermal degradation rate and the initial degradation temperature. Also, higher ash content in the rice husk resulted in higher residual weight at 700 C. Rice husk could be degraded to the extent of 73--80%.

  7. Marker-assisted backcrossing: a useful method for rice improvement.

    PubMed

    Hasan, Muhammad Mahmudul; Rafii, Mohd Y; Ismail, Mohd R; Mahmood, Maziah; Rahim, Harun A; Alam, Md Amirul; Ashkani, Sadegh; Malek, Md Abdul; Latif, Mohammad Abdul

    2015-03-04

    The world's population is increasing very rapidly, reducing the cultivable land of rice, decreasing table water, emerging new diseases and pests, and the climate changes are major issues that must be addressed to researchers to develop sustainable crop varieties with resistance to biotic and abiotic stresses. However, recent scientific discoveries and advances particularly in genetics, genomics and crop physiology have opened up new opportunities to reduce the impact of these stresses which would have been difficult if not impossible as recently as the turn of the century. Marker assisted backcrossing (MABC) is one of the most promising approaches is the use of molecular markers to identify and select genes controlling resistance to those factors. Regarding this, MABC can contribute to develop resistant or high-yielding or quality rice varieties by incorporating a gene of interest into an elite variety which is already well adapted by the farmers. MABC is newly developed efficient tool by which using large population sizes (400 or more plants) for the backcross F1 generations, it is possible to recover the recurrent parent genotype using only two or three backcrosses. So far, many high yielding, biotic and abiotic stresses tolerance, quality and fragrance rice varieties have been developed in rice growing countries through MABC within the shortest timeframe. Nowadays, MABC is being used widely in plant breeding programmes to develop new variety/lines especially in rice. This paper reviews recent literature on some examples of variety/ line development using MABC strategy.

  8. Research in rice fields

    USGS Publications Warehouse

    ,

    2000-01-01

    Between 1987 and 1999, 2.4-3 million acres of rice were planted annually nationwide. Rice fields are a major component of the contemporary landscapes in the Gulf Coastal Plain, the Mississippi Alluvial Valley, and Central Valley of California. In 1998, approximately 600,000 acres of rice were planted in Louisiana. In the Louisiana plant commodities report for 1998, total value for rice was over $350 million; sugarcane was the only plant commodity that exceeded this value. Louisiana has over 2,000 rice farmers supporting over 12,000 jobs in the state. Rice fields in the United States receive high use by wildlife, especially shorebirds, wading birds, and waterfowl. Waterbirds use rice fields for food, shelter, and breeding habitat.

  9. Phosphorus and Iron Deficiencies Influences Rice Shoot Growth in an Oxygen Dependent Manner: Insight from Upland and Lowland Rice.

    PubMed

    Mongon, Jenjira; Chaiwong, Nanthana; Bouain, Nadia; Prom-U-Thai, Chanakan; Secco, David; Rouached, Hatem

    2017-03-10

    Rice is the main staple crop for one-third of the world population. To maximize yields, large quantities and constant input of fertilizers containing essential nutrients such as phosphorus (P) and iron (Fe) are added. Rice can germinate in both aerobic and anaerobic conditions, but the crosstalk between oxygen (O₂) and nutrients such as P and Fe on plant growth remains obscure. The aim of this work was to test whether such interactions exist, and, if so, if they are conserved between up- and lowland rice varieties. To do so, we assessed shoot and root biomass as well as inorganic phosphate (Pi) accumulation in four rice varieties, including two lowland rice varieties Nipponbare and Suphanburi 1 (SPR1) (adapted to non-aerated condition) and two upland rice varieties CMU122 and Sew Mae Jun (SMJ) (adapted to aerated condition) under various conditions of Pi and/or Fe deficiencies, in aerated and non-areated solution. Under these different experimental conditions, our results revealed that the altered shoot biomass in Nipponbare and SPR1 was O₂-dependent but to a lesser extent in CMU122 and SMJ cultivars. In this perspective, discovering the biological significance and molecular basis of these mineral elements and O₂ signal interaction is needed to fully appreciate the performance of plants to multiple environmental changes.

  10. Phosphorus and Iron Deficiencies Influences Rice Shoot Growth in an Oxygen Dependent Manner: Insight from Upland and Lowland Rice

    PubMed Central

    Mongon, Jenjira; Chaiwong, Nanthana; Bouain, Nadia; Prom-u-thai, Chanakan; Secco, David; Rouached, Hatem

    2017-01-01

    Rice is the main staple crop for one-third of the world population. To maximize yields, large quantities and constant input of fertilizers containing essential nutrients such as phosphorus (P) and iron (Fe) are added. Rice can germinate in both aerobic and anaerobic conditions, but the crosstalk between oxygen (O2) and nutrients such as P and Fe on plant growth remains obscure. The aim of this work was to test whether such interactions exist, and, if so, if they are conserved between up- and lowland rice varieties. To do so, we assessed shoot and root biomass as well as inorganic phosphate (Pi) accumulation in four rice varieties, including two lowland rice varieties Nipponbare and Suphanburi 1 (SPR1) (adapted to non-aerated condition) and two upland rice varieties CMU122 and Sew Mae Jun (SMJ) (adapted to aerated condition) under various conditions of Pi and/or Fe deficiencies, in aerated and non-areated solution. Under these different experimental conditions, our results revealed that the altered shoot biomass in Nipponbare and SPR1 was O2-dependent but to a lesser extent in CMU122 and SMJ cultivars. In this perspective, discovering the biological significance and molecular basis of these mineral elements and O2 signal interaction is needed to fully appreciate the performance of plants to multiple environmental changes. PMID:28287426

  11. Genetics, Physiological Mechanisms and Breeding of Flood-Tolerant Rice (Oryza sativa L.).

    PubMed

    Singh, Anuradha; Septiningsih, Endang M; Balyan, Harendra S; Singh, Nagendra K; Rai, Vandna

    2017-01-09

    Flooding of rice fields is a serious problem in the river basins of South and South-East Asia where about 15 Mha of lowland rice cultivation is regularly affected. Flooding creates hypoxic conditions resulting in poor germination and seedling establishment. Flash flooding, where rice plants are completely submerged for 10-15 d during their vegetative stage, causes huge losses. Water stagnation for weeks to months also leads to substantial yield losses when large parts of rice aerial tissues are inundated. The low-yielding traditional varieties and landraces of rice adapted to these flooding conditions have been replaced by flood-sensitive high-yielding rice varieties. The 'FR13A' rice variety and the Submergence 1A (SUB1A) gene were identified for flash flooding and subsequently introgressed to high-yielding rice varieties. The challenge is to find superior alleles of the SUB1A gene, or even new genes that may confer greater tolerance to submergence. Similarly, genes have been identified in tolerant landraces of rice for their ability to survive by rapid stem elongation (SNORKEL1 and SNORKEL2) during deep-water flooding, and for anaerobic germination ability (TPP7). Research on rice genotypes and novel genes that are tolerant to prolonged water stagnation is in progress. These studies will greatly assist in devising more efficient and precise molecular breeding strategies for developing climate-resilient high-yielding rice varieties for flood-prone regions. Here we review the state of our knowledge of flooding tolerance in rice and its application in varietal improvement.

  12. Estimating Evapotrnspiration in a Rice Field Using a Remote-Sensing Based Two Source Energy Balance Model

    NASA Astrophysics Data System (ADS)

    Han, K.; Kustas, W. P.; Anderson, M. C.; Gao, F.; Lee, K.; Hong, S.; Zhang, Y.

    2013-12-01

    Evapotranspiration monitoring of rice, a main cereal and food source of Monsoon Asia, is important not only for sustaining stable grain production and for effective water use through precise water management, but also provides a means for early warning of and response to drought. The remote-sensing based two source energy balance model (TSEB) estimates of evapotranspiration (ET) over a wide variety of land cover types using ground, airborne and satellite imagery and meteorological data without time-consuming and/or expensive field measurements such as measurements of daily decrease of flooding water depth and eddy covariance-based flux tower observations. We, therefore, evaluated the TSEB model at local sites, Icheon and Kimje, with energy flux tower and ground-based thermal-infrared temperature measurement collected over cultivated rice fields and applied the model for estimating ET over rice cropping region encompassing an area 16km x 16km scale in South Korea using Landsat imagery. The TSEB model required modification to the soil heat flux algorithm because rice typically grows in saturated soils and/or standing water for about 75% of the rice growing season. Half-hourly energy flux data, including net radiation, sensible heat, latent heat (corresponding to ET), and soil heat, at two field sites were acquired using eddy-covariance method. The root mean square difference values between predicted and observed latent heat flux ranged between 10% and 25% of the average observed latent heat flux. This is comparable to the measurement uncertainty, suggesting that the TSEB model can provide reliable ET estimation for rice fields. Applying the TSEB model with Landsat imagery over a 16km x 16km domain encompassing the Kimje flux tower site was also performed. Leaf area index for the study area at the Landsat resolution was estimated using MODIS leaf area index products as a reference. Atmospheric correction of the land surface temperature was carried out using MODTRAN

  13. Cooked rice texture and rice flour pasting properties; impacted by rice temperature during milling.

    PubMed

    Saleh, Mohammed; Meullenet, Jean-Francois

    2015-03-01

    Rice milling plays a key factor in determining rice quality and value. Therefore accurate quality assessments are critical to the rice industry. This study was undertaken to assess the effect of exposing rice to elevated temperatures during milling, on cooked rice texture and rice flour pasting properties. Two long (Cybonnett and Francis) and one medium (Jupiter) rice (oryzae sativa L.) cultivars were milled using McGill laboratory mill for 30 and 40 s after warmed up the mill before milling. Four different milling temperatures per milling duration were achieved. Cooked rice texture properties were assessed using a uniaxial compression test and rice flour pasting properties measured using a TA-2000 rheometer. Results of this study showed that exposure of rice to high temperatures during milling significantly decreased cooked rice firmness. An increase in milled rice temperature after milling from 10.0 to 13.3 °C resulted in a 5.4 and 8.1 N decrease in cooked rice firmness. Although not always significant, the increase in milled rice temperature during milling resulted in an increase in cooked rice stickiness. The increase in milling temperature also showed significant increase in rice flour pasting properties. Changes in rice functional characteristics were attributed to the changes occurring to rice chemical constituents due to temperature exposure as indicated by the increase in rice protein hydrophobicity. Proteins are known to affect rice starch water holding capacity and other starch gelatinization properties.

  14. Genetic variation architecture of mitochondrial genome reveals the differentiation in Korean landrace and weedy rice.

    PubMed

    Tong, Wei; He, Qiang; Park, Yong-Jin

    2017-03-03

    Mitochondrial genome variations have been detected despite the overall conservation of this gene content, which has been valuable for plant population genetics and evolutionary studies. Here, we describe mitochondrial variation architecture and our performance of a phylogenetic dissection of Korean landrace and weedy rice. A total of 4,717 variations across the mitochondrial genome were identified adjunct with 10 wild rice. Genetic diversity assessment revealed that wild rice has higher nucleotide diversity than landrace and/or weedy, and landrace rice has higher diversity than weedy rice. Genetic distance was suggestive of a high level of breeding between landrace and weedy rice, and the landrace showing a closer association with wild rice than weedy rice. Population structure and principal component analyses showed no obvious difference in the genetic backgrounds of landrace and weedy rice in mitochondrial genome level. Phylogenetic, population split, and haplotype network evaluations were suggestive of independent origins of the indica and japonica varieties. The origin of weedy rice is supposed to be more likely from cultivated rice rather than from wild rice in mitochondrial genome level.

  15. Genetic variation architecture of mitochondrial genome reveals the differentiation in Korean landrace and weedy rice

    PubMed Central

    Tong, Wei; He, Qiang; Park, Yong-Jin

    2017-01-01

    Mitochondrial genome variations have been detected despite the overall conservation of this gene content, which has been valuable for plant population genetics and evolutionary studies. Here, we describe mitochondrial variation architecture and our performance of a phylogenetic dissection of Korean landrace and weedy rice. A total of 4,717 variations across the mitochondrial genome were identified adjunct with 10 wild rice. Genetic diversity assessment revealed that wild rice has higher nucleotide diversity than landrace and/or weedy, and landrace rice has higher diversity than weedy rice. Genetic distance was suggestive of a high level of breeding between landrace and weedy rice, and the landrace showing a closer association with wild rice than weedy rice. Population structure and principal component analyses showed no obvious difference in the genetic backgrounds of landrace and weedy rice in mitochondrial genome level. Phylogenetic, population split, and haplotype network evaluations were suggestive of independent origins of the indica and japonica varieties. The origin of weedy rice is supposed to be more likely from cultivated rice rather than from wild rice in mitochondrial genome level. PMID:28256554

  16. Gelatinization temperature of rice explained by polymorphisms in starch synthase.

    PubMed

    Waters, Daniel L E; Henry, Robert J; Reinke, Russell F; Fitzgerald, Melissa A

    2006-01-01

    The cooking quality of rice is associated with the starch gelatinization temperature (GT). Rice genotypes with low GT have probably been selected for their cooking quality by humans during domestication. We now report polymorphisms in starch synthase IIa (SSIIa) that explain the variation in rice starch GT. Sequence analysis of the eight exons of SSIIa identified significant polymorphism in only exon 8. These single nucleotide polymorphisms (SNPs) were determined in 70 diverse genotypes of rice. Two SNPs could classify all 70 genotypes into either high GT or low GT types which differed in GT by 8 degrees C. 'A' rather than 'G' at base 2412 determined whether a methionine or valine was present at the corresponding amino acid residue in SSIIa, whilst two adjacent SNPs at bases 2543 and 2544 coded for either leucine (GC) or phenylalanine (TT). Rice varieties with high GT starch had a combination of valine and leucine at these residues. In contrast, rice varieties with low GT starch had a combination of either methionine and leucine or valine and phenylalanine at these same residues. At least two distinct polymorphisms have apparently been selected for their desirable cooking qualities in the domestication of rice.

  17. Food variety and biodiversity: Econutrition.

    PubMed

    Wahlqvist, M L; Specht, R L

    1998-12-01

    Both annual biomass production and biodiversity at any locality on earth are continually under threat as the population of Homo sapiens steadily increases, with the resultant pollution of atmosphere, soil and water. Today, environmental degradation and global warming (with its effect on evaporative aerodynamics and cellular respiration) have increased at an alarming rate. The ABP of all terrestrial plant communities (natural or cultivated) is slowly declining, thus reducing the energy supply of component plants and resident animals; in turn, the biodiversity of all the world's ecosystems, plant and animal, is threatened. The maintenance of biodiversity is important to human health for several reasons: (i) a varied food supply is essential to maintain the health of the omnivorous human species; (ii) a range of diverse food sources is necessary to safe-guard against climatic and pestilent disasters which may affect one or more of the food sources; (iii) a diversity of plants and animals may provide a rich source of medicinal material, essential for the extraction of undiscovered therapeutic compounds; (iv) intact ecosystems of indigenous plants and animals appear to act as a buffer to the spread of invasive plants and animals, and of pathogens and toxins, thus contributing to the health of populations nearby; and (v) the 'spiritual' values of exploring the diversity of plants, animals and ecosystems in an area appear to have a beneficial effect on mental health, strengthening the feeling of 'belonging to the landscape'. The variety of foods, their energy contents and food values, consumed throughout the year is amenable to scientific enquiry; as is the amount of energy expended in this collection or production. The control and management of food production and of water supplies, with attention to safety issues, has led to an improvement in life expectancy for a proportion of the world's population. The question is at what point might human health be disadvantaged by

  18. A feasibility study on identification of Basmati (aromatic) rice using SAR data

    NASA Astrophysics Data System (ADS)

    Jain, Varunika; Patnaik, C.; Panigrahy, S.

    2014-12-01

    Rice areas in India are being mapped for acreage estimation using Synthetic Aperture Radar (SAR) data under forecasting agricultural output using space, agrometeorology and land-based observations (FASAL) program for over a decade now. Under this study, an attempt was made to segregate rice areas based on variety in parts of Punjab state. Data acquisition was done at critical stages of rice growth. The shift in transplantation in temporal domain and difference in canopy volume formed the basis of characterization of rice crop into two different varieties namely aromatic and non-aromatic. Multitemporal HH polarization data along with rate of change of cross polarization ratio (HH/HV) from July to September 2011 was used. The aromatic rice could be separated from normal rice with 91% accuracy.

  19. Climate change: implications for the yield of edible rice.

    PubMed

    Zhao, Xiangqian; Fitzgerald, Melissa

    2013-01-01

    Global warming affects not only rice yield but also grain quality. A better understanding of the effects of climate factors on rice quality provides information for new breeding strategies to develop varieties of rice adapted to a changing world. Chalkiness is a key trait of physical quality, and along with head rice yield, is used to determine the price of rice in all markets. In the present study, we show that for every ∼1% decrease in chalkiness, an increase of ∼1% in head rice yield follows, illustrating the dual impact of chalk on amount of marketable rice and its value. Previous studies in controlled growing conditions report that chalkiness is associated with high temperature. From 1980-2009 at IRRI, Los Baños, the Philippines, annual minimum and mean temperatures, and diurnal variation changed significantly. The objective of this study was to determine how climate impacts chalkiness in field conditions over four wet and dry seasons. We show that low relative humidity and a high vapour pressure deficit in the dry season associate with low chalk and high head rice yield in spite of higher maximum temperature, but in the opposite conditions of the wet season, chalk is high and head rice yield is low. The data therefore suggest that transpirational cooling is a key factor affecting chalkiness and head rice yield, and global warming per se might not be the major factor that decreases the amount and quality of rice, but other climate factors in combination, that enable the crop to maintain a cool canopy.

  20. The relationship between translucency of rice grain and gelatinization of starch in the grain during cooking.

    PubMed

    He, G; Suzuki, H

    1987-08-01

    The soaked and nonsoaked rice grains were cooked by the excess water method and the steamer method, and subjected to Ranghino's test, X-ray diffraction, and microscopic observation. The starch granules in the nonsoaked rice were gelatinized at the same time as the grains became translucent during cooking. However, when the grains of medium amylose varieties and waxy rice were presoaked, the starch granules were not fully gelatinized in the translucent grains cooked for Ranghino's cooking time. The gelatinization of starch granules proceeded faster in the soaked rice and by the excess water method than that in the nonsoaked rice and by the steamer method. The cooking time and gelatinization time correlated negatively with the water content after soaking, and positively with the amylose content in the rice grains. The japonica rices were gelatinized fully in less than 20 min when the amount of water added for cooking was adequate.

  1. Studies on mineral nutrition and safety of wild rice (Oryza L.).

    PubMed

    Jiang, Shuli; Shi, Chunhai; Wu, Jianguo

    2009-01-01

    Mineral element contents of five wild rice were analyzed, including mineral nutrient elements such as phosphorus (P), potassium (K), calcium (Ca), sodium (Na), magnesium (Mg), iron (Fe), zinc (Zn), copper (Cu), manganese (Mn) and selenium (Se), and the potential toxic elements arsenic (As), mercury (Hg), lead (Pb) and cadmium (Cd). The results showed that the contents of K, Mg, Fe, Zn, Cu, Mn and Se in five wild rice materials were much higher than the cultivate variety Zhou 903 in both brown and milled rice. Wild rice also had lower potential toxic element contents of Hg, Pb and Cd compared with Zhou 903 in brown rice and milled rice, respectively. Among five wild rice samples, WR-3 from Uganda had the highest level of P, K, Ca, Na, Mg, Fe, Zn, Mn and Se, and the lowest contents of Hg, Pb and Cd.

  2. Rice industrial processing worldwide and impact on macro- and micronutrient content, stability, and retention.

    PubMed

    Atungulu, Griffiths G; Pan, Zhongli

    2014-09-01

    Various processing methods are used in the food industry worldwide to produce numerous rice products with desirable sensory qualities based on cultural and cooking preferences and nutritional considerations. The processes result in variable degrees of macro- and micronutrient content, stability, and retention, depending on rice variety and original nutritional quality. In this article, modern and traditional premilling, milling, and postmilling processing methods of different rice types are comprehensively reviewed. The implications of industrial rice processing methods, especially milling, as well as techniques for nutrient extraction, transfer, and enhancement, such as rice parboiling, sprouting, and fortification, for macro- and micronutrient content and consumer acceptance of the products, are documented. Socioeconomic constraints facing various aspects of rice processing methods are also discussed. This article reviews up-to-date research on rice industrial processing worldwide and aims to benefit engineers dealing with food processing, nutritionists and dieticians, food companies, education and research institutions, and quality-control and safety managers.

  3. 7 CFR 906.13 - Variety or varieties.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 7 Agriculture 8 2010-01-01 2010-01-01 false Variety or varieties. 906.13 Section 906.13 Agriculture Regulations of the Department of Agriculture (Continued) AGRICULTURAL MARKETING SERVICE (Marketing... oranges; (d) white seeded grapefruit; (e) white seedless grapefruit; (f) pink and red seeded...

  4. 7 CFR 906.13 - Variety or varieties.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 7 Agriculture 8 2011-01-01 2011-01-01 false Variety or varieties. 906.13 Section 906.13 Agriculture Regulations of the Department of Agriculture (Continued) AGRICULTURAL MARKETING SERVICE (Marketing... oranges; (d) white seeded grapefruit; (e) white seedless grapefruit; (f) pink and red seeded...

  5. Evaluation of Rice Resistance to Southern Rice Black-Streaked Dwarf Virus and Rice Ragged Stunt Virus through Combined Field Tests, Quantitative Real-Time PCR, and Proteome Analysis

    PubMed Central

    Wang, Zhenchao; Yu, Lu; Jin, Linhong; Wang, Wenli; Zhao, Qi; Ran, Longlu; Li, Xiangyang; Chen, Zhuo; Guo, Rong; Wei, Yongtian; Yang, Zhongcheng; Liu, Enlong; Hu, Deyu; Song, Baoan

    2017-01-01

    Diseases caused by southern rice black-streaked dwarf virus (SRBSDV) and rice ragged stunt virus (RRSV) considerably decrease grain yield. Therefore, determining rice cultivars with high resistance to SRBSDV and RRSV is necessary. In this study, rice cultivars with high resistance to SRBSDV and RRSV were evaluated through field trials in Shidian and Mangshi county, Yunnan province, China. SYBR Green I-based quantitative real-time polymerase chain reaction (qRT-PCR) analysis was used to quantitatively detect virus gene expression levels in different rice varieties. The following parameters were applied to evaluate rice resistance: acre yield (A.Y.), incidence of infected plants (I.I.P.), virus load (V.L.), disease index (D.I.), and insect quantity (I.Q.) per 100 clusters. Zhongzheyou1 (Z1) and Liangyou2186 (L2186) were considered the most suitable varieties with integrated higher A.Y., lower I.I.P., V.L., D.I. and I.Q. features. In order to investigate the mechanism of rice resistance, comparative label-free shotgun liquid chromatography tandem-mass spectrometry (LC-MS/MS) proteomic approaches were applied to comprehensively describe the proteomics of rice varieties’ SRBSDV tolerance. Systemic acquired resistance (SAR)-related proteins in Z1 and L2186 may result in the superior resistance of these varieties compared with Fengyouxiangzhan (FYXZ). PMID:28241456

  6. Constitutive expression of McCHIT1-PAT enhances resistance to rice blast and herbicide, but does not affect grain yield in transgenic glutinous rice.

    PubMed

    Zeng, Xiao-Fang; Li, Lei; Li, Jian-Rong; Zhao, De-Gang

    2016-01-01

    To produce new rice blast- and herbicide-resistant transgenic rice lines, the McCHIT1 gene encoding the class I chitinase from Momordica charantia and the herbicide resistance gene PAT were introduced into Lailong (Oryza sativa L. ssp. Japonica), a glutinous local rice variety from Guizhou Province, People's Republic of China. Transgenic lines were identified by ß-glucuronidase (GUS) histochemical staining, PCR, and Southern blot analyses. Agronomic traits, resistance to rice blast and herbicide, chitinase activities, and transcript levels of McCHIT1 were assessed in the T2 progeny of three transgenic lines (L1, L8, and L10). The results showed that the introduction of McCHIT1-PAT into Lailong significantly enhanced herbicide and blast resistance. After infection with the blast fungus Magnaporthe oryzae, all of the T2 progeny exhibited less severe lesion symptoms than those of wild type. The disease indices were 100% for wild type, 65.66% for T2 transgenic line L1, 59.69% for T2 transgenic line L8, and 79.80% for T2 transgenic line L10. Transgenic lines expressing McCHIT1-PAT did not show a significant difference from wild type in terms of malondialdehyde (MDA) content, polyphenol oxidase (PPO) activity, and superoxide dismutase (SOD) activity in the leaves. However, after inoculation with M. oryzae, transgenic plants showed significantly higher SOD and PPO activities and lower MDA contents in leaves, compared with those in wild-type leaves. The transgenic and the wild-type plants did not show significant differences in grain yield parameters including plant height, panicles per plant, seeds per panicle, and 1000-grain weight. Therefore, the transgenic plants showed increased herbicide and blast resistance, with no yield penalty.

  7. Responses of Super Rice (Oryza sativa L.) to Different Planting Methods for Grain Yield and Nitrogen-Use Efficiency in the Single Cropping Season

    PubMed Central

    Chen, Song; Wang, Danying; Xu, Chunmei; Ji, Chenglin; Zhang, Xiaoguo; Zhao, Xia; Zhang, Xiufu; Chauhan, Bhagirath Singh

    2014-01-01

    To break the yield ceiling of rice production, a super rice project was developed in 1996 to breed rice varieties with super high yield. A two-year experiment was conducted to evaluate yield and nitrogen (N)-use response of super rice to different planting methods in the single cropping season. A total of 17 rice varieties, including 13 super rice and four non-super checks (CK), were grown under three N levels [0 (N0), 150 (N150), and 225 (N225) kg ha−1] and two planting methods [transplanting (TP) and direct-seeding in wet conditions (WDS)]. Grain yield under WDS (7.69 t ha−1) was generally lower than TP (8.58 t ha−1). However, grain yield under different planting methods was affected by N rates as well as variety groups. In both years, there was no difference in grain yield between super and CK varieties at N150, irrespective of planting methods. However, grain yield difference was dramatic in japonica groups at N225, that is, there was an 11.3% and 14.1% average increase in super rice than in CK varieties in WDS and TP, respectively. This suggests that high N input contributes to narrowing the yield gap in super rice varieties, which also indicates that super rice was bred for high fertility conditions. In the japonica group, more N was accumulated in super rice than in CK at N225, but no difference was found between super and CK varieties at N0 and N150. Similar results were also found for N agronomic efficiency. The results suggest that super rice varieties have an advantage for N-use efficiency when high N is applied. The response of super rice was greater under TP than under WDS. The results suggest that the need to further improve agronomic and other management practices to achieve high yield and N-use efficiency for super rice varieties in WDS. PMID:25111805

  8. Responses of super rice (Oryza sativa L.) to different planting methods for grain yield and nitrogen-use efficiency in the single cropping season.

    PubMed

    Chen, Song; Wang, Danying; Xu, Chunmei; Ji, Chenglin; Zhang, Xiaoguo; Zhao, Xia; Zhang, Xiufu; Chauhan, Bhagirath Singh

    2014-01-01

    To break the yield ceiling of rice production, a super rice project was developed in 1996 to breed rice varieties with super high yield. A two-year experiment was conducted to evaluate yield and nitrogen (N)-use response of super rice to different planting methods in the single cropping season. A total of 17 rice varieties, including 13 super rice and four non-super checks (CK), were grown under three N levels [0 (N0), 150 (N150), and 225 (N225) kg ha-1] and two planting methods [transplanting (TP) and direct-seeding in wet conditions (WDS)]. Grain yield under WDS (7.69 t ha-1) was generally lower than TP (8.58 t ha-1). However, grain yield under different planting methods was affected by N rates as well as variety groups. In both years, there was no difference in grain yield between super and CK varieties at N150, irrespective of planting methods. However, grain yield difference was dramatic in japonica groups at N225, that is, there was an 11.3% and 14.1% average increase in super rice than in CK varieties in WDS and TP, respectively. This suggests that high N input contributes to narrowing the yield gap in super rice varieties, which also indicates that super rice was bred for high fertility conditions. In the japonica group, more N was accumulated in super rice than in CK at N225, but no difference was found between super and CK varieties at N0 and N150. Similar results were also found for N agronomic efficiency. The results suggest that super rice varieties have an advantage for N-use efficiency when high N is applied. The response of super rice was greater under TP than under WDS. The results suggest that the need to further improve agronomic and other management practices to achieve high yield and N-use efficiency for super rice varieties in WDS.

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

    PubMed

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

    2016-07-01

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

  10. Recent Advances in the Measurement of Arsenic, Cadmium, and Mercury in Rice and Other Foods

    PubMed Central

    Punshon, Tracy

    2015-01-01

    Trace element analysis of foods is of increasing importance because of raised consumer awareness and the need to evaluate and establish regulatory guidelines for toxic trace metals and metalloids. This paper reviews recent advances in the analysis of trace elements in food, including challenges, state-of-the art methods, and use of spatially resolved techniques for localizing the distribution of As and Hg within rice grains. Total elemental analysis of foods is relatively well-established but the push for ever lower detection limits requires that methods be robust from potential matrix interferences which can be particularly severe for food. Inductively coupled plasma mass spectrometry (ICP-MS) is the method of choice, allowing for multi-element and highly sensitive analyses. For arsenic, speciation analysis is necessary because the inorganic forms are more likely to be subject to regulatory limits. Chromatographic techniques coupled to ICP-MS are most often used for arsenic speciation and a range of methods now exist for a variety of different arsenic species in different food matrices. Speciation and spatial analysis of foods, especially rice, can also be achieved with synchrotron techniques. Sensitive analytical techniques and methodological advances provide robust methods for the assessment of several metals in animal and plant-based foods, in particular for arsenic, cadmium and mercury in rice and arsenic speciation in foodstuffs. PMID:25938012

  11. Recent Advances in the Measurement of Arsenic, Cadmium, and Mercury in Rice and Other Foods.

    PubMed

    Jackson, Brian P; Punshon, Tracy

    2015-03-01

    Trace element analysis of foods is of increasing importance because of raised consumer awareness and the need to evaluate and establish regulatory guidelines for toxic trace metals and metalloids. This paper reviews recent advances in the analysis of trace elements in food, including challenges, state-of-the-art methods, and use of spatially resolved techniques for localizing the distribution of arsenic and mercury within rice grains. Total elemental analysis of foods is relatively well-established, but the push for ever lower detection limits requires that methods be robust from potential matrix interferences, which can be particularly severe for food. Inductively coupled plasma mass spectrometry (ICP-MS) is the method of choice, allowing for multi-element and highly sensitive analyses. For arsenic, speciation analysis is necessary because the inorganic forms are more likely to be subject to regulatory limits. Chromatographic techniques coupled to ICP-MS are most often used for arsenic speciation, and a range of methods now exist for a variety of different arsenic species in different food matrices. Speciation and spatial analysis of foods, especially rice, can also be achieved with synchrotron techniques. Sensitive analytical techniques and methodological advances provide robust methods for the assessment of several metals in animal- and plant-based foods, particularly for arsenic, cadmium, and mercury in rice and arsenic speciation in foodstuffs.

  12. A Rare Allele of GS2 Enhances Grain Size and Grain Yield in Rice.

    PubMed

    Hu, Jiang; Wang, Yuexing; Fang, Yunxia; Zeng, Longjun; Xu, Jie; Yu, Haiping; Shi, Zhenyuan; Pan, Jiangjie; Zhang, Dong; Kang, Shujing; Zhu, Li; Dong, Guojun; Guo, Longbiao; Zeng, Dali; Zhang, Guangheng; Xie, Lihong; Xiong, Guosheng; Li, Jiayang; Qian, Qian

    2015-10-05

    Grain size determines grain weight and affects grain quality. Several major quantitative trait loci (QTLs) regulating grain size have been cloned; however, our understanding of the underlying mechanism that regulates the size of rice grains remains fragmentary. Here, we report the cloning and characterization of a dominant QTL, grain size on chromosome 2 (GS2), which encodes Growth-Regulating Factor 4 (OsGRF4), a transcriptional regulator. GS2 localizes to the nucleus and may act as a transcription activator. A rare mutation of GS2 affecting the binding site of a microRNA, OsmiR396c, causes elevated expression of GS2/OsGRF4. The increase in GS2 expression leads to larger cells and increased numbers of cells, which thus enhances grain weight and yield. The introduction of this rare allele of GS2/OsGRF4 into rice cultivars could significantly enhance grain weight and increase grain yield, with possible applications in breeding high-yield rice varieties.

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed

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

    2015-04-01

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

  15. Towards understanding of molecular interactions between rice and the brown planthopper.

    PubMed

    Cheng, Xiaoyan; Zhu, Lili; He, Guangcun

    2013-05-01

    The brown planthopper (BPH) is the most notorious pest of rice (Oryza sativa). Studies of rice-BPH interaction have contributed to development of new rice varieties, offering an effective means for long-lasting control of BPH. Here, we review the status of knowledge of the molecular basis of rice-BPH interaction, from the perspective of immunity. The BPH has complicated feeding behaviors on rice, which are mainly related to host resistance. Now, 24 resistance genes have been detected in rice, indicating gene-for-gene relationships with biotypes of the BPH. However, only one BPH resistance gene (Bph14) was identified and characterized using map-based cloning. Bph14 encodes an immune receptor of NB-LRR family, providing a means for studying the molecular mechanisms of rice resistance to BPH. Plant hormones (e.g. salicylic acid and jasmonate/ethylene), Ca(2+), mitogen-activated protein kinases (MAPKs), and OsRac1 play important roles in the immune response of rice to BPH. Signal transduction leads to modifying expression of defense-related genes and defense mechanisms against BPH, including sieve tube sealing, production of secondary metabolites, and induction of proteinase inhibitor. A model for the molecular interactions between rice and the BPH is proposed, although many details remain to be investigated that are valuable for molecular design of BPH-resistant rice varieties.

  16. Rice chloroplast-localized heat shock protein 70, OsHsp70CP1, is essential for chloroplast development under high-temperature conditions.

    PubMed

    Kim, Sung-Ryul; An, Gynheung

    2013-06-15

    Heat is a primary abiotic stress that reduces crop yields. At the seedling stage, we identified heat-sensitive mutants that carried T-DNA inserted into a heat shock protein 70 gene, OsHsp70CP1. When grown under a constant high temperature (40°C), the seedling leaves developed severe chlorosis whereas plants grown at a constant 27°C showed a normal phenotype. This indicated that OsHsp70CP1 is essential for chloroplast differentiation from the proplastids under high temperatures. Transient expression analyses revealed that OsHsp70CP1 was localized to the stroma. OsHsp70CP1 was dominantly expressed in photosynthetic tissues; transcripts were greatly increased by heat stress. Some transcripts for plastid RNA metabolism were impaired in the mutant while others were not, demonstrating that a subset of nuclear-encoded proteins are substrates of OsHsp70CP1.

  17. Determinants for grading Malaysian rice

    NASA Astrophysics Data System (ADS)

    ChePa, Noraziah; Yusoff, Nooraini; Ahmad, Norhayati

    2016-08-01

    Due to un-uniformity of rice grading practices in Malaysia, zones which actively producing rice in Malaysia are using their own way of grading rice. Rice grading is important in determining rice quality and its subsequent price in the market. It is an important process applied in the rice production industry with the purpose of ensuring that the rice produced for the market meets the quality requirements of consumer. Two important aspects that need to be considered in determining rice grades are grading technique and determinants to be used for grading (usually referred as rice attributes). This article proposes the list of determinants to be used in grading Malaysian rice. Determinants were explored through combination of extensive literature review and series of interview with the domain experts and practitioners. The proposed determinants are believed to be beneficial to BERNAS in improving the current Malaysian rice grading process.

  18. Improvement of single wavelength-based Thai jasmine rice identification with elliptic Fourier descriptor and neural network analysis

    NASA Astrophysics Data System (ADS)

    Suwansukho, Kajpanya; Sumriddetchkajorn, Sarun; Buranasiri, Prathan

    2012-11-01

    Instead of considering only the amount of fluorescent signal spatially distributed on the image of milled rice grains this paper shows how our single-wavelength spectral-imaging-based Thai jasmine (KDML105) rice identification system can be improved by analyzing the shape and size of the image of each milled rice variety especially during the image threshold operation. The image of each milled rice variety is expressed as chain codes and elliptic Fourier coefficients. After that, a feed-forward back-propagation neural network model is applied, resulting in an improved average FAR of 11.0% and FRR of 19.0% in identifying KDML105 milled rice from the unwanted four milled rice varieties.

  19. Improvement in shelf life of rough and brown rice using infrared radiation heating

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The objective of this study was to investigate the effect of IR heating and tempering treatments on storage stability of rough and brown rice. Samples of freshly harvested medium grain rice variety M206 with initial moisture content of 25.03±0.21% (d.b.) were used. They were dried using infrared (IR...

  20. A new micro-chamber method for selecting sheath blight tolerant rice

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Dr. Shannon Pinson’s role as an applied Plant Geneticist is to develop new knowledge and techniques that allow breeders to be more efficient and successful at developing improved rice varieties. While visiting various rice researchers in Bangladesh in 2002, Dr. Pinson gained some knowledge and ideas...

  1. Rice breeding trends over 30 years for predicting response to climate change

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Rice has been produced in the United States since pre-revolutionary days. Currently around 3 million acres are harvested each year with 84% of the acreage occurring in the southern US. Public breeding efforts, which began in the early 1920’s, have produced about 150 rice varieties for production in ...

  2. Relating raw rice color and composition to cooked rice color.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Traditionally, the color of milled rice is economically important. The whiter the rice the more it is preferred by consumers and the more value it has in the market place. Little attention has been given to relating raw rice color to cooked milled rice color and, specifically, to determining the i...

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

    PubMed Central

    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

  4. Alternative uses of rice-straw in California. Final report

    SciTech Connect

    Bainbridge, D.A.

    1997-03-01

    Interconnectedness and complexity are the hallmarks of almost every environmental problem and opportunity including the challenge of rice straw management in California. Although attempts are often made to solve environmental problems by working on single aspects, this rarely works, just as treating symptoms may do little to resolve diseases. The rice straw problem includes the physical system of the atmosphere, air basins, soils, and local and regional watersheds, and reaches the global scale with concern over atmospheric contribution of methane and implications for global warming. It includes the biological system of the rice crop, soil organisms, crop pests, and wildlife (both beneficial and harmful). And finally, it includes the economic and social systems of the rice grower, farm families, farm service industries, rural communities, the regional population, rice consumers around the world, fishermen and women, hunters, manufacturers of harvesting equipment, medical services, and potentially, builders and home buyers in the region.

  5. [Effects of Rice Cultivar and Typical Soil Improvement Measures on the Uptake of Cd in Rice Grains].

    PubMed

    Wang, Mei-e; Peng, Chi; Chen, Wei-ping

    2015-11-01

    Cadmium pollution of rice is a big problem in agricultural food safety. The accident "Cd rice" occurred last year in Youxian County, Hunan Province caused serious social panic. In this study, trials on "Cd rice" controlling techniques specific to the Cd pollution in paddy soil in Youxian were investigated. It was suggested that the average Cd contents in rice grains of the rice variety "Zhu Liang You 06" in Datongqiao and Wangling were 0.167 and 0.127 mg x kg(-1), respectively, which were only equal to 20% of the contents of other varieties. The trials for stabilizing agents revealed that treatments of lime and mineral fertilizer decreased Cd contents in rice grains to 20-30% of the control. Plastic film-mulched treatment decreased the rice grain Cd to 50%. And combined treatment of plastic film-mulched and biochar and silicon foliar-fertilizer decreased 80% of rice Cd content. Single treatments of silicon foliar-fertilizer and combined treatment of silicon foliar-fertilizer and topdressing fertilizer decreased more than 90% of Cd content. Results of BCR revealed that the percentage of cationic exchangeable and/or carbonate associated Cd fraction was more than 55% for most of the soil samples. Lime treatment significantly decreased the percentage of cationic exchangeable and/or carbonate and oxides of Fe and Mn associated Cd and increased the crystalline structure of clay minerals associated Cd. The change rate reached about 20%. Our results suggested concentration of soil Cd and pH were the two significant factors impacting the uptake of Cd by rice grains.

  6. Changes in physical, cooking, textural properties and crystallinity upon iron fortification of red rice (Jyothi).

    PubMed

    Pandey, Shruti; Mr, Asha; A, Jayadep

    2016-02-01

    The present study is an investigation, into one of the varieties of paddy (Jyothi) its fortification with sodium iron EDTA salt, its physical properties, cooking characteristics, color, texture and characterization studies. Fortification was done at two concentrations 1.88 g/kg (T1 corresponding Iron content 0.25 g/Kg) and 3.39 g/kg (T2 corresponding Iron content 0.45 g/Kg). It was found that the iron content increased 2.5 folds after fortification, as compared to control sample. The results revealed that, there was significant difference between the physical properties of rice in the control, fortified brown and milled rice. The cooking parameters for control and fortified brown rice viz. cooking time, volume expansion water uptake were quite close to the control sample. The cooking time for fortified rice was 1-2 min high as compared to control, other parameters remained same. In case of milled rice, the cooking time and volume expansion for control milled rice and fortified was almost same; however the water uptake was higher for fortified milled rice as compared to control milled rice. The texture of fortified brown rice was hard as compared to fortified milled rice, although the taste was found satisfactory. The colour was significantly different in brown and milled rice. X-ray diffraction results revealed the polycrystalline nature of the fortified sample, was somewhat less crystalline as compared to control sample.

  7. Rice (Oryza) hemoglobins

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  8. Making rice even healthier!

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Rice is a naturally healthy food, but what if it could be made even healthier? Would Americans eat more rice if it could be advertised to be a 'New and Improved' source of calcium to promote bone growth, or iron to prevent anemia? Grocery stores are full of foods that are vitamin enhanced to attract...

  9. QTL Analysis for Resistance to Blast Disease in U.S. Weedy Rice.

    PubMed

    Liu, Yan; Qi, Xinshuai; Gealy, Dave R; Olsen, Kenneth M; Caicedo, Ana L; Jia, Yulin

    2015-07-01

    Understanding the genetic architecture of adaptation is of great importance in evolutionary biology. U.S. weedy rice is well adapted to the local conditions in U.S. rice fields. Rice blast disease is one of the most destructive diseases of cultivated rice worldwide. However, information about resistance to blast in weedy rice is limited. Here, we evaluated the disease reactions of 60 U.S. weedy rice accessions with 14 blast races, and investigated the quantitative trait loci (QTL) associated with blast resistance in two major ecotypes of U.S. weedy rice. Our results revealed that U.S. weedy rice exhibited a broad resistance spectrum. Using genotyping by sequencing, we identified 28 resistance QTL in two U.S. weedy rice ecotypes. The resistance QTL with relatively large and small effects suggest that U.S. weedy rice groups have adapted to blast disease using two methods, both major resistance (R) genes and QTL. Three genomic loci shared by some of the resistance QTL indicated that these loci may contribute to no-race-specific resistance in weedy rice. Comparing with known blast disease R genes, we found that the R genes at these resistance QTL are novel, suggesting that U.S. weedy rice is a potential source of novel blast R genes for resistant breeding.

  10. Methane Emissions From Global Paddy Rice Agriculture - a New Estimate Based on DNDC Model Simulations

    NASA Astrophysics Data System (ADS)

    Hagen, S. C.; Li, C.; Salas, W.; Ingraham, P.; Li, J.; Beach, R.; Frolking, S.

    2012-12-01

    Roughly one-quarter of global methane emissions to the atmosphere come from the agricultural sector. Agricultural emissions are dominated by livestock (ruminants) and paddy-rice agriculture. We report on a new estimate of global methane emissions from paddy rice c.2010, based on DNDC model simulations of rice cropping around the world. We first generated a global map of rice cropping at 0.5°-resolution, based on existing global crop maps and various other published data. For each 0.5° grid cell that has rice agriculture, we simulated all rice cropping systems that our mapping indicated to be occurring there - irrigated and/or rainfed; single-rice, double-rice, triple-rice, and/or rice-rotated with other upland crops - under local climate and soil conditions, with assumptions about crop management (e.g., fertilizer type and amount, irrigation, flooding frequency and duration, manure application, tillage, crop residue management). We estimate global paddy rice emissions at 23 Tg CH4/yr from 120 Mha of rice paddies (land area) and 160 Mha of rice cropping (harvested area) for the baseline management scenario. We also report on the spatial distribution of these emissions, and the impacts of various management alternatives (flooding methods, fertilizer types, crop residue incorporation etc.) on yield, soil carbon sequestration and emissions of methane and nitrous oxide. For example, simulations with continuous flooding on all paddies increased simulated global paddy rice emissions to 33 Tg CH4/yr, while simulations where all fertilizer was applied as ammonium sulfate reduced simulated global paddy rice emissions to about 19 Tg CH4/yr. Simulated global paddy rice yield was about 320 Tg C in grain.

  11. Effects of shading on starch pasting characteristics of indica hybrid rice (Oryza sativa L.).

    PubMed

    Wang, Li; Deng, Fei; Ren, Wan-Jun; Yang, Wen-Yu

    2013-01-01

    Rice is an important staple crop throughout the world, but environmental stress like low-light conditions can negatively impact crop yield and quality. Using pot experiments and field experiments, we studied the effects of shading on starch pasting viscosity and starch content with six rice varieties for three years, using the Rapid Visco Analyser to measure starch pasting viscosity. Shading at different growth stages and in different rice varieties all affected the starch pasting characteristics of rice. The effects of shading on starch pasting viscosity at middle and later growth stages were greater than those at earlier stages. Shading enhanced breakdown but reduced hold viscosity and setback at tillering-elongation stage. Most pasting parameters changed significantly with shading after elongation stage. Furthermore, the responses of different varieties to shading differed markedly. The change scope of starch pasting viscosity in Dexiang 4103 was rather small after heading, while that in IIyou 498 and Gangyou 906 was small before heading. We observed clear tendencies in peak viscosity, breakdown, and pasting temperature of the five rice varieties with shading in 2010 and 2011. Correlation analysis indicated that the rice amylose content was negatively correlated with breakdown, but was positively correlated with setback. Based on our results, IIyou 498, Gangyou 906, and Dexiang 4103 had higher shade endurance, making these varieties most suitable for high-quality rice cultivation in low-light regions.

  12. Involvement of ASR genes in aluminium tolerance mechanisms in rice.

    PubMed

    Arenhart, Rafael Augusto; Lima, Julio César de; Pedron, Marcelo; Carvalho, Fabricio E L; Silveira, Joaquim Albenisio Gomes da; Rosa, Silvia Barcelos; Caverzan, Andreia; Andrade, Claudia M B; Schünemann, Mariana; Margis, Rogério; Margis-Pinheiro, Márcia

    2013-01-01

    Among cereal crops, rice is considered the most tolerant to aluminium (Al). However, variability among rice genotypes leads to remarkable differences in the degree of Al tolerance for distinct cultivars. A number of studies have demonstrated that rice plants achieve Al tolerance through an unknown mechanism that is independent of root tip Al exclusion. We have analysed expression changes of the rice ASR gene family as a function of Al treatment. The gene ASR5 was differentially regulated in the Al-tolerant rice ssp. Japonica cv. Nipponbare. However, ASR5 expression did not respond to Al exposure in Indica cv. Taim rice roots, which are highly Al sensitive. Transgenic plants carrying RNAi constructs that targeted the ASR genes were obtained, and increased Al susceptibility was observed in T1 plants. Embryogenic calli of transgenic rice carrying an ASR5-green fluorescent protein fusion revealed that ASR5 was localized in both the nucleus and cytoplasm. Using a proteomic approach to compare non-transformed and ASR-RNAi plants, a total of 41 proteins with contrasting expression patterns were identified. We suggest that the ASR5 protein acts as a transcription factor to regulate the expression of different genes that collectively protect rice cells from Al-induced stress responses.

  13. Proposing nutrients and nutrient levels for rice fortification.

    PubMed

    de Pee, Saskia

    2014-09-01

    Micronutrient deficiencies are often linked to low dietary diversity. Rice fortification could substantially increase micronutrient intake in countries where rice is a staple food. The World Health Organization (WHO) interim consensus statement on maize and wheat flour fortification is based on the premise of the public health importance of specific micronutrient deficiencies and evidence of the benefits of increased micronutrient intake. Since this rationale for maize and wheat flour also applies to rice, it is recommended to fortify rice with iron, folic acid, vitamin B12, vitamin A, and zinc, as well as with thiamin, vitamin B6, and niacin, as polished rice has low levels of these micronutrients. To achieve intake that meets the estimated average requirement of adults, the following levels are recommended where rice consumption is 150-300 g/cap/day (mg/100 g): iron, 7; folic acid, 0.13; vitamin B12, 0.001; vitamin A, 0.15; zinc, 6; thiamin, 0.5; niacin, 7; and vitamin B6, 0.6. These concentrations can be achieved at a 1:100 blending ratio of fortified:unfortified kernels. The costs of rice fortification are largely determined by the manufacturing of the fortified kernels rather than by the number of micronutrients that are added. These are general recommendations that can be adjusted locally, and monitoring and impact evaluation should accompany the introduction of rice fortification.

  14. Human exposure to mercury in a compact fluorescent lamp manufacturing area: By food (rice and fish) consumption and occupational exposure.

    PubMed

    Liang, Peng; Feng, Xinbin; Zhang, Chan; Zhang, Jin; Cao, Yucheng; You, Qiongzhi; Leung, Anna Oi Wah; Wong, Ming-Hung; Wu, Sheng-Chun

    2015-03-01

    To investigate human Hg exposure by food consumption and occupation exposure in a compact fluorescent lamp (CFL) manufacturing area, human hair and rice samples were collected from Gaohong town, Zhejiang Province, China. The mean values of total mercury (THg) and methylmercury (MeHg) concentrations in local cultivated rice samples were significantly higher than in commercial rice samples which indicated that CFL manufacturing activities resulted in Hg accumulation in local rice samples. For all of the study participants, significantly higher THg concentrations in human hair were observed in CFL workers compared with other residents. In comparison, MeHg concentrations in human hair of residents whose diet consisted of local cultivated rice were significantly higher than those who consumed commercial rice. These results demonstrated that CFL manufacturing activities resulted in THg accumulation in the hair of CFL workers. However, MeHg in hair were mainly affected by the sources of rice of the residents.

  15. Allele distributions at hybrid incompatibility loci facilitate the potential for gene flow between cultivated and weedy rice in the US.

    PubMed

    Craig, Stephanie M; Reagon, Michael; Resnick, Lauren E; Caicedo, Ana L

    2014-01-01

    The accumulation of independent mutations over time in two populations often leads to reproductive isolation. Reproductive isolation between diverging populations may be reinforced by barriers that occur either pre- or postzygotically. Hybrid sterility is the most common form of postzygotic isolation in plants. Four postzygotic sterility loci, comprising three hybrid sterility systems (Sa, s5, DPL), have been recently identified in Oryza sativa. These loci explain, in part, the limited hybridization that occurs between the domesticated cultivated rice varieties, O. sativa spp. japonica and O. sativa spp. indica. In the United States, cultivated fields of japonica rice are often invaded by conspecific weeds that have been shown to be of indica origin. Crop-weed hybrids have been identified in crop fields, but at low frequencies. Here we examined the possible role of these hybrid incompatibility loci in the interaction between cultivated and weedy rice. We identified a novel allele at Sa that seemingly prevents loss of fertility in hybrids. Additionally, we found wide-compatibility type alleles at strikingly high frequencies at the Sa and s5 loci in weed groups, and a general lack of incompatible alleles between crops and weeds at the DPL loci. Our results suggest that weedy individuals, particularly those of the SH and BRH groups, should be able to freely hybridize with the local japonica crop, and that prezygotic factors, such as differences in flowering time, have been more important in limiting weed-crop gene flow in the past. As the selective landscape for weedy rice changes due to increased use of herbicide resistant strains of cultivated rice, the genetic barriers that hinder indica-japonica hybridization cannot be counted on to limit the flow of favorable crop genes into weeds.

  16. Thermogravimetric analysis of rice husks in an air atmosphere

    SciTech Connect

    Mansaray, K.G.; Ghaly, A.E.

    1998-08-01

    In rice-producing countries, large amounts of rice husks are generated as waste material for which there is no ready use and in some cases may have a negative value because of the cost of disposal. Most of these countries depend on fossil fuels for their energy uses, and rice husk can be used to supplement such energy sources using thermochemical conversion processes. However, efficient operation of thermochemical conversion systems requires a thorough understanding of the influence of the influence of the composition and thermal properties of rice husks on their behavior during the conversion process. In this study, the thermal behavior of four rice husk varieties (Lemont, ROK 14, CP 4, and Pa Potho) was examined at three heating rates (10, 20, and 50 C/min) in stationary air atmosphere. The thermal degradation rate in active and passive pyrolysis zones, the initial degradation temperature, and the residual weight at 600 C were determined. Increasing the heating rate increased both the thermal degradation rate and the residual weight and decreased the initial degradation temperature. The higher the cellulosic content of the rice husk, the higher the thermal degradation rate and the initial degradation temperature. Also, higher ash content in the rice husk resulted in higher residual weight at 600 C.

  17. RiceATM: a platform for identifying the association between rice agronomic traits and miRNA expression

    PubMed Central

    Liu, Wei-Ting; Yang, Chia-Chun; Chen, Rong-Kuen; Jwo, Woei-Shyuan; Wu, Chih-Wen; Ting, Wen-Yen; Shung, Dah-Pyng; Liu, Chun-Chi; Chen, Jeremy J.W.

    2016-01-01

    MicroRNAs (miRNAs) are known to play critical roles in plant development and stress-response regulation, and they frequently display multi-targeting characteristics. The control of defined rice phenotypes occurs through multiple genes; however, evidence demonstrating the relationship between agronomic traits and miRNA expression profiles is lacking. In this study, we investigated eight yield-related traits in 187 local rice cultivars and profiled the expression levels of 193 miRNAs in these cultivars using microarray analyses. By integrating the miRBase database, the rice annotation project database, and the miRanda and psRNATarget web servers, we constructed a database (RiceATM) that can be employed to investigate the association between rice agronomic traits and miRNA expression. The functions of this platform include phenotype selection, sample grouping, microarray data pretreatment, statistical analysis and target gene predictions. To demonstrate the utility of RiceATM, we used the database to identify four miRNAs associated with the heading date and validated their expression trends in the cultivars with early or late heading date by real-time PCR. RiceATM is a useful tool for researchers seeking to characterize the role of certain miRNAs for a specific phenotype and discover potential biomarkers for breeding or functional studies. Database URL: http://syslab3.nchu.edu.tw/rice/ PMID:28025342

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

    PubMed

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

    2007-11-01

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

  19. Effects of landscape features on waterbird use of rice fields

    USGS Publications Warehouse

    King, S.; Elphick, C.S.; Guadagnin, D.; Taft, O.; Amano, T.

    2010-01-01

    Literature is reviewed to determine the effects of landscape features on waterbird use of fields in regions where rice (Oryza sativa) is grown. Rice-growing landscapes often consist of diverse land uses and land cover, including rice fields, irrigation ditches, other agricultural fields, grasslands, forests and natural wetlands. Numerous studies indicate that local management practices, such as water depth and timing of flooding and drawdown, can strongly influence waterbird use of a given rice field. However, the effects of size and distribution of rice fields and associated habitats at a landscape scale have received less attention. Even fewer studies have focused on local and landscape effects simultaneously. Habitat connectivity, area of rice, distance to natural wetlands, and presence and distance to unsuitable habitat can be important parameters influencing bird use of rice fields. However, responses to a given landscape vary with landscape structure, scale of analysis, among taxa and within taxa among seasons. A lack of multi-scale studies, particularly those extending beyond simple presence and abundance of a given species, and a lack of direct tests comparing the relative importance of landscape features with in-field management activities limits understanding of the importance of landscape in these systems and hampers waterbird conservation and management.

  20. Selenium Characterization in the Global Rice Supply Chain

    SciTech Connect

    Williams, Paul N.; Lombi, Enzo; Sun, Guo-Xin; Scheckel, Kirk; Zhu, Yong-Guan; Feng, Xinbin; Zhu, Jianming; Carey, Anne-Marie; Adomako, Eureka; Lawgali, Youseff; Deacon, Claire; Meharg, Andrew A.

    2009-08-13

    For up to 1 billion people worldwide, insufficient dietary intake of selenium (Se) is a serious health constraint. Cereals are the dominant Se source for those on low protein diets, as typified by the global malnourished population. With crop Se content constrained largely by underlying geology, regional soil Se variations are often mirrored by their locally grown staples. Despite this, the Se concentrations of much of the world's rice, the mainstay of so many, is poorly characterized, for both total Se content and Se speciation. In this study, 1092 samples of market sourced polished rice were obtained. The sampled rice encompassed dominant rice producing and exporting countries. Rice from the U.S. and India were found to be the most enriched, while mean average levels were lowest in Egyptian rice: {approx}32-fold less than their North American equivalents. By weighting country averages by contribution to either global production or export, modeled baseline values for both were produced. Based on a daily rice consumption of 300 g day{sup -1}, around 75% of the grains from the production and export pools would fail to provide 70% of daily recommended Se intakes. Furthermore, Se localization and speciation characterization using X-ray fluorescence ({mu}-XRF) and X-ray absorption near edge structure ({mu}-XANES) techniques were investigated in a Se-rich sample. The results revealed that the large majority of Se in the endosperm was present in organic forms.

  1. [Impacts of climate warming on growth period and yield of rice in Northeast China during recent two decades].

    PubMed

    Hou, Wen-jia; Geng, Ting; Chen, Qun; Chen, Chang-qing

    2015-01-01

    By using rice growth period, yield and climate observation data during the recent two decades, the impact of climate warming on rice in Northeast China was investigated by mathematical statistics methods. The results indicated that in the three provinces of Northeast China, the average, maximum and minimum temperatures in rice growing season were on the. rise, and the rainfall presented a downward trend during 1989-2009. Compared to 1990s, the rice whole growth periods of Heilongjiang, Jilin and Liaoning provinces in 2000s were prolonged 14 d, 4.5 d and 5.1 d, respectively. The increase of temperature in May, June and September could extend the rice growth period, while that in July would shorten the growth duration. The rice growth duration of registered varieties and experiment sites had a similar increasing trend in Northeast China except for the Heilongjiang Province, and the extension of registered varieties growth period was the main factor causing the prolonged growth period of rice at experiment sites. The change in daily average, minimum and maximum temperatures all could affect the rice yield in Northeast China. The increasing temperature significantly increased the rice yield in Heilongjiang Province, especially in the west region of Sanjiang Plain. Except for the south of Liaoning Province, rice yields in other regions of Northeast China were promoted by increasing temperature. Proper measures for breeding, cultivation and farming, could be adopted to fully improve the adaptation of rice to climate warming in Northeast China.

  2. [Temperature differences of air-rice plant under different irrigated water depths at spiking stage].

    PubMed

    Zhang, Bin; Zheng, Jian-chu; Huang, Shan; Tian, Yun-lu; Peng, Lan; Bian, Xin-min; Zhang, Wei-jian

    2008-01-01

    With rice cultivars Yangdao 6, Yangjing 9538 and Wuxiangjing 14 as test materials, field experiment was conducted to study the effects of 3 irrigated water depths (0 cm, 2-4 cm, and > 10 cm) on the temperature of different parts of rice plant at spiking stage. The results showed that from 10:30 to 15:00 on sunny days, irrigated water depth on paddy field had significant effects on the temperature of field surface, middle part of rice plant, and rice spike. The higher the water depth on field surface, the lower the temperature of rice plant and rice spike. At the water level > 10 cm, the average temperature differences between air and the rice spike, middle part of rice plant and field surface of these three cultivars were 1.37, 2.98 and 4.12 degrees C higher than those at the water depth of 0 cm, and 0.67, 1.59 and 2.17 degrees C higher than those at the water depth of 2-4 cm, respectively. In addition, the temperature differences were 0.71, 1.39 and 1.95 degrees C higher at the water depth of 2-4 cm than those at the water depth of 0 cm, respectively. Obvious temperature differences of air-rice plant were also observed among the three rice varieties under different irrigated water depths. The analysis of the characteristics of temperature transfer among field surface, middle part of plant and rice spike indicated that the temperature transfer patterns under all test water management regimes accorded with the principles of energy transfer, suggesting that keeping proper water depth on the field surface at rice spiking stage contributed great to the decrease of rice spike temperature and the alleviation of rice heat injury.

  3. Title: Rice Crop Monitoring by Fusing Microwave and Optical Satellite Data

    NASA Astrophysics Data System (ADS)

    Oyoshi, K.; Takeuchi, W.; LE Toan, T.; Sobue, S.

    2015-12-01

    Rapid population and economic growth, and the increase in extreme weather events, are destabilizing global food security. In Asia, rice is a staple cereal crop, and the continent accounts for about 90% of global rice production and consumption. The Group on Earth Observations (GEO) Global Agricultural Monitoring (GLAM) was launched in 2011 to utilize remote sensing tools to enhance crop production projections in order to promote food security and foster sustainable economic growth. Asia---‒Rice Crop Estimation & Monitoring (Asia---‒RiCE) is a component of GEOGLAM, and aims to use remote sensing tools to develop rice---‒related information such as maps of paddy fields, rice growing conditions, yield, and production. However, in some regions in Southeast Asia, rice is planted and harvested more than twice a year, and the crop calendar is quite complicated. In addition, rice is mainly cultivated in the rainy season, and the high density of cloud cover during that season limits the observations that can be made from space using only optical sensors. In contrast, Synthetic Aperture Radar (SAR) is a robust tool because it penetrates cloud cover; however, the revisit frequency of a single SAR satellite is limited, making it difficult to capture the complicated rice crop calendar in Asia. In this research, time---‒series SAR data were fused with optical data to monitor rice crops in Southeast Asia with complicated crop calendars. In addition, a microwave radiometer that also penetrates clouds and has a high revisit frequency but a coarse spatial resolution (greater than several kilometers), was used. The integrated use of a large variety of satellite data enables us to periodically monitor surface conditions such as water inundation, transplanting, and rice crop growth and harvesting, which in turn enables us to examine rice planted areas, rice crop calendars, and rice growing conditions in order to estimate rice production.

  4. Advances to improve the eating and cooking qualities of rice by marker-assisted breeding.

    PubMed

    Phing Lau, Wendy Chui; Latif, Mohammad Abdul; Y Rafii, Mohd; Ismail, Mohd Razi; Puteh, Adam

    2016-01-01

    The eating and cooking qualities of rice are heavily emphasized in breeding programs because they determine market values and they are the appealing attributes sought by consumers. Conventional breeding has developed traditional varieties with improved eating and cooking qualities. Recently, intensive genetic studies have pinpointed the genes that control eating and cooking quality traits. Advances in genetic studies have developed molecular techniques, thereby allowing marker-assisted breeding (MAB) for improved eating and cooking qualities in rice. MAB has gained the attention of rice breeders for the advantages it can offer that conventional breeding cannot. There have been successful cases of using MAB to improve the eating and cooking qualities in rice over the years. Nevertheless, MAB should be applied cautiously given the intensive effort needed for genotyping. Perspectives from conventional breeding to marker-assisted breeding will be discussed in this review for the advancement of the eating and cooking qualities of fragrance, amylose content (AC), gel consistency (GC) and gelatinization temperature (GT) in rice. These four parameters are associated with eating and cooking qualities in rice. The genetic basis of these four parameters is also included in this review. MAB is another approach to rice variety improvement and development in addition to being an alternative to genetic engineering. The MAB approach shortens the varietal development time, and is therefore able to deliver improved rice varieties to farmers within a shorter period of time.

  5. Evaluation of anaerobic biodegradability of forage rice straw fertilized with livestock waste.

    PubMed

    Zhou, Sheng; Iino, Hiroshi; Nakashimada, Yutaka; Hosomi, Masaaki

    2012-01-01

    Fertilizing livestock waste for forage rice production can remove nitrogen and reduce the need for chemical fertilizers. Furthermore, rice straw can be used for biogas production. Here, the growth characteristics of different forage rice varieties in Japanese paddy fields fertilized with liquid cattle waste were investigated. Six experimental plots were established in a paddy field planted with three varieties of forage rice developed for livestock feed. Methane production potential assays were then conducted to investigate the anaerobic digestion characteristics of the stems and leaves of these three varieties. The total methane production potential of the Leafstar variety was higher than that of other varieties, while its lag phase was significantly shorter. Co-digestion of ethanol fermentation residue with Leafstar straw revealed that the NH(4)(+)-N concentration decreased as the C/N ratio increased. Additionally, the methane production potential of the mixed substrate was higher than that of ethanol fermentation residue or forage rice straw applied alone. Hence, Leafstar forage rice is a promising variety for establishment of agricultural resource recycling systems in which higher straw biomass can be achieved by applying liquid cattle waste and more biogas can be produced due to the potential for increased methane production.

  6. Improving the nutritional value of Golden Rice through increased pro-vitamin A content.

    PubMed

    Paine, Jacqueline A; Shipton, Catherine A; Chaggar, Sunandha; Howells, Rhian M; Kennedy, Mike J; Vernon, Gareth; Wright, Susan Y; Hinchliffe, Edward; Adams, Jessica L; Silverstone, Aron L; Drake, Rachel

    2005-04-01

    "Golden Rice" is a variety of rice engineered to produce beta-carotene (pro-vitamin A) to help combat vitamin A deficiency, and it has been predicted that its contribution to alleviating vitamin A deficiency would be substantially improved through even higher beta-carotene content. We hypothesized that the daffodil gene encoding phytoene synthase (psy), one of the two genes used to develop Golden Rice, was the limiting step in beta-carotene accumulation. Through systematic testing of other plant psys, we identified a psy from maize that substantially increased carotenoid accumulation in a model plant system. We went on to develop "Golden Rice 2" introducing this psy in combination with the Erwinia uredovora carotene desaturase (crtI) used to generate the original Golden Rice. We observed an increase in total carotenoids of up to 23-fold (maximum 37 microg/g) compared to the original Golden Rice and a preferential accumulation of beta-carotene.

  7. Genotype diversity in structure of amylopectin of waxy rice and its influence on gelatinization properties.

    PubMed

    Lin, Jheng-Hua; Singh, Harinder; Ciao, Jhih-Ying; Kao, Wen-Tzu; Huang, Wei-Hsiang; Chang, Yung-Ho

    2013-02-15

    A set of 13 waxy rice genotypes prepared by chemically-induced mutation of non-waxy rice variety TNG67 and 7 waxy rice varieties widely planted in Taiwan were screened for various structural and gelatinization properties of starches. Wide variation on physicochemical properties and molecular structure of amylopectin for the 20 waxy rice starches were obtained and relationship between gelatinization properties and molecular structure of starch were discussed. More attributes on swelling and gelatinization thermal properties, comparing to pasting attributes, showed significant correlation with molecular structure parameters. The swelling and gelatinization thermal properties of waxy rice starch did not show significant correlation with molecular size of amylopectin, while significant correlations were found between the swelling or gelatinization thermal properties and chain length of amylopectin. Results suggest that the swelling and pasting of waxy starch is essentially dominated by granule architecture and is dependent on the interactions among amylopectin chains.

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

    PubMed

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

    2015-08-01

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

  9. New Developments in Forage Varieties

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Forage crops harvested for hay or haylage or grazed support dairy, beef, sheep and horse production. Additional livestock production from reduced forage acreage supports the need for forage variety improvement. The Consortium for Alfalfa Improvement is a partnership model of government, private no...

  10. Brunei English: A Developing Variety

    ERIC Educational Resources Information Center

    O'Hara-Davies, Breda

    2010-01-01

    A considerable amount of time has elapsed since the existence of a distinct variety of English, Brunei English (BNE), was mooted in the early 1990s. A subsequent study conducted by Svalberg in 1998 suggested that BNE was then in its infancy and that its speakers were largely unaware of the differences between it and Standard British English (STE).…

  11. Cross Cultural Varieties of Politeness.

    ERIC Educational Resources Information Center

    Hondo, Junko; Goodman, Bridget

    2001-01-01

    The treatment of politeness features is particularly revealing of the complex dynamics that language teachers face given the cultural variety present in schools and colleges. Along with its positive contributions to the learning environment, the growing student diversity poses a significant challenge for both students and educators. This paper…

  12. Sugarcane Variety Census: Florida 2010

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The Florida sugarcane industry produces about 25% of all sugar produced in the U.S. Varieties originate from two sources, a private breeding and selection program of the United States Sugar Corporation in Clewiston, Florida and a public program at Canal Point, Florida supported by the USDA-Agricultu...

  13. Sugarcane Variety Census: Florida 2008

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The Florida sugarcane industry produces about 25% of all sugar produced in the U.S. Varieties originate from two sources, a private breeding and selection program of the United States Sugar Corporation in Clewiston, Florida and a public program at Canal Point, Florida supported by the USDA-Agricultu...

  14. Sugarcane Variety Census: Florida 2007

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The Florida sugarcane industry produces about 25% of all sugar produced in the U.S. Varieties originate from two sources, a private breeding and selection program of the United States Sugar Corporation in Clewiston, Florida and a public program at Canal Point, Florida supported by the USDA-Agricultu...

  15. Chapter 3: Seed and Varieties

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Seed is one of the most important factors in sugarbeet production. Seed selection is one of the most important decisions a grower can make. Without a uniform plant population of a sugarbeet variety adapted to the growing region, the producer will have difficulty achieving economical crop production....

  16. Image recognition of clipped stigma traces in rice seeds

    NASA Astrophysics Data System (ADS)

    Cheng, F.; Ying, YB

    2005-11-01

    The objective of this research is to develop algorithm to recognize clipped stigma traces in rice seeds using image processing. At first, the micro-configuration of clipped stigma traces was observed with electronic scanning microscope. Then images of rice seeds were acquired with a color machine vision system. A digital image-processing algorithm based on morphological operations and Hough transform was developed to inspect the occurrence of clipped stigma traces. Five varieties of Jinyou402, Shanyou10, Zhongyou207, Jiayou and you3207 were evaluated. The algorithm was implemented with all image sets using a Matlab 6.5 procedure. The results showed that the algorithm achieved an average accuracy of 96%. The algorithm was proved to be insensitive to the different rice seed varieties.

  17. Transcriptional and Post-transcriptional Mechanisms Limit Heading Date 1 (Hd1) Function to Adapt Rice to High Latitudes

    PubMed Central

    Landini, Martina; Brambilla, Vittoria; Gómez-Ariza, Jorge; Takagi, Hiroki; Terauchi, Ryohei; Mantovani, Roberto

    2017-01-01

    Rice flowering is controlled by changes in the photoperiod that promote the transition to the reproductive phase as days become shorter. Natural genetic variation for flowering time has been largely documented and has been instrumental to define the genetics of the photoperiodic pathway, as well as providing valuable material for artificial selection of varieties better adapted to local environments. We mined genetic variation in a collection of rice varieties highly adapted to European regions and isolated distinct variants of the long day repressor HEADING DATE 1 (Hd1) that perturb its expression or protein function. Specific variants allowed us to define novel features of the photoperiodic flowering pathway. We demonstrate that a histone fold domain scaffold formed by GRAIN YIELD, PLANT HEIGHT AND HEADING DATE 8 (Ghd8) and several NF-YC subunits can accommodate distinct proteins, including Hd1 and PSEUDO RESPONSE REGULATOR 37 (PRR37), and that the resulting OsNF-Y complex containing Hd1 can bind a specific sequence in the promoter of HEADING DATE 3A (Hd3a). Artificial selection has locally favored an Hd1 variant unable to assemble in such heterotrimeric complex. The causal polymorphism was defined as a single conserved lysine in the CCT domain of the Hd1 protein. Our results indicate how genetic variation can be stratified and explored at multiple levels, and how its description can contribute to the molecular understanding of basic developmental processes. PMID:28068345

  18. PRIN: a predicted rice interactome network

    PubMed Central

    2011-01-01

    Background Protein-protein interactions play a fundamental role in elucidating the molecular mechanisms of biomolecular function, signal transductions and metabolic pathways of living organisms. Although high-throughput technologies such as yeast two-hybrid system and affinity purification followed by mass spectrometry are widely used in model organisms, the progress of protein-protein interactions detection in plants is rather slow. With this motivation, our work presents a computational approach to predict protein-protein interactions in Oryza sativa. Results To better understand the interactions of proteins in Oryza sativa, we have developed PRIN, a Predicted Rice Interactome Network. Protein-protein interaction data of PRIN are based on the interologs of six model organisms where large-scale protein-protein interaction experiments have been applied: yeast (Saccharomyces cerevisiae), worm (Caenorhabditis elegans), fruit fly (Drosophila melanogaster), human (Homo sapiens), Escherichia coli K12 and Arabidopsis thaliana. With certain quality controls, altogether we obtained 76,585 non-redundant rice protein interaction pairs among 5,049 rice proteins. Further analysis showed that the topology properties of predicted rice protein interaction network are more similar to yeast than to the other 5 organisms. This may not be surprising as the interologs based on yeast contribute nearly 74% of total interactions. In addition, GO annotation, subcellular localization information and gene expression data are also mapped to our network for validation. Finally, a user-friendly web interface was developed to offer convenient database search and network visualization. Conclusions PRIN is the first well annotated protein interaction database for the important model plant Oryza sativa. It has greatly extended the current available protein-protein interaction data of rice with a computational approach, which will certainly provide further insights into rice functional genomics and

  19. Arsenic speciation in Australian-grown and imported rice on sale in Australia: implications for human health risk.

    PubMed

    Rahman, M Azizur; Rahman, Mohammad Mahmudur; Reichman, Suzie M; Lim, Richard P; Naidu, Ravi

    2014-06-25

    Rice is an important route of arsenic (As) exposure to humans, especially populations with rice-based diets. Human health risk of As varies greatly with rice variety and country of origin. The purpose of the present study was to determine total and speciated As in Australian-grown and imported rice on sale in Australia to assess their health risk to consumers. The total As (tAs) concentrations in Australian-grown organic brown, medium grain brown, and organic white rice were 438±23, 287±03, and 283±18 μg kg(-1) dry weight (d wt), respectively. In Bangladeshi, Indian, Pakistani, and Thai rice imported and on sale in Australia, tAs concentrations were 56±05, 92±10, 82±06 and 172±24 μg kg(-1), respectively. Asian rice contained mainly inorganic As (iAs; 86-99%), whereas 18-26% of the tAs in Australian-grown rice was dimethylarsinic acid (DMA). Relatively higher concentrations of tAs in Australian-grown rice than that in imported rice of Asian origin suggest that Australian-grown rice may be a health risk for the consumers. It was estimated that Australian-grown organic brown rice can contribute up to 98% of the FAO/WHO recommended maximum tolerable daily intake limit of iAs (2.1 μg kg(-1) body wt day(-1)) for Asian immigrants. However, other Australian consumers including European immigrants are unlikely to be at risk to As from rice diets due to their lower rice consumption rates than that of Asian immigrants. The risk assessment showed that imported rice on sale in Australia was likely to pose a lower health risk to consumers than Australian-grown rice.

  20. ON THE RELATION BETWEEN THE KINDS OF WINTER CROPS AND THE OCCURRENCE OF THE BACTERIAL LEAF BLIGHT OF RICE PLANT

    DTIC Science & Technology

    The present report, as a part of the research on the ecology of rice leaf blight , is the result of an investigation to determine whether there was a...difference in the occurrence of rice leaf blight on the post-winter crop-fields according to the variety of winter crops. In order to make comparisons...outbreak of rice leaf blight , cultivation procedures, flooding, wind and drainage systems, the winter crops were different from each other, two adjoining

  1. Genetic diversity for mycorrhizal symbiosis and phosphate transporters in rice.

    PubMed

    Jeong, Kwanho; Mattes, Nicolas; Catausan, Sheryl; Chin, Joong Hyoun; Paszkowski, Uta; Heuer, Sigrid

    2015-11-01

    Phosphorus (P) is a major plant nutrient and developing crops with higher P-use efficiency is an important breeding goal. In this context we have conducted a comparative study of irrigated and rainfed rice varieties to assess genotypic differences in colonization with arbuscular mycorrhizal (AM) fungi and expression of different P transporter genes. Plants were grown in three different soil samples from a rice farm in the Philippines. The data show that AM symbiosis in all varieties was established after 4 weeks of growth under aerobic conditions and that, in soil derived from a rice paddy, natural AM populations recovered within 6 weeks. The analysis of AM marker genes (AM1, AM3, AM14) and P transporter genes for the direct Pi uptake (PT2, PT6) and AM-mediated pathway (PT11, PT13) were largely in agreement with the observed root AM colonization providing a useful tool for diversity studies. Interestingly, delayed AM colonization was observed in the aus-type rice varieties which might be due to their different root structure and might confer an advantage for weed competition in the field. The data further showed that P-starvation induced root growth and expression of the high-affinity P transporter PT6 was highest in the irrigated variety IR66 which also maintained grain yield under P-deficient field conditions.

  2. Glycaemic and insulin responses, glycaemic index and insulinaemic index values of rice between three Asian ethnic groups.

    PubMed

    Tan, V M H; Wu, T; Henry, C J; Lee, Y S

    2015-04-28

    Asians exhibit larger glycaemic response (GR) and insulin response (IR) than Caucasians, predisposing to an increased risk of type 2 diabetes mellitus (T2DM). We aimed to determine the GR and IR as well as the glycaemic index (GI) and insulinaemic index (II) of two rice varieties among three ethnic groups in Singapore. A total of seventy-five healthy males (twenty-five Chinese, twenty-five Malay and twenty-five Asian-Indians) were served the available equivalent carbohydrate amounts (50 g) of test foods (Jasmine rice and Basmati rice) and a reference food (glucose) on separate occasions. Postprandial blood glucose and plasma insulin concentrations were measured at fasting ( -5 and 0 min) and at 15, 30, 45, 60, 90 and 120 min after food consumption. Using the trapezoidal rule, GR, IR, GI and II values were determined. The GR did not differ between ethnic groups for Jasmine rice and Basmati rice. The IR was consistently higher for Jasmine rice (P=0·002) and Basmati rice (P=0·002) among Asian-Indians, probably due to compensatory hyperinsulinaemia to maintain normoglycaemia. The GI and II of both rice varieties did not differ significantly between ethnicities. The overall mean GI for Jasmine rice and Basmati rice were 91 (sd 21) and 59 (sd 15), respectively. The overall mean II for Jasmine rice was 76 (sd 26) and for Basmati rice was 57 (sd 24). We conclude that the GI values presented for Jasmine rice and Basmati rice were applicable to all three ethnic groups in Singapore. Future studies should include deriving the II for greater clinical utility in the prevention and management of T2DM.

  3. Cross-fertilization for enhancing tocotrienol biosynthesis in rice plants and QTL analysis of their F2 progenies.

    PubMed

    Sookwong, Phumon; Murata, Kazumasa; Nakagawa, Kiyotaka; Shibata, Akira; Kimura, Toshiyuki; Yamaguchi, Masayuki; Kojima, Yoichiro; Miyazawa, Teruo

    2009-06-10

    As rice bran tocotrienol (T3) has been known to have a wide range of physiological functions (e.g., antiangiogenesis), we aimed at developing a T3-rich rice variety for nutraceutical purposes. T3 content in more than 250 kinds of rice bran samples were investigated, and Milyang23 was found as the best variety rich in T3. The variety was therefore chosen for cross-fertilization with Koshihikari. Among obtained F(2) progenies, some of them became improved in T3 content (up to 2-fold of reference Koshihikari). QTL analysis of the F(2) progenies revealed five putative loci corresponding to T3 biosynthesis, in which the main loci were located near a marker RM3827 on chromosome 6. The results show that cross-breeding is effective in improving rice bran T3 and provides more genetic understanding on T3 biosynthesis in rice plants.

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

    PubMed

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

    2015-02-01

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

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  6. Micronutrient-Fortified Rice Can Increase Hookworm Infection Risk: A Cluster Randomized Trial

    PubMed Central

    de Gier, Brechje; Campos Ponce, Maiza; Perignon, Marlene; Fiorentino, Marion; Khov, Kuong; Chamnan, Chhoun; de Boer, Michiel R.; Parker, Megan E.; Burja, Kurt; Dijkhuizen, Marjoleine A.; Berger, Jacques; Polman, Katja; Wieringa, Frank T.

    2016-01-01

    Background Fortification of staple foods is considered an effective and safe strategy to combat micronutrient deficiencies, thereby improving health. While improving micronutrient status might be expected to have positive effects on immunity, some studies have reported increases in infections 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 n = 506). Intestinal parasite infection was measured in fecal samples by Kato-Katz method at baseline and after three and seven months. In a subgroup (N = 330), fecal calprotectin was measured by ELISA as a marker for intestinal inflammation. Results Baseline prevalence of hookworm infection was 18.6%, 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 baseline prevalence was high (>15%), and only by UltraRice_original in schools with low baseline prevalence. Neither hookworm infection nor fortified rice was related to fecal calprotectin. Conclusions Consumption of rice fortified with micronutrients can increase hookworm prevalence, especially in environments with high infection pressure. When considering fortification of staple foods, a careful risk-benefit analysis is warranted, taking into account severity of

  7. Effects of climate change on suitable rice cropping areas, cropping systems and crop water requirements in southern China

    SciTech Connect

    Ye, Qing; Yang, Xiaoguang; Dai, Shuwei; Chen, Guangsheng; Li, Yong; Zhang, Caixia

    2015-06-05

    Here, we discuss that rice is one of the main crops grown in southern China. Global climate change has significantly altered the local water availability and temperature regime for rice production. In this study, we explored the influence of climate change on suitable rice cropping areas, rice cropping systems and crop water requirements (CWRs) during the growing season for historical (from 1951 to 2010) and future (from 2011 to 2100) time periods. The results indicated that the land areas suitable for rice cropping systems shifted northward and westward from 1951 to 2100 but with different amplitudes.

  8. Functional analysis of rice NPR1-like genes reveals that OsNPR1/NH1 is the rice orthologue conferring disease resistance with enhanced herbivore susceptibility.

    PubMed

    Yuan, Yuexing; Zhong, Sihui; Li, Qun; Zhu, Zengrong; Lou, Yonggen; Wang, Linyou; Wang, Jianjun; Wang, Muyang; Li, Qiaoli; Yang, Donglei; He, Zuhua

    2007-03-01

    The key regulator of salicylic acid (SA)-mediated resistance, NPR1, is functionally conserved in diverse plant species, including rice (Oryza sativa L.). Investigation in depth is needed to provide an understanding of NPR1-mediated resistance and a practical strategy for the improvement of disease resistance in the model crop rice. The rice genome contains five NPR1-like genes. In our study, three rice homologous genes, OsNPR1/NH1, OsNPR2/NH2 and OsNPR3, were found to be induced by rice bacterial blight Xanthomonas oryzae pv. oryzae and rice blast Magnaporthe grisea, and the defence molecules benzothiadiazole, methyl jasmonate and ethylene. We confirmed that OsNPR1 is the rice orthologue by complementing the Arabidopsis npr1 mutant. Over-expression of OsNPR1 conferred disease resistance to bacterial blight, but also enhanced herbivore susceptibility in transgenic plants. The OsNPR1-green fluorescent protein (GFP) fusion protein was localized in the cytoplasm and moved into the nucleus after redox change. Mutations in its conserved cysteine residues led to the constitutive localization of OsNPR1(2CA)-GFP in the nucleus and also abolished herbivore hypersensitivity in transgenic rice. Different subcellular localizations of OsNPR1 antagonistically regulated SA- and jasmonic acid (JA)-responsive genes, but not SA and JA levels, indicating that OsNPR1 might mediate antagonistic cross-talk between the SA- and JA-dependent pathways in rice. This study demonstrates that rice has evolved an SA-mediated systemic acquired resistance similar to that in Arabidopsis, and also provides a practical approach for the improvement of disease resistance without the penalty of decreased herbivore resistance in rice.

  9. Portable x-ray fluorescence for assessing trace elements in rice and rice products: Comparison with inductively coupled plasma-mass spectrometry.

    PubMed

    Fleming, David E B; Foran, Kelly A; Kim, Jong Sung; Guernsey, Judy R

    2015-10-01

    Portable x-ray fluorescence (XRF) was investigated as a means of assessing trace elements in rice and rice products. Using five measurement trials of 180 s real time, portable XRF was first used to detect arsenic (As), manganese (Mn), iron (Fe), nickel (Ni), copper (Cu), and zinc (Zn) in a variety of rice samples. The same samples were then microwave-digested and used to determine elemental concentrations using inductively coupled plasma-mass spectrometry (ICP-MS). The concentrations of As, Mn, Fe, Cu, and Zn determined by ICP-MS were found to be consistent with other recent studies involving various types of rice and rice products. When assessing for As, Mn, Fe, Cu, and Zn, comparison of results between XRF amplitude and ICP-MS concentration (wet weight) demonstrated a linear relationship with a significant correlation. A significant correlation between XRF amplitude and ICP-MS concentration was not found when assessing for Ni.

  10. Shaping a better rice plant.

    PubMed

    Springer, Nathan

    2010-06-01

    Two studies describe how regulatory variation at the rice gene OsSPL14 can lead to altered plant morphology and improve grain yield. These studies support the possibility of improving rice yield through changing plant architecture.

  11. Allele mining and enhanced genetic recombination for rice breeding.

    PubMed

    Leung, Hei; Raghavan, Chitra; Zhou, Bo; Oliva, Ricardo; Choi, Il Ryong; Lacorte, Vanica; Jubay, Mona Liza; Cruz, Casiana Vera; Gregorio, Glenn; Singh, Rakesh Kumar; Ulat, Victor Jun; Borja, Frances Nikki; Mauleon, Ramil; Alexandrov, Nickolai N; McNally, Kenneth L; Sackville Hamilton, Ruaraidh

    2015-12-01

    Traditional rice varieties harbour a large store of genetic diversity with potential to accelerate rice improvement. For a long time, this diversity maintained in the International Rice Genebank has not been fully used because of a lack of genome information. The publication of the first reference genome of Nipponbare by the International Rice Genome Sequencing Project (IRGSP) marked the beginning of a systematic exploration and use of rice diversity for genetic research and breeding. Since then, the Nipponbare genome has served as the reference for the assembly of many additional genomes. The recently completed 3000 Rice Genomes Project together with the public database (SNP-Seek) provides a new genomic and data resource that enables the identification of useful accessions for breeding. Using disease resistance traits as case studies, we demonstrated the power of allele mining in the 3,000 genomes for extracting accessions from the GeneBank for targeted phenotyping. Although potentially useful landraces can now be identified, their use in breeding is often hindered by unfavourable linkages. Efficient breeding designs are much needed to transfer the useful diversity to breeding. Multi-parent Advanced Generation InterCross (MAGIC) is a breeding design to produce highly recombined populations. The MAGIC approach can be used to generate pre-breeding populations with increased genotypic diversity and reduced linkage drag. Allele mining combined with a multi-parent breeding design can help convert useful diversity into breeding-ready genetic resources.

  12. Improved antioxidant activity of BKOS Thai jasmine rice.

    PubMed

    Semsang, N; Kawaree, R; Cutler, R W; Chundet, R; Yu, L D; Anuntalabhochai, S

    2012-01-01

    Thai jasmine rice (Oryza sativa L. cv. KDML105) is highly valued due to its subtle aroma, robust seed characteristics and high nutritional quality. Low-energy ion-beam bombardment was chosen to improve the quality of jasmine rice by mutation induction. One mutated variety, named BKOS, was found to exhibit a deep purple colour due to an increased accumulation of anthocyanin. The total phenolic content and antioxidant activities of cooked and uncooked rice extracts were compared with KDML105, BKOS and other rice mutants created by a low-energy ion beam. The BKOS extracts showed the highest total phenol content (0.140 and 0.096 mg of gallic acid equivalent (GAE) g(-1) dry extract from uncooked and cooked rice, respectively). The BKOS extracts also had improved antioxidant activities, determined using three standard methods: 2,2'-diphenyl-1-picrylhdrazyl (DPPH) free radical scavenging, ABTS radical cation (ABTS•(+)) decolourisation and ferric-reducing antioxidant power assays. BKOS extracts showed 2-2.5-fold increased levels for each method. Interestingly, there was no significant difference between the antioxidant activities of the cooked and uncooked BKOS rice extracts. The increased quantity of antioxidants in this anthocyanin-based natural product could allow antioxidants to be consumed by a wider population than what is currently possible.

  13. Dark septate endophyte decreases stress on rice plants.

    PubMed

    Santos, Silvana Gomes Dos; Silva, Paula Renata Alves da; Garcia, Andres Calderin; Zilli, Jerri Édson; Berbara, Ricardo Luis Louro

    Abiotic stress is one of the major limiting factors for plant development and productivity, which makes it important to identify microorganisms capable of increasing plant tolerance to stress. Dark septate endophytes can be symbionts of plants. In the present study, we evaluated the ability of dark septate endophytes isolates to reduce the effects of water stress in the rice varieties Nipponbare and Piauí. The experiments were performed under gnotobiotic conditions, and the water stress was induced with PEG. Four dark septate endophytes were isolated from the roots of wild rice (Oryza glumaepatula) collected from the Brazilian Amazon. Plant height as well as shoot and root fresh and dry matter were measured. Leaf protein concentrations and antioxidant enzyme activity were also estimated. The dark septate endophytes were grown in vitro in Petri dishes containing culture medium; they exhibited different levels of tolerance to salinity and water stress. The two rice varieties tested responded differently to inoculation with dark septate endophytes. Endophytes promoted rice plant growth both in the presence and in the absence of a water deficit. Decreased oxidative stress in plants in response to inoculation was observed in nearly all inoculated treatments, as indicated by the decrease in antioxidant enzyme activity. Dark septate endophytes fungi were shown to increase the tolerance of rice plants to stress caused by water deficiency.

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

    PubMed

    Swamy, B P Mallikarjuna; Kumar, Arvind

    2013-12-01

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

  15. [Photosynthetic and water physiological characteristics of weedy rice in northern China].

    PubMed

    Gao, Qi; Ma, Dian-Rong; Kong, De-Xiu; Wang, Wen-Jia; Tong, Hui; Zhao, Ming-Hui; Xu, Zheng-Jin; Chen, Wen-Fu

    2013-11-01

    Weedy rice is an important germplasm source of rice, which has the characteristics of cold-, drought-, and barren tolerance. Taking 88 accessions of weedy rice and 4 varieties of cultivated rice in northern China as test materials, this paper studied the photosynthetic characteristics (photosynthetic rate, transpiration rate, and stomatal conductance), water physiological characteristics, and their interrelationships of weedy rice in northern China. There existed greater differences in the photosynthetic and water physiological characteristics among the weedy rice accessions, possessing abundant diversity. The photosynthetic rate of the accessions was from 12.47 micromol CO2 x m(-2) x s(-1) to 28.67 micromol CO2 X m(-2) x s(-1), and the instantaneous water use efficiency was from 1.39 mg x g(-1) to 3.40 mg x g(-1). Among the photosynthetic parameters, intercellular CO2 concentration had the smallest variable coefficient, while stomatal conductance had the largest one. The photosynthetic rate had significant conic relationships with transpiration rate and stomatal conductance, and had a linear relationship with intercellular CO2 concentration. The significant conic relationships also existed between the instantaneous water use efficiency and the transpiration rate and stomatal conductance. The excellent features of weedy rice could be used to improve the cultivated rice varieties.

  16. Rice bran extracts inhibit invasion and intracellular replication of Salmonella typhimurium in mouse and porcine intestinal epithelial cells

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Dietary rice bran supplementation has been shown to inhibit Salmonella fecal shedding in animals. The aim of this study was to determine if bran extracts from two distinct rice varieties, Lijiangxintuanheigu (LTH) and Sanhuangzhan-2 (SHZ-2), differentially inhibit Salmonella enterica serover Typhimu...

  17. Niclosamide inhibits leaf blight caused by Xanthomonas oryzae in rice

    PubMed Central

    Kim, Sung-Il; Song, Jong Tae; Jeong, Jin-Yong; Seo, Hak Soo

    2016-01-01

    Rice leaf blight, which is caused by the bacterial pathogen Xanthomonas oryzae pv. oryzae (Xoo), results in huge losses in grain yield. Here, we show that Xoo-induced rice leaf blight is effectively controlled by niclosamide, an oral antihelminthic drug and molluscicide, which also functions as an anti-tumor agent. Niclosamide directly inhibited the growth of the three Xoo strains PXO99, 10208 and K3a. Niclosamide moved long distances from the site of local application to distant rice tissues. Niclosamide also increased the levels of salicylate and induced the expression of defense-related genes such as OsPR1 and OsWRKY45, which suppressed Xoo-induced leaf wilting. Niclosamide had no detrimental effects on vegetative/reproductive growth and yield. These combined results indicate that niclosamide can be used to block bacterial leaf blight in rice with no negative side effects. PMID:26879887

  18. Evolution of Compatibility Range in the Rice-Magnaporthe oryzae System: An Uneven Distribution of R Genes Between Rice Subspecies.

    PubMed

    Gallet, Romain; Fontaine, Colin; Bonnot, François; Milazzo, Joëlle; Tertois, Christophe; Adreit, Henri; Ravigné, Virginie; Fournier, Elisabeth; Tharreau, Didier

    2016-04-01

    Efficient strategies for limiting the impact of pathogens on crops require a good understanding of the factors underlying the evolution of compatibility range for the pathogens and host plants, i.e., the set of host genotypes that a particular pathogen genotype can infect and the set of pathogen genotypes that can infect a particular host genotype. Until now, little is known about the evolutionary and ecological factors driving compatibility ranges in systems implicating crop plants. We studied the evolution of host and pathogen compatibility ranges for rice blast disease, which is caused by the ascomycete Magnaporthe oryzae. We challenged 61 rice varieties from three rice subspecies with 31 strains of M. oryzae collected worldwide from all major known genetic groups. We determined the compatibility range of each plant variety and pathogen genotype and the severity of each plant-pathogen interaction. Compatibility ranges differed between rice subspecies, with the most resistant subspecies selecting for pathogens with broader compatibility ranges and the least resistant subspecies selecting for pathogens with narrower compatibility ranges. These results are consistent with a nested distribution of R genes between rice subspecies.

  19. Using NOAA/AVHRR based remote sensing data and PCR method for estimation of Aus rice yield in Bangladesh

    NASA Astrophysics Data System (ADS)

    Nizamuddin, Mohammad; Akhand, Kawsar; Roytman, Leonid; Kogan, Felix; Goldberg, Mitch

    2015-06-01

    Rice is a dominant food crop of Bangladesh accounting about 75 percent of agricultural land use for rice cultivation and currently Bangladesh is the world's fourth largest rice producing country. Rice provides about two-third of total calorie supply and about one-half of the agricultural GDP and one-sixth of the national income in Bangladesh. Aus is one of the main rice varieties in Bangladesh. Crop production, especially rice, the main food staple, is the most susceptible to climate change and variability. Any change in climate will, thus, increase uncertainty regarding rice production as climate is major cause year-to-year variability in rice productivity. This paper shows the application of remote sensing data for estimating Aus rice yield in Bangladesh using official statistics of rice yield with real time acquired satellite data from Advanced Very High Resolution Radiometer (AVHRR) sensor and Principal Component Regression (PCR) method was used to construct a model. The simulated result was compared with official agricultural statistics showing that the error of estimation of Aus rice yield was less than 10%. Remote sensing, therefore, is a valuable tool for estimating crop yields well in advance of harvest, and at a low cost.

  20. [Climatic suitability of single cropping rice planting region in China].

    PubMed

    Duan, Ju-Qi; Zhou, Guang-Sheng

    2012-02-01

    To clarify the leading climate factors affecting the distribution of single cropping rice planting region in China at national and annual temporal scales and to reveal the potential distribution and climatic suitability divisions of this planting region in China could not only provide scientific basis for optimizing the allocation of single cropping rice production, modifying planting pattern, and introducing fine varieties, but also ensure the food security of China. In this paper, the potential climate factors affecting the single cropping rice distribution in China at regional and annual scales were selected from related literatures, and the single cropping rice geographic information from the national agro-meteorological observation stations of China Meteorological Administration (CMA), together with the maximum entropy model (MaxEnt) and spatial analyst function of Arc-GIS software, were adopted to clarify the leading climate factors affecting the potential distribution of single cropping rice planting region in China, and to construct a model about the relationships between the potential distribution of the planting region and the climate. The results showed that annual precipitation, moisture index, and days of not less than 18 degrees C stably were the leading climate factors affecting the potential distribution of single cropping rice planting region in China, with their cumulative contribution rate reached 94.5% of all candidate climate factors. The model constructed in this paper could well simulate the potential distribution of single cropping rice planting region in China. According to the appearance frequency, the low, medium and high climatic suitability divisions of single cropping rice planting region in China were clarified, and the climate characteristics of the planting region in each climatic suitability division were analyzed.

  1. Unravelling the proteomic profile of rice meiocytes during early meiosis

    PubMed Central

    Collado-Romero, Melania; Alós, Enriqueta; Prieto, Pilar

    2014-01-01

    Transfer of genetic traits from wild or related species into cultivated rice is nowadays an important aim in rice breeding. Breeders use genetic crosses to introduce desirable genes from exotic germplasms into cultivated rice varieties. However, in many hybrids there is only a low level of pairing (if existing) and recombination at early meiosis between cultivated rice and wild relative chromosomes. With the objective of getting deeper into the knowledge of the proteins involved in early meiosis, when chromosomes associate correctly in pairs and recombine, the proteome of isolated rice meiocytes has been characterized by nLC-MS/MS at every stage of early meiosis (prophase I). Up to 1316 different proteins have been identified in rice isolated meiocytes in early meiosis, being 422 exclusively identified in early prophase I (leptotene, zygotene, or pachytene). The classification of proteins in functional groups showed that 167 were related to chromatin structure and remodeling, nucleic acid binding, cell-cycle regulation, and cytoskeleton. Moreover, the putative roles of 16 proteins which have not been previously associated to meiosis or were not identified in rice before, are also discussed namely: seven proteins involved in chromosome structure and remodeling, five regulatory proteins [such as SKP1 (OSK), a putative CDK2 like effector], a protein with RNA recognition motifs, a neddylation-related protein, and two microtubule-related proteins. Revealing the proteins involved in early meiotic processes could provide a valuable tool kit to manipulate chromosome associations during meiosis in rice breeding programs. The data have been deposited to the ProteomeXchange with the PXD001058 identifier. PMID:25104955

  2. [Testing of germination rate of hybrid rice seeds based on near-infrared reflectance spectroscopy].

    PubMed

    Li, Yi-nian; Jiang, Dan; Liu, Ying-ying; Ding, Wei-min; Ding, Qi-shuo; Zha, Liang-yu

    2014-06-01

    Germination rate of rice seeds was measured according to technical stipulation of germination testing for agricultural crop seeds at present. There existed many faults for this technical stipulation such as long experimental period, more costing and higher professional requirement. A rapid and non-invasive method was put forward to measure the germination rate of hybrid rice seeds based on near-infrared reflectance spectroscopy. Two varieties of hybrid rice seeds were aged artificially at temperature 45 degrees C and humidity 100% condition for 0, 24, 48, 72, 96, 120 and 144 h. Spectral data of 280 samples for 2 varieties of hybrid rice seeds with different aging time were acquired individually by near-infrared spectra analyzer. Spectral data of 280 samples for 2 varieties of hybrid rice seeds were randomly divided into calibration set (168 samples) and prediction set (112 samples). Gormination rate of rice seed with different aging time was tested. Regression model was established by using partial least squares (PLS). The effect of the different spectral bands on the accuracy of models was analyzed and the effect of the different spectral preprocessing methods on the accuracy of models was also compared. Optimal model was achieved under the whole bands and by using standardization and orthogonal signal correction (OSC) preprocessing algorithms with CM2000 software for spectral data of 2 varieties of hybrid rice seeds, the coefficient of determination of the calibration set (Rc) and that of the prediction set (Rp) were 0.965 and 0.931 individually, standard error of calibration set (SEC) and that of prediction set (SEP) were 1.929 and 2.899 respectively. Relative error between tested value and predicted value for prediction set of rice seeds is below 4.2%. The experimental results show that it is feasible that rice germination rate is detected rapidly and nondestructively by using the near-infrared spectroscopy analysis technology.

  3. Optimizing hill seeding density for high-yielding hybrid rice in a single rice cropping system in South China.

    PubMed

    Wang, Danying; Chen, Song; Wang, Zaiman; Ji, Chenglin; Xu, Chunmei; Zhang, Xiufu; Chauhan, Bhagirath Singh

    2014-01-01

    Mechanical hill direct seeding of hybrid rice could be the way to solve the problems of high seeding rates and uneven plant establishment now faced in direct seeded rice; however, it is not clear what the optimum hill seeding density should be for high-yielding hybrid rice in the single-season rice production system. Experiments were conducted in 2010 and 2011 to determine the effects of hill seeding density (25 cm×15 cm, 25 cm×17 cm, 25 cm×19 cm, 25 cm×21 cm, and 25 cm×23 cm; three to five seeds per hill) on plant growth and grain yield of a hybrid variety, Nei2you6, in two fields with different fertility (soil fertility 1 and 2). In addition, in 2012 and 2013, comparisons among mechanical hill seeding, broadcasting, and transplanting were conducted with three hybrid varieties to evaluate the optimum seeding density. With increases in seeding spacing from 25 cm×15 cm to 25 cm×23 cm, productive tillers per hill increased by 34.2% and 50.0% in soil fertility 1 and 2. Panicles per m2 declined with increases in seeding spacing in soil fertility 1. In soil fertility 2, no difference in panicles per m2 was found at spacing ranging from 25 cm×17 cm to 25 cm×23 cm, while decreases in the area of the top three leaves and aboveground dry weight per shoot at flowering were observed. Grain yield was the maximum at 25 cm×17 cm spacing in both soil fertility fields. Our results suggest that a seeding density of 25 cm×17 cm was suitable for high-yielding hybrid rice. These results were verified through on-farm demonstration experiments, in which mechanical hill-seeded rice at this density had equal or higher grain yield than transplanted rice.

  4. Optimizing Hill Seeding Density for High-Yielding Hybrid Rice in a Single Rice Cropping System in South China

    PubMed Central

    Wang, Danying; Chen, Song; Wang, Zaiman; Ji, Chenglin; Xu, Chunmei; Zhang, Xiufu; Chauhan, Bhagirath Singh

    2014-01-01

    Mechanical hill direct seeding of hybrid rice could be the way to solve the problems of high seeding rates and uneven plant establishment now faced in direct seeded rice; however, it is not clear what the optimum hill seeding density should be for high-yielding hybrid rice in the single-season rice production system. Experiments were conducted in 2010 and 2011 to determine the effects of hill seeding density (25 cm×15 cm, 25 cm×17 cm, 25 cm×19 cm, 25 cm×21 cm, and 25 cm×23 cm; three to five seeds per hill) on plant growth and grain yield of a hybrid variety, Nei2you6, in two fields with different fertility (soil fertility 1 and 2). In addition, in 2012 and 2013, comparisons among mechanical hill seeding, broadcasting, and transplanting were conducted with three hybrid varieties to evaluate the optimum seeding density. With increases in seeding spacing from 25 cm×15 cm to 25 cm×23 cm, productive tillers per hill increased by 34.2% and 50.0% in soil fertility 1 and 2. Panicles per m2 declined with increases in seeding spacing in soil fertility 1. In soil fertility 2, no difference in panicles per m2 was found at spacing ranging from 25 cm×17 cm to 25 cm×23 cm, while decreases in the area of the top three leaves and aboveground dry weight per shoot at flowering were observed. Grain yield was the maximum at 25 cm×17 cm spacing in both soil fertility fields. Our results suggest that a seeding density of 25 cm×17 cm was suitable for high-yielding hybrid rice. These results were verified through on-farm demonstration experiments, in which mechanical hill-seeded rice at this density had equal or higher grain yield than transplanted rice. PMID:25290342

  5. Proposal of a growth chamber for growing Super-Dwarf Rice in Space Agriculture

    NASA Astrophysics Data System (ADS)

    Hirai, Hiroaki; Kitaya, Yoshiaki; Tsukamoto, Koya; Yamashita, Youichirou; Hirai, Takehiro

    Space agriculture needs to be considered to supply food for space crew who stay in space over an extended time period. So far crops such as wheat, onion, oat, pea and lettuce grew to explore the possibility of space agriculture. Although rice is a staple food for most of the world, research on rice cultivation in space has not been done much. Rice grains are nutrient-rich with carbohydrate, protein and dietary fiber. Moreover, rice is a high yield crop and harvested grains have a long shelf life. However, the plant height of standard rice cultivars is relatively long, requiring much space. In addition, rice plants require higher light intensities for greater yield. For these reasons, it is difficult to establish facilities for rice culture in a limited space with a low cost. We propose to employee a super-dwarf cultivar and a small growth chamber with a new type of LEDs. The super-dwarf rice is a short-grain japonica variety and the plant height is approximately 20 cm that is one-fifth as tall as standard cultivars. The LED light used as a light source for this study can provide full spectrum of 380 nm to 750 nm. Air temperature and humidity were controlled by a Peltier device equipped in the chamber. The characteristics of the new type of LEDs and other equipments of the chamber and the ground based performance of super-dwarf rice plants grown in the chamber will be reported.

  6. Methane potential and biodegradability of rice straw, rice husk and rice residues from the drying process.

    PubMed

    Contreras, L M; Schelle, H; Sebrango, C R; Pereda, I

    2012-01-01

    Agricultural solid residues are a potential renewable energy source. Rice harvesting and production in Sancti Spíritus province, Cuba, currently generates residues without an environmentally sustainable disposal route. Rice residues (rice straw, rice husk and rice residues from the drying process) are potentially an important carbon source for anaerobic digestion. For this paper, rice residues were placed for 36 days retention time in anaerobic batch reactor environments at both mesophilic (37 °C) and thermophilic (55 °C) conditions. Biogas and methane yield were determined as well as biogas composition. The results showed that rice straw as well as rice residues from the drying process had the highest biogas and methane yield. Temperature played an important role in determining both biogas yield and kinetics. In all cases, rice straw produced the highest yields; under mesophilic conditions the biogas yield was 0.43 m(3) kg(VS)(-1), under thermophilic conditions biogas yield reached 0.52 m(3) kg(VS)(-1). In the case of the rice husk, the biodegradability was very low. Methane content in all batches was kept above 55% vol. All digested material had a high carbon:nitrogen (C:N) ratio, even though significant biodegradation was recorded with the exception of rice husk. A first-order model can be used to describe the rice crop residues fermentation effectively.

  7. Differential activation of genes related to aluminium tolerance in two contrasting rice cultivars.

    PubMed

    Roselló, Maite; Poschenrieder, Charlotte; Gunsé, Benet; Barceló, Juan; Llugany, Mercè

    2015-11-01

    Rice (Oryza sativa) is a highly Al-tolerant crop. Among other mechanisms, a higher expression of STAR1/STAR2 (sensitive to Al rhizotoxicity1/2) genes and of Nrat1 (NRAMP Aluminium Transporter 1), and ALS1 (Aluminium sensitive 1) can at least in part be responsible for the inducible Al tolerance in this species. Here we analysed the responses to Al in two contrasting rice varieties. All analysed toxicity/tolerance markers (root elongation, Evans blue, morin and haematoxylin staining) indicated higher Al-tolerance in variety Nipponbare, than in variety Modan. Nipponbare accumulated much less Al in the roots than Modan. Aluminium supply caused stronger expression of STAR1 in Nipponbare than in Modan. A distinctively higher increase of Al-induced abscisic acid (ABA) accumulation was found in the roots of Nipponbare than in Modan. Highest ABA levels were observed in Nipponbare after 48 h exposure to Al. This ABA peak was coincident in time with the highest expression level of STAR1. It is proposed that ABA may be required for cell wall remodulation facilitated by the enhanced UDP-glucose transport to the walls through STAR1/STAR2. Contrastingly, in the roots of Modan the expression of both Nrat1 coding for a plasma membrane Al-transporter and of ALS1 coding for a tonoplast-localized Al transporter was considerably enhanced. Moreover, Modan had a higher Al-induced expression of ASR1 a gene that has been proposed to code for a reactive oxygen scavenging protein. In conclusion, the Al-exclusion strategy of Nipponbare, at least in part mediated by STAR1 and probably regulated by ABA, provided better protection against Al toxicity than the accumulation and internal detoxification strategy of Modan mediated by Nrat1, ALS1 and ARS1.

  8. Dematerialization: Variety, caution, and persistence.

    PubMed

    Ausubel, Jesse H; Waggoner, Paul E

    2008-09-02

    Dematerialization, represented by declining consumption per GDP of energy or of goods, offers some hope for rising environmental quality with development. The declining proportion of income spent on staples as affluence grows, which income elasticity <1.0 measures, makes dematerialization widespread. Further, as learning improves efficiency of resource use, the intensity of environmental impact per production of staples often declines. We observe that combinations of low income elasticity for staples and of learning by producers cause a variety of dematerializations and declining intensities of impact, from energy use and carbon emission to food consumption and fertilizer use, globally and in countries ranging from the United States and France to China, India, Brazil, and Indonesia. Because dematerialization and intensity of impact are ratios of parameters that may be variously defined and are sometimes difficult to estimate, their fluctuations must be interpreted cautiously. Nevertheless, substantial declining intensity of impact, and especially, dematerialization persisted between 1980 and 2006.

  9. Neglecting rice milling yield and quality underestimates economic losses from high-temperature stress.

    PubMed

    Lyman, Nathaniel B; Jagadish, Krishna S V; Nalley, L Lanier; Dixon, Bruce L; Siebenmorgen, Terry

    2013-01-01

    Future increases in global surface temperature threaten those worldwide who depend on rice production for their livelihoods and food security. Past analyses of high-temperature stress on rice production have focused on paddy yield and have failed to account for the detrimental impact of high temperatures on milling quality outcomes, which ultimately determine edible (marketable) rice yield and market value. Using genotype specific rice yield and milling quality data on six common rice varieties from Arkansas, USA, combined with on-site, half-hourly and daily temperature observations, we show a nonlinear effect of high-temperature stress exposure on yield and milling quality. A 1 °C increase in average growing season temperature reduces paddy yield by 6.2%, total milled rice yield by 7.1% to 8.0%, head rice yield by 9.0% to 13.8%, and total milling revenue by 8.1% to 11.0%, across genotypes. Our results indicate that failure to account for changes in milling quality leads to understatement of the impacts of high temperatures on rice production outcomes. These dramatic losses result from reduced paddy yield and increased percentages of chalky and broken kernels, which together decrease the quantity and market value of milled rice. Recently published estimates show paddy yield reductions of up to 10% across the major rice-producing regions of South and Southeast Asia due to rising temperatures. The results of our study suggest that the often-cited 10% figure underestimates the economic implications of climate change for rice producers, thus potentially threatening future food security for global rice producers and consumers.

  10. Automatic mapping of rice fields in the Sacramento Valley for water resources management

    NASA Astrophysics Data System (ADS)

    Zhong, L.; Yin, H.; Reyes, E.; Chung, F. I.

    2015-12-01

    Water use by rice fields is one of the most important components in hydrologic model simulation of the Sacramento Valley, California. In this study, rice fields were mapped by an automatic approach using Landsat imagery. The automatic approach is advantageous for its capacity of mapping rice fields repeatedly, consistently and timely without the need to collect training data. Seasonal dynamics of Enhanced Vegetation Index (EVI) and Normalized Difference Moisture Index (NDMI) were employed to identify rice based on its phenological characteristics. Classification could be conducted around planting date for early response to cropland use change, or for the full growing season to monitor rice growth. Two studies are illustrated as the applications of this mapping method: 1. A rice map was produced before mid-June to forecast rice acreage and water use in the 2015 drought. Due to continuous drought, rice acreage in the Sacramento Valley reached the historical minimum of the past 20 years in 2014, and further reduction is occurring in 2015. A quantitative measure of rice field extent is needed to forecast rice water use as early as possible. The automatic mapping method utilized the spectral dynamics during initial flooding to identify rice fields. Based on the map product, the forecast of rice water demand was made to facilitate the simulation of current-year hydrologic conditions. 2. Rice field extent has been mapped since 1989 and phenological metrics have been derived to study the change in growing season. The increasing use of short-season rice varieties and special weather condition (like El Nino in 2015) may alter the seasonal pattern of water demand by rice. Rice fields were identified based on the temporal profiles of NDMI and EVI derived from series of segmented images. Validation using field survey data and other land use maps showed a promising accuracy. The start and the end of the growing season and other phenological metrics were extracted from object

  11. The potential of rice to offer solutions for malnutrition and chronic diseases.

    PubMed

    Dipti, Sharifa Sultana; Bergman, Christine; Indrasari, Siti Dewi; Herath, Theja; Hall, Robert; Lee, Hueihong; Habibi, Fatemeh; Bassinello, Priscila Zaczuk; Graterol, Eduardo; Ferraz, Julie P; Fitzgerald, Melissa

    2012-07-02

    It is internationally accepted that malnutrition and chronic diseases in developing countries are key limitations to achieving the Millennium Development Goals. In many developing countries, rice is the primary source of nutrition. In those countries, the major forms of malnutrition are Fe-induced anaemia, Zn deficiency and Vitamin A deficiency, whereas the major chronic disease challenges are Type II diabetes, cardiovascular disease and some cancers. There is a growing corpus of evidence regarding both limitations and opportunities as to how rice could be an effective vehicle by which to tackle key nutrition and health related problems in countries with limited resources. Rice breeding programs are able to focus on developing new varieties carrying enhanced amounts of either Fe, Zn or beta-carotene because of large public investment, and the intuitive link between providing a mineral/vitamin to cure a deficiency in that mineral/vitamin. By contrast, there has been little investment in progressing the development of particular varieties for potential impact on chronic diseases. In this review article we focus on the broad battery of evidence linking rice-related nutritional limitations to their impact on a variety of human health issues. We discuss how rice might offer sometimes even simple solutions to rectifying key problems through targeted biofortification strategies and finally, we draw attention to how recent technological (-omics) developments may facilitate untold new opportunities for more rapidly generating improved rice varieties specifically designed to meet the current and future nutritional needs of a rapidly expanding global population.

  12. Whole Genome Sequencing of Elite Rice Cultivars as a Comprehensive Information Resource for Marker Assisted Selection

    PubMed Central

    Duitama, Jorge; Silva, Alexander; Sanabria, Yamid; Cruz, Daniel Felipe; Quintero, Constanza; Ballen, Carolina; Lorieux, Mathias; Scheffler, Brian; Farmer, Andrew; Torres, Edgar; Oard, James; Tohme, Joe

    2015-01-01

    Current advances in sequencing technologies and bioinformatics revealed the genomic background of rice, a staple food for the poor people, and provided the basis to develop large genomic variation databases for thousands of cultivars. Proper analysis of this massive resource is expected to give novel insights into the structure, function, and evolution of the rice genome, and to aid the development of rice varieties through marker assisted selection or genomic selection. In this work we present sequencing and bioinformatics analyses of 104 rice varieties belonging to the major subspecies of Oryza sativa. We identified repetitive elements and recurrent copy number variation covering about 200 Mbp of the rice genome. Genotyping of over 18 million polymorphic locations within O. sativa allowed us to reconstruct the individual haplotype patterns shaping the genomic background of elite varieties used by farmers throughout the Americas. Based on a reconstruction of the alleles for the gene GBSSI, we could identify novel genetic markers for selection of varieties with high amylose content. We expect that both the analysis methods and the genomic information described here would be of great use for the rice research community and for other groups carrying on similar sequencing efforts in other crops. PMID:25923345

  13. Effect of enhanced UV-B radiation on methane emission in a paddy field and rice root exudation of low-molecular-weight organic acids.

    PubMed

    He, Yongmei; Zhan, Fangdong; Li, Yuan; Xu, Weiwei; Zu, Yanqun; Yue, Ming

    2016-06-08

    A local rice variety, "Baijiaolaojing", was grown in a paddy field in the Yuanyang rice terraces under ambient and supplemental levels of ultraviolet-B (UV-B, 280-315 nm) radiation. The effects of enhanced UV-B radiation (5 and 10 kJ m(-2) d(-1)) on methane emissions in the paddy field were evaluated using a closed-chamber gas chromatography-based system, and the contents of low-molecular-weight organic acids (LMWOAs) in root exudates were determined by high-performance liquid chromatography (HPLC). Peaks in methane emissions in the paddy field were detected at 60, 80 and 100 days after rice transplantation. The highest level of cumulative methane emissions occurred at the tillering stage, followed by the jointing-booting and maturity stages. The lowest level was found at the flowering stage. The enhanced UV-B radiation did not change the seasonal variation in methane emissions in the paddy field; however, it induced a significant increase in the flux of methane emissions at the jointing-booting and maturity stages, as well as a significant increase in the cumulative flux of methane emissions throughout the growth period. In addition, the enhanced UV-B radiation caused an increase in the contents of oxalic acid and succinic acid and a decrease in the contents of tartaric acid and malic acid in rice root exudates. Furthermore, a significant positive correlation (r = 0.725, p < 0.01) was found between the content of oxalic acid and the methane emissions in the paddy field. The results indicated that enhanced UV-B radiation promoted methane emissions in the paddy field, which was closely associated with its impact on the exudation of LMWOAs by rice roots.

  14. 7 CFR 920.6 - Varieties.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... Orders; Fruits, Vegetables, Nuts), DEPARTMENT OF AGRICULTURE KIWIFRUIT GROWN IN CALIFORNIA Definitions § 920.6 Varieties. Varieties means and includes all classifications or subdivisions of kiwifruit....

  15. 7 CFR 920.6 - Varieties.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... ORDERS; FRUITS, VEGETABLES, NUTS), DEPARTMENT OF AGRICULTURE KIWIFRUIT GROWN IN CALIFORNIA Definitions § 920.6 Varieties. Varieties means and includes all classifications or subdivisions of kiwifruit....

  16. 7 CFR 920.6 - Varieties.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... ORDERS; FRUITS, VEGETABLES, NUTS), DEPARTMENT OF AGRICULTURE KIWIFRUIT GROWN IN CALIFORNIA Definitions § 920.6 Varieties. Varieties means and includes all classifications or subdivisions of kiwifruit....

  17. 7 CFR 920.6 - Varieties.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... Orders; Fruits, Vegetables, Nuts), DEPARTMENT OF AGRICULTURE KIWIFRUIT GROWN IN CALIFORNIA Definitions § 920.6 Varieties. Varieties means and includes all classifications or subdivisions of kiwifruit....

  18. 7 CFR 920.6 - Varieties.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... Orders; Fruits, Vegetables, Nuts), DEPARTMENT OF AGRICULTURE KIWIFRUIT GROWN IN CALIFORNIA Definitions § 920.6 Varieties. Varieties means and includes all classifications or subdivisions of kiwifruit....

  19. Organic Rice Production: Challenges and Opportunities

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The market demand for organically produced rice has grown steadily with the majority of the acreage now being located in Texas and California. A wide range of organic products are marketed including conventional long and medium grain rice, aromatic or scented rice, rice with colored bran, and rice f...

  20. STV11 encodes a sulphotransferase and confers durable resistance to rice stripe virus.

    PubMed

    Wang, Qi; Liu, Yuqiang; He, Jun; Zheng, Xiaoming; Hu, Jinlong; Liu, Yanling; Dai, Huimin; Zhang, Yingxin; Wang, Baoxiang; Wu, Weixun; Gao, He; Zhang, Yunhui; Tao, Xiaorong; Deng, Huafeng; Yuan, Dingyang; Jiang, Ling; Zhang, Xin; Guo, Xiuping; Cheng, Xianian; Wu, Chuanyin; Wang, Haiyang; Yuan, Longping; Wan, Jianmin

    2014-09-09

    Rice stripe virus (RSV) causes one of the most serious viral diseases of rice (Oryza sativa L.), but the molecular basis of RSV resistance has remained elusive. Here we show that the resistant allele of rice STV11 (STV11-R) encodes a sulfotransferase (OsSOT1) catalysing the conversion of salicylic acid (SA) into sulphonated SA (SSA), whereas the gene product encoded by the susceptible allele STV11-S loses this activity. Sequence analyses suggest that the STV11-R and STV11-S alleles were predifferentiated in different geographic populations of wild rice, Oryza rufipogon, and remained prevalent in cultivated indica and japonica rice varieties, respectively. Introgression of the STV11-R allele into susceptible cultivars or heterologous transfer of STV11-R into tobacco plants confers effective resistance against RSV. Our results shed new insights into plant viral defense mechanisms and suggest effective means of breeding RSV-resistant crops using molecular marker-assisted selection or genetic engineering.

  1. The durably resistant rice cultivar Digu activates defence gene expression before the full maturation of Magnaporthe oryzae appressorium.

    PubMed

    Li, Weitao; Liu, Ya; Wang, Jing; He, Min; Zhou, Xiaogang; Yang, Chao; Yuan, Can; Wang, Jichun; Chern, Mawsheng; Yin, Junjie; Chen, Weilan; Ma, Bingtian; Wang, Yuping; Qin, Peng; Li, Shigui; Ronald, Pamela; Chen, Xuewei

    2016-04-01

    Rice blast caused by the fungal pathogen Magnaporthe oryzae is one of the most destructive diseases worldwide. Although the rice-M. oryzae interaction has been studied extensively, the early molecular events that occur in rice before full maturation of the appressorium during M. oryzae invasion are unknown. Here, we report a comparative transcriptomics analysis of the durably resistant rice variety Digu and the susceptible rice variety Lijiangxintuanheigu (LTH) in response to infection by M. oryzae (5, 10 and 20 h post-inoculation, prior to full development of the appressorium). We found that the transcriptional responses differed significantly between these two rice varieties. Gene ontology and pathway analyses revealed that many biological processes, including extracellular recognition and biosynthesis of antioxidants, terpenes and hormones, were specifically activated in Digu shortly after infection. Forty-eight genes encoding receptor kinases (RKs) were significantly differentially regulated by M. oryzae infection in Digu. One of these genes, LOC_Os08g10300, encoding a leucine-rich repeat RK from the LRR VIII-2 subfamily, conferred enhanced resistance to M. oryzae when overexpressed in rice. Our study reveals that a multitude of molecular events occur in the durably resistant rice Digu before the full maturation of the appressorium after M. oryzae infection and that membrane-associated RKs play important roles in the early response.

  2. Development and characterization of rice bran cookies.

    PubMed

    Sangronis, E; Sancio, M

    1990-01-01

    Four cookie formulas (A, B, C and D) were prepared by combining stabilized rice bran with flour of other locally produced cereals. A Hedonic Scale from 1 to 7 was used to test acceptability; and Proximate Composition, Protein Efficiency Ratio (PER), Chemical Score (C.S.) and NDpCal% were determined. Sensory evaluation of the products did not detect a significant preference (p = 0.05) for any of the tested cookies. The formula A (30% rice bran), with the highest average score in flavor (6.2) and the highest PER (0.9) was selected for a consumer test among children ages 4 to 7, resulting in an acceptability of 100%.

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

    NASA Astrophysics Data System (ADS)

    Suwansukho, Kajpanya; Sumriddetchkajorn, Sarun; Buranasiri, Prathan

    2013-06-01

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

  4. Rice: chemistry and technology.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Rice has taken center stage this last decade, not only as an important provider of nourishment for the world’s population, but as a grain now recognized as having many unique nutritional and functional attributes with potential to be captured in a multitude of value-added food and non-food applicati...

  5. Rice bran phytonutrients

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The bran layer of the whole grain rice contains potential health-beneficial compounds. These include vitamin E homologs (tocopherols, tocotrienols), oryzanol fractions, simple phenolics and poly-phenolics. These are antioxidants that are believed to provide protection against diseases such as cancer...

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

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 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...

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

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 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...

  8. 7 CFR 868.310 - Grades and grade requirements for the classes Long Grain Milled Rice, Medium Grain Milled Rice...

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 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...

  9. 7 CFR 868.310 - Grades and grade requirements for the classes Long Grain Milled Rice, Medium Grain Milled Rice...

    Code of Federal Regulations, 2010 CFR

    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...

  10. 7 CFR 868.310 - Grades and grade requirements for the classes Long Grain Milled Rice, Medium Grain Milled Rice...

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 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...

  11. Rice Glycosyltransferase (GT) Phylogenomic Database

    DOE Data Explorer

    Ronald, Pamela

    The Ronald Laboratory staff at the University of California-Davis has a primary research focus on the genes of the rice plant. They study the role that genetics plays in the way rice plants respond to their environment. They created the Rice GT Database in order to integrate functional genomic information for putative rice Glycosyltransferases (GTs). This database contains information on nearly 800 putative rice GTs (gene models) identified by sequence similarity searches based on the Carbohydrate Active enZymes (CAZy) database. The Rice GT Database provides a platform to display user-selected functional genomic data on a phylogenetic tree. This includes sequence information, mutant line information, expression data, etc. An interactive chromosomal map shows the position of all rice GTs, and links to rice annotation databases are included. The format is intended to "facilitate the comparison of closely related GTs within different families, as well as perform global comparisons between sets of related families." [From http://ricephylogenomics.ucdavis.edu/cellwalls/gt/genInfo.shtml] See also the primary paper discussing this work: Peijian Cao, Laura E. Bartley, Ki-Hong Jung and Pamela C. Ronalda. Construction of a Rice Glycosyltransferase Phylogenomic Database and Identification of Rice-Diverged Glycosyltransferases. Molecular Plant, 2008, 1(5): 858-877.

  12. Establishment of a high efficiency Agrobacterium-mediated transformation system of rice (Oryza sativa L.).

    PubMed

    Ozawa, Kenjirou

    2009-04-01

    Technologies for transformation of rice have been developed to meet the requirements of functional genomics in order to enable the production of transgenic rice plants with useful agricultural characters. However, many rice varieties are not efficiently transformed by Agrobacterium. We have succeeded in establishing a highly efficient transformation system in rice by co-cultivating rice calli with Agrobacterium on three filter papers moistened with enriched N6 or DKN media instead of using solid media. Rice calli immersed in Agrobacterium suspension (EHA101, Agrobacterium concentration of OD600=0.04) were co-cultured on three pieces of filter paper (9cm in diameter) moistened with 5.5mL of N6 or DKN liquid co-cultivation medium supplemented with 2,4-d (2mg/L), proline (10mM), casein hydrolysate (300mg/L), sucrose (30g/L), glucose (5g/L), l-cysteine (100mg/L) and acetosyringone (15mg/L) at 25°C for 3 days in the dark. Compared with the transformation efficiency of calli co-cultivated on solid media, transformation efficiency was increased by about fivefold by using the filter paper method for many varieties of rice, including those that previously yielded much poor transformation rates.

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

    PubMed

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

    2015-05-01

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

  14. Soil amendments and cultivar selection can improve rice yield in salt-influenced (tsunami-affected) paddy fields in Sri Lanka.

    PubMed

    Reichenauer, Thomas G; Panamulla, Sunil; Subasinghe, Siripala; Wimmer, Bernhard

    2009-10-01

    The tsunami disaster in the Indian Ocean in December 2004 caused devastation of agricultural soils by salt water over wide areas. Many rice fields located close to the coast were affected by the flood of seawater. Electric conductivity (EC) of soils in tsunami-affected rice fields was found to be higher compared to unaffected fields 2 years after the tsunami. Four soil amendments (gypsum, dolomite, cinnamon ash and rice-husk-charcoal) were tested for their influence on improving the yield parameters of rice grown in a tsunami-affected and a non-affected area. Yield parameters were compared with an untreated control of the same cultivar (AT362) and with a salt resistant rice variety (AT354). The salt resistant variety had the highest grain yield. The two amendments gypsum and rice-husk-charcoal led to an increase in grain yield compared to the untreated control, whereas dolomite and cinnamon ash had no significant effect on grain yield.

  15. The socio-economic impacts of rice policies implementation in rural Burma/Myanmar.

    PubMed

    Thawnghmung, Ardeth Maung

    2003-01-01

    This paper, focusing on two rice-farming villages where the Burmese government has experimented with a variety of agricultural programmes, explores the problems associated with rice implementation processes. In particular it looks at the basic structure and operation of agricultural administration — salary and income of government officials, the predominance of military officers in civilian ministries and departments, the creation of departments with overlapping responsibilities, and the hierarchical structure of the Agricultural Ministry — and highlight their limitations. It provides another aspect to evaluating the roots of poverty among average rice farmers.

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

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

  17. Methane production, emission and possible control measures in the rice agriculture

    NASA Astrophysics Data System (ADS)

    Wang, Mingxing; Shangguan, Xingjian; Shen, Renxing; Reiner, Wassmann; Wolfgang, Seiler

    1993-09-01

    In the rice field methane is produced in the soil layer with depths of 2 25 cm. The vertical profile of methane production rate in the paddy soil during the water covering period differs from that in the paddy soil in dry phase. Only a small part, about 30%, of the produced methane is emitted to the atmosphere through rice plant, air bubbles, and molecular diffusion. Therefore, the methane emission rate from the rice field depends not only on the methane production rate in the soil, but also on the transport efficiency of the rice plant, air bubble formation that in turn depends on the production rate, and molecular diffusion. Field measurements show that methane emission rates from a particular rice field have very large diurnal, seasonal and interannual variations, which are related to soil characteristics, water regime, farming procedure, local climate, and rice growing activities. The relationship between the methane emission rate and the above mentioned factors is very complicated. The emission rates from different rice fields differ greatly not only in the absolute value, but also in the temporal variation patterns. Methane emission rate from the rice field may be significantly reduced by scientific management of fertilizer and irrigation. While the use of SO{4/2-} containing fertilizer and fermented organic fertilizer may reduce the methane emission significantly, the most promising measure for reducing methane emission from rice field is the frequent drainage irrigation procedure.

  18. Deforestation and Rice: Using Methods in Modeling and Remote Sensing to Project Patterns of Forest Change in Eastern Madagascar

    NASA Astrophysics Data System (ADS)

    Armstrong, A. H.; Fatoyinbo, T. E.; Fischer, R.; Huth, A.; Shugart, H. H.

    2013-12-01

    review) Madagascar FORMIX3 Model (see Huth and Ditzer, 2000) by incorporating rice economy, selective logging and political stability modules into the model to control certain species groups (i.e. selective harvest) and fire frequency (encroachment). The improved FORMIX3 model was then used to investigate and project forest growth response to a variety of impact scenarios ranging from an increase in overall deforestation to a decrease in deforestation and increase in protection enforcement. Our findings showed a significant positive correlation between increasing deforestation rates and higher local rice prices due to political regime and international market factors. This research resulted in the first quantitative analysis of the relationship between the international rice market and local land-use in terms of slash and burn agriculture, illegal logging of precious hardwood in Madagascar.

  19. Life cycle GHG evaluation of organic rice production in northern Thailand.

    PubMed

    Yodkhum, Sanwasan; Gheewala, Shabbir H; Sampattagul, Sate

    2017-03-09

    Greenhouse gas (GHG) emission is one of the serious international environmental issues that can lead to severe damages such as climate change, sea level rise, emerging disease and many other impacts. Rice cultivation is associated with emissions of potent GHGs such as methane and nitrous oxide. Thai rice has been massively exported worldwide however the markets are becoming more competitive than ever since the green market has been hugely promoted. In order to maintain the same level or enhance of competitiveness, Thai rice needs to be considered for environmentally conscious products to meet the international environmental standards. Therefore, it is necessary to evaluate the greenhouse gas emissions throughout the life cycle of rice production in order to identify the major emission sources and possible reduction strategies. In this research, the rice variety considered is Khao Dawk Mali 105 (KDML 105) cultivated by organic practices. The data sources were Don-Chiang Organic Agricultural Cooperative (DCOAC), Mae-teang district, Chiang Mai province, Thailand and the Office of Agricultural Economics (OAE) of Thailand with onsite records and interviews of farmers in 2013. The GHG emissions were calculated from cradle-to-farm by using the Life Cycle Assessment (LCA) approach and the 2006 IPCC Guideline for National Greenhouse Gas Inventories. The functional unit is defined as 1 kg of paddy rice at farm gate. Results showed that the total GHG emissions of organic rice production were 0.58 kg CO2-eq per kg of paddy rice. The major source of GHG emission was from the field emissions accounting for 0.48 kg CO2-eq per kg of paddy rice, about 83% of total, followed by land preparation, harvesting and other stages (planting, cultivation and transport of raw materials) were 9, 5 and 3% of total, respectively. The comparative results clearly showed that the GHG emissions of organic paddy rice were considerably lower than conventional rice production due to the advantages

  20. Remote sensing based change analysis of rice environments in Odisha, India.

    PubMed

    Gumma, Murali Krishna; Mohanty, Samarendu; Nelson, Andrew; Arnel, Rala; Mohammed, Irshad A; Das, Satya Ranjan

    2015-01-15

    The rainfed rice-growing environment is perhaps one of the most vulnerable to water stress such as drought and floods. It is important to determine the spatial extent of the stress-prone areas to effectively and efficiently promote proper technologies (e.g., stress-tolerant varieties) to tackle the problem of sustainable food production. This study was conducted in Odisha state located in eastern India. Odisha is predominantly a rainfed rice ecosystem (71% rainfed and 29% canal irrigated during kharif-monsoon season), where rice is the major crop and staple food of the people. However, rice productivity in Odisha is one of the lowest in India and a significant decline (9%) in rice cultivated area was observed in 2002 (a drought year). The present study analyzed the temporal rice cropping pattern in various ecosystems and identified the stress-prone areas due to submergence (flooding) and water shortage. The spatial distribution of rice areas was mapped using MODIS (MOD09Q1) 250-m 8-day time-series data (2000-2010) and spectral matching techniques. The mapped rice areas were strongly correlated (R(2) = 90%) with district-level statistics. Also the class accuracy based on field-plot data was 84.8%. The area under the rainfed rice ecosystem continues to dominate, recording the largest share among rice classes across all the years. The use of remote-sensing techniques is rapid, cost-effective, and reliable to monitor changes in rice cultivated area over long periods of time and estimate the reduction in area cultivated due to abiotic stress such as water stress and submergence. Agricultural research institutes and line departments in the government can use these techniques for better planning, regular monitoring of land-use changes, and dissemination of appropriate technologies.

  1. Accelerated Solvent Extraction of Insecticides from Rice Hulls, Rice Bran, and Polished Rice Grains.

    PubMed

    Teló, Gustavo Mack; Senseman, Scott Allen; Marchesan, Enio; Camargo, Edinalvo Rabaioli; Carson, Katherine

    2017-03-01

    Analysis of pesticide residues in irrigated rice grains is important for food security. In this study, we analyzed accelerated solvent extraction (ASE) conditions for the extraction of thiamethoxam and chlorantraniliprole insecticides from rice hulls, rice bran, and polished rice grains. Several variables, including extraction solvent, extraction temperature, extraction pressure, cell size, static extraction time, and sample concentration, were investigated. The average recoveries of the three matrixes were between 89.7 and 109.7% at the fortification level of 0.75 mg/kg. The optimum ASE operating conditions were acetonitrile (100%) as extraction solvent, extraction temperature of 75°C for rice hulls and 100°C for rice bran and polished rice grains, extraction cell pressure of 10.3 MPa, 22 mL cell size, and two extraction cycles. The total extraction time was approximately 25 min. The extracted volume was evaporated to dryness and the residues were redissolved in 2 mL acetonitrile after 1 min of vortex-shaking. Thiamethoxam and chlorantraniliprole were analyzed by ultra-HPLC with tandem MS. In conclusion, ASE in rice hulls, rice bran, and polished rice grains offers the possibility of a fast and simple method for obtaining a quantitative extraction of the studied pesticides.

  2. Development and field performance of nitrogen use efficient rice lines for Africa.

    PubMed

    Selvaraj, Michael Gomez; Valencia, Milton Orlando; Ogawa, Satoshi; Lu, Yingzhi; Wu, Liying; Downs, Christopher; Skinner, Wayne; Lu, Zhongjin; Kridl, Jean C; Ishitani, Manabu; van Boxtel, Jos

    2016-11-27

    Nitrogen (N) fertilizers are a major input cost in rice production, and its excess application leads to major environmental pollution. Development of rice varieties with improved nitrogen use efficiency (NUE) is essential for sustainable agriculture. Here, we report the results of field evaluations of marker-free transgenic NERICA4 (New Rice for Africa 4) rice lines overexpressing barley alanine amino transferase (HvAlaAT) under the control of a rice stress-inducible promoter (pOsAnt1). Field evaluations over three growing seasons and two rice growing ecologies (lowland and upland) revealed that grain yield of pOsAnt1:HvAlaAT transgenic events was significantly higher than sibling nulls and wild-type controls under different N application rates. Our field results clearly demonstrated that this genetic modification can significantly increase the dry biomass and grain yield compared to controls under limited N supply. Increased yield in transgenic events was correlated with increased tiller and panicle number in the field, and evidence of early establishment of a vigorous root system in hydroponic growth. Our results suggest that expression of the HvAlaAT gene can improve NUE in rice without causing undesirable growth phenotypes. The NUE technology described in this article has the potential to significantly reduce the need for N fertilizer and simultaneously improve food security, augment farm economics and mitigate greenhouse gas emissions from the rice ecosystem.

  3. Rice Area Inter Annual Variation through a Remote Sensing Based Mapping Algorithm

    NASA Astrophysics Data System (ADS)

    Elshorbagy, A. M.; Imam, E. H.; Nour, M. H.

    2013-10-01

    Rice is the main water-consuming crop planted in Egypt Delta. Constrained with the limited water resources, mapping rice is essential for any better water resources management. Xiao (2005) developed an algorithm for rice mapping by studying the dynamics of three vegetation indices the normalized difference vegetation index (NDVI), the Enhanced Vegetation Index (EVI) and the Land surface water index (LSWI). Rice main differentiating feature is being planted in flooded land. Thus moisture sensitive index like LSWI will temporally exceed the EVI or the NDVI signalling rice transplanting. Xiao (2005) utilized MODIS free satellite imagery (500 m spatial resolution). However its coarse resolution combined with the Egyptian complex landscape raised the need for the algorithm modification. In this piece of work a low - cost rice mapping algorithm was developed. The multi resolution (MODIS 250 m red and near infrared bands) and (MODIS 500 m - shortwave infrared and blue bands) were utilized. The arable land was mapped through the utilization of the NDVI and applying it on MODIS 250 m (fine spatial resolution) scenes. The MODIS fine temporal resolution (MOD09A1 product) was utilized to study the LSWI, NDVI and EVI dynamics throughout the rice planting season. The non-arable land from MODIS 250 m was then used to refine the rice area calculated from the MODIS 500 m imagery. The algorithm was applied on the Egypt delta region in years 2008, 2009, and 2010. The mapped rice areas were enhanced from the MODIS 250 m arable mapping module and the results of the algorithm were validated against annual areas reports. There was good agreement between the estimated areas from the algorithm and the reports. Inter annual variation in rice areas was successfully mapped. In addition, the rice area and probable transplanting dates conforms to local planting practices. The findings of this study indicate that the algorithm can be used for rice mapping on a timely and frequent manner.

  4. Overexpression of acetylcholinesterase gene in rice results in enhancement of shoot gravitropism.

    PubMed

    Yamamoto, Kosuke; Shida, Satoshi; Honda, Yoshihiro; Shono, Mariko; Miyake, Hiroshi; Oguri, Suguru; Sakamoto, Hikaru; Momonoki, Yoshie S

    2015-09-25

    Acetylcholine (ACh), a known neurotransmitter in animals and acetylcholinesterase (AChE) exists widely in plants, although its role in plant signal transduction is unclear. We previously reported AChE in Zea mays L. might be related to gravitropism based on pharmacological study using an AChE inhibitor. Here we clearly demonstrate plant AChE play an important role as a positive regulator in the gravity response of plants based on a genetic study. First, the gene encoding a second component of the ACh-mediated signal transduction system, AChE was cloned from rice, Oryza sativa L. ssp. Japonica cv. Nipponbare. The rice AChE shared high homology with maize, siratro and Salicornia AChEs. Similar to animal and other plant AChEs, the rice AChE hydrolyzed acetylthiocholine and propionylthiocholine, but not butyrylthiocholine. Thus, the rice AChE might be characterized as an AChE (E.C.3.1.1.7). Similar to maize and siratro AChEs, the rice AChE exhibited low sensitivity to the AChE inhibitor, neostigmine bromide, compared with the electric eel AChE. Next, the functionality of rice AChE was proved by overexpression in rice plants. The rice AChE was localized in extracellular spaces of rice plants. Further, the rice AChE mRNA and its activity were mainly detected during early developmental stages (2 d-10 d after sowing). Finally, by comparing AChE up-regulated plants with wild-type, we found that AChE overexpression causes an enhanced gravitropic response. This result clearly suggests that the function of the rice AChE relate to positive regulation of gravitropic response in rice seedlings.

  5. Plant physiological and soil characteristics associated with methane and nitrous oxide emission from rice paddy.

    PubMed

    Baruah, K K; Gogoi, Boby; Gogoi, P

    2010-01-01

    Methane (CH4) and nitrous oxide (N2O) are important greenhouse gases causing global warming and climate change. Efforts were made to analyze the CH4 and N2O flux in relation to plant and soil factors from rice (Oryza sativa L.) paddy. Ten popularly grown rice varieties namely Rashmisali, Bogajoha, Basmuthi, Lalkalamdani, Choimora (traditional varieties); Mahsuri, Moniram, Kushal, Gitesh and Profulla (high yielding varieties = HYV) were grown during monsoon season of July 2006. The CH4 and N2O emissions were measured the date of transplanting onwards at weekly interval along with soil and plant parameters. The seasonal integrated CH4 and N2O emission (Esif) from rice ranged from 8.13 g m(-2) to 13.00 g m(-2) and 121.63 mg N2O-N m(-2) to 189.46 mg N2O-N m(-2), respectively. Variety Gitesh emitted less N2O and CH4 amongst all the rice varieties. Both CH4 and N2O emission exhibited a significant positive correlation with leaf area, leaf number, tiller number and root dry weight. Soil organic carbon of the experimental field was associated with both CH4 and N2O emission whereas nitrate-N content of soil was associated with N2O emission. Methane emission showed significant positive correlations with soil temperature and crop photosynthetic rate. Traditional rice varieties with profuse vegetative growth recorded higher CH4 and N2O fluxes compared to HYVs. Gitesh and Kushal having low seasonal CH4 and N2O emission with higher yield potential can be recommended as low greenhouse gas emitting rice varieties.

  6. Field Trials Reveal Ecotype-Specific Responses to Mycorrhizal Inoculation in Rice

    PubMed Central

    Diedhiou, Abdala Gamby; Mbaye, Fatou Kine; Mbodj, Daouda; Faye, Mathieu Ndigue; Pignoly, Sarah; Ndoye, Ibrahima; Djaman, Koffi; Gaye, Souleymane; Kane, Aboubacry; Laplaze, Laurent; Manneh, Baboucarr; Champion, Antony

    2016-01-01

    The overuse of agricultural chemicals such as fertilizer and pesticides aimed at increasing crop yield results in environmental damage, particularly in the Sahelian zone where soils are fragile. Crop inoculation with beneficial soil microbes appears as a good alternative for reducing agricultural chemical needs, especially for small farmers. This, however, requires selecting optimal combinations of crop varieties and beneficial microbes tested in field conditions. In this study, we investigated the response of rice plants to inoculation with arbuscular mycorrhizal fungi (AMF) and plant growth promoting bacteria (PGPB) under screenhouse and field conditions in two consecutive seasons in Senegal. Evaluation of single and mixed inoculations with AMF and PGPB was conducted on rice (Oryza sativa) variety Sahel 202, on sterile soil under screenhouse conditions. We observed that inoculated plants, especially plants treated with AMF, grew taller, matured earlier and had higher grain yield than the non-inoculated plants. Mixed inoculation trials with two AMF strains were then conducted under irrigated field conditions with four O. sativa varieties, two O. glaberrima varieties and two interspecific NERICA varieties, belonging to 3 ecotypes (upland, irrigated, and rainfed lowland). We observed that the upland varieties had the best responses to inoculation, especially with regards to grain yield, harvest index and spikelet fertility. These results show the potential of using AMF to improve rice production with less chemical fertilizers and present new opportunities for the genetic improvement in rice to transfer the ability of forming beneficial rice-microbe associations into high yielding varieties in order to increase further rice yield potentials. PMID:27907023

  7. Genetic diversity and classification of Oryza sativa with emphasis on Chinese rice germplasm

    PubMed Central

    Wang, C-H; Zheng, X-M; Xu, Q; Yuan, X-P; Huang, L; Zhou, H-F; Wei, X-H; Ge, S

    2014-01-01

    Despite extensive studies on cultivated rice, the genetic structure and subdivision of this crop remain unclear at both global and local scales. Using 84 nuclear simple sequence repeat markers, we genotyped a panel of 153 global rice cultivars covering all previously recognized groups and 826 cultivars representing the diversity of Chinese rice germplasm. On the basis of model-based grouping, neighbour-joining tree and principal coordinate analysis, we confirmed the widely accepted five major groups of rice cultivars (indica, aus, aromatic, temperate japonica and tropical japonica), and demonstrated that rayada rice was unique in genealogy and should be treated as a new (the sixth) major group of rice germplasm. With reference to the global classification of rice cultivars, we identified three major groups (indica, temperate japonica and tropical japonica) in Chinese rice germplasm and showed that Chinese temperate japonica contained higher diversity than that of global samples, whereas Chinese indica and tropical japonica maintained slightly lower diversity than that present in the global samples. Particularly, we observed that all seasonal, drought-tolerant and endosperm types occurred within each of three major groups of Chinese cultivars, which does not support previous claims that seasonal differentiation exists in Indica and drought-tolerant differentiation is present in Japonica. It is most likely that differentiation of cultivar types arose multiple times stemming from artificial selection for adaptation to local environments. PMID:24326293

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

    PubMed Central

    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

  9. Overexpression of rice serotonin N-acetyltransferase 1 in transgenic rice plants confers resistance to cadmium and senescence and increases grain yield.

    PubMed

    Lee, Kyungjin; Back, Kyoungwhan

    2017-04-01

    While ectopic overexpression of serotonin N-acetyltransferase (SNAT) in plants has been accomplished using animal SNAT genes, ectopic overexpression of plant SNAT genes in plants has not been investigated. Because the plant SNAT protein differs from that of animals in its subcellular localization and enzyme kinetics, its ectopic overexpression in plants would be expected to give outcomes distinct from those observed from overexpression of animal SNAT genes in transgenic plants. Consistent with our expectations, we found that transgenic rice plants overexpressing rice (Oryza sativa) SNAT1 (OsSNAT1) did not show enhanced seedling growth like that observed in ovine SNAT-overexpressing transgenic rice plants, although both types of plants exhibited increased melatonin levels. OsSNAT1-overexpressing rice plants did show significant resistance to cadmium and senescence stresses relative to wild-type controls. In contrast to tomato, melatonin synthesis in rice seedlings was not induced by selenium and OsSNAT1 transgenic rice plants did not show tolerance to selenium. T2 homozygous OsSNAT1 transgenic rice plants exhibited increased grain yield due to increased panicle number per plant under paddy field conditions. These benefits conferred by ectopic overexpression of OsSNAT1 had not been observed in transgenic rice plants overexpressing ovine SNAT, suggesting that plant SNAT functions differently from animal SNAT in plants.

  10. Rice develop wavy seminal roots in response to light stimulus.

    PubMed

    Wang, Shu-Jen; Ho, Chia-Hsun; Chen, Hsiang-Wen

    2011-09-01

    Rice (Oryza sativa L.) seminal roots are the primary roots to emerge from germinated seeds. Here, we demonstrate that the photomorphology of the seminal roots was diverse among rice varieties, and the light-induced wavy roots were found mostly in indica-type rice varieties. The light-induced wavy morphology in rice seminal roots has been different with curling or coiling roots in some other specific conditions, such as high air humidity or high nitrogen nutrient. The efficiency of light-induced root waving was developmental stage dependent. The wavy root phenotype was caused by asymmetric cell growth around the stele. Using the inhibitors to block auxin polar transport and fatty acid oxygenation, the role of auxin and oxylipins in the morphogenesis of light-induced wavy roots was investigated. Expressions of genes encoded in the enzymes involved in fatty acid oxygenation in light-exposed roots were monitored by reverse transcriptase-polymerase chain reaction. Our results suggested that auxin polar transport was essential for inducing wavy seminal roots by light stimulus. In addition, the ketol oxylipins derived from allene oxide synthase (EC 4.2.1.92)-mediated fatty acid oxygenation function as intracellular signals for triggering the light-induced wavy root phenotype.

  11. Overexpression of the rice carotenoid cleavage dioxygenase 1 gene in Golden Rice endosperm suggests apocarotenoids as substrates in planta.

    PubMed

    Ilg, Andrea; Yu, Qiuju; Schaub, Patrick; Beyer, Peter; Al-Babili, Salim

    2010-08-01

    Carotenoids are converted by carotenoid cleavage dioxygenases that catalyze oxidative cleavage reactions leading to apocarotenoids. However, apocarotenoids can also be further truncated by some members of this enzyme family. The plant carotenoid cleavage dioxygenase 1 (CCD1) subfamily is known to degrade both carotenoids and apocarotenoids in vitro, leading to different volatile compounds. In this study, we investigated the impact of the rice CCD1 (OsCCD1) on the pigmentation of Golden Rice 2 (GR2), a genetically modified rice variety accumulating carotenoids in the endosperm. For this purpose, the corresponding cDNA was introduced into the rice genome under the control of an endosperm-specific promoter in sense and anti-sense orientations. Despite high expression levels of OsCCD1 in sense plants, pigment analysis revealed carotenoid levels and patterns comparable to those of GR2, pleading against carotenoids as substrates in rice endosperm. In support, similar carotenoid contents were determined in anti-sense plants. To check whether OsCCD1 overexpressed in GR2 endosperm is active, in vitro assays were performed with apocarotenoid substrates. HPLC analysis confirmed the cleavage activity of introduced OsCCD1. Our data indicate that apocarotenoids rather than carotenoids are the substrates of OsCCD1 in planta.

  12. The politics of Golden Rice.

    PubMed

    Dubock, Adrian

    2014-07-03

    Genetic knowledge applicable to crop improvement has erupted over the past 60 years, and the techniques of introducing genes from one organism to another have enabled new varieties of crops not achievable by previously available methodologies of crop breeding. Research and particularly development of these GMO-crops to a point where they are useful for growers and consumers in most countries is subject to complex national and international rules arising out of the UN's Cartagena Protocol on Biosafety to the Convention on Biological Diversity, with 167 country signatories. (The USA and Canada are not signatories.) The Protocol was developed based on concerns initially expressed in the 1970's that such technology presented unusual risks to man and the environment. Those ideas have comprehensively and authoritatively been proven to be wrong. The Protocol has nevertheless spawned significant regulatory obstacles to the development of GMO-crop technology at great cost to global society and in conflict with many other UN objectives. The suspicion induced by the Protocol is also widely used, overtly or covertly, for political purposes. These points are illustrated by reference to the not-for-profit Golden Rice project.

  13. The politics of Golden Rice

    PubMed Central

    Dubock, Adrian

    2014-01-01

    Genetic knowledge applicable to crop improvement has erupted over the past 60 years, and the techniques of introducing genes from one organism to another have enabled new varieties of crops not achievable by previously available methodologies of crop breeding. Research and particularly development of these GMO-crops to a point where they are useful for growers and consumers in most countries is subject to complex national and international rules arising out of the UN's Cartagena Protocol on Biosafety to the Convention on Biological Diversity, with 167 country signatories. (The USA and Canada are not signatories.) The Protocol was developed based on concerns initially expressed in the 1970's that such technology presented unusual risks to man and the environment. Those ideas have comprehensively and authoritatively been proven to be wrong. The Protocol has nevertheless spawned significant regulatory obstacles to the development of GMO-crop technology at great cost to global society and in conflict with many other UN objectives. The suspicion induced by the Protocol is also widely used, overtly or covertly, for political purposes. These points are illustrated by reference to the not-for-profit Golden Rice project. PMID:25437240

  14. Phytotoxicity of arsenate and salinity on early seedling growth of rice (Oryza sativa L.): a threat to sustainable rice cultivation in South and South-East Asia.

    PubMed

    Rahman, M Mamunur; Rahman, M Azizur; Maki, T; Hasegawa, H

    2012-05-01

    Arsenic (As) contamination is an important environmental consequence in some parts of salinity-affected South (S) and South-East (SE) Asia. In this study, we investigated the individual and combined phytotoxicity of arsenic (As) [arsenate; As(V)] and salinity (NaCl) on early seedling growth (ESG) of saline-tolerant and non-tolerant rice varieties. Germination percentage (GP), germination speed (GS) and vigor index (VI) of both saline-tolerant and non-tolerant rice varieties decreased significantly (p > 0.01) with increasing As(V) and NaCl concentrations. The highest GP (91%) was observed for saline non-tolerant BRRI dhan28 and BRRI dhan49, while the lowest (62%) was for saline-tolerant BRRI dhan47. The ESG parameters, such as weights and relative lengths of plumule and radicle, also decreased significantly (p < 0.01) with increasing As(V) and NaCl concentrations. Relative radicle length was more affected than plumule length by As(V) and NaCl. Although VI of saline-tolerant and non-tolerant rice seedlings showed significant variation (p < 0.05), weights and lengths of plumule and radicle of different rice varieties did not show significant variation for As(V) and NaCl treatments. Results reveal that the combined phytotoxicity of As(V) and NaCl on rice seed germination and ESG are greater than their individual toxicities, and some saline-tolerant rice varieties are more resistant to the combined phytotoxicity of As(V) and NaCl than the saline non-tolerant varieties.

  15. Determinants of rice residue burning in the field.

    PubMed

    Haider, Mohammed Ziaul

    2013-10-15

    This study determines the factors that influence rice residue burning in the field. We consider the southwest region of Bangladesh as the study site. Our results indicate that while straw length, low-elevation land, and distance of the plot from homestead positively and significantly influence the rice residue burning decision, residue price negatively and significantly influences the residue burning decision of farmers. Our study proposes subsidies for the purchase of new varieties of seeds and/or education in order to persuade farmers to move to short-straw varieties on high/medium-elevation lands as policy interventions for handling the residue burning issue. Another option might be to switch from residue burning to incorporation. Research and development efforts into shortening straw length and shortening the time period between planting and harvesting time are among other options that would mitigate the problem under consideration.

  16. High Temperature Induced Glume Closure Resulted in Lower Fertility in Hybrid Rice Seed Production

    PubMed Central

    Yan, Haoliang; Zhang, Binglin; Zhang, Yunbo; Chen, Xinlan; Xiong, Hui; Matsui, Tsutomu; Tian, Xiaohai

    2017-01-01

    Predicted climate changes, in particular, the increased dimension and frequency of heat waves, are expected to affect crop growth in the future seriously. Hybrid rice relies on seed production from male sterile and restorer lines. Experiments were conducted over two consecutive years to compare the high temperature tolerance of parents of different hybrid rice combinations, in terms of fertility rate, flowering pattern, pollination and physiological parameters of the lodicule. Three male sterile lines and a broad compatibility restorer line (as pollen donor and conventional variety as well) were grown to heading stage and then treated with average daily temperatures of 26°C (range 23–30°C), 28°C (25–32°C), and 30°C (26–34°C), respectively, continued for 5–7 days each in a natural light phytotron which simulated the local typical high temperature weather in the field. The results indicated that male sterile lines were more sensitive to high temperature than the restorer line for fertility rate, and the sensitivity varied between varieties. The fertility rate of the restorer line was maintained at about 90% under the high temperature treatments, while it decreased in the male sterile lines by 23.3 and 48.1% at 28 and 30°C, respectively. The fertility rate of the most sensitive line declined by 70%, and the tolerant line declined by 34% at 30°C. Glume closure in the male sterile lines was a major reason for the reduced fertility rate under high temperature, which is closely correlated with carbohydrates content and the vascular bundle pattern in the lodicule. The present study identified a useful trait to select male sterile lines with high temperature tolerance for seed production. PMID:28105031

  17. Rice planting systems, global warming and outbreaks of Nilaparvata lugens (Stål).

    PubMed

    Hu, G; Cheng, X N; Qi, G J; Wang, F Y; Lu, F; Zhang, X X; Zhai, B P

    2011-04-01

    Brown Planthopper (BPH, Nilaparvata lugens (Stål)) is one of the most serious pests of rice in both temperate and tropical regions of East and South Asia and has become especially problematic over the past few years. In order to analyze the effect of the change of rice cropping system on the population dynamics of BPH, field surveys of the occurrence and distribution of BPH were performed and other relevant data, including light trap data and ovary dissection data were collected in nearly 40 Chinese counties encompassing six provinces (or municipalities), including Hainan, Guangxi, Anhui, Shanghai, Fujian and Guangdong from April to October in 2007.The mixed planting areas of single- and double-cropping rice in China include Hubei, South and Central Anhui, North Hunan, and North Jiangxi. In these areas, double-cropping rice has now been greatly reduced and single-cropping rice has been rapidly increasing since 1997. The surveys revealed that when the immigration peak of BPH occurred in June and July, the single-cropping rice was at the tillering to booting stage and fit for BPH, but early rice had already matured and most of late rice had not yet been transplanted. BPH immigrants from southern rice areas prefer to inhabit and breed in single-cropping rice paddies. Moreover, farming activities between early rice and late rice interrupted the continuous growth of BPH populations in double-cropping rice paddies. As a result, in comparison with data collected 30 years ago, the spatiotemporal dynamics and migration patterns of BPH have dramatically changed in the lower-middle reaches of the Yangtze River. In the mixed planting areas, due to their high suitability, the BPH population in single-cropping rice grew so quickly that it caused serious local damage and there was mass emigration of macropterous progeny to the Yangtze River Delta in late August and early September.Global warming may also affect BPH populations, where results suggest steadily warmer autumns have

  18. Selection Under Domestication: Evidence for a Sweep in the Rice Waxy Genomic Region

    PubMed Central

    Olsen, Kenneth M.; Caicedo, Ana L.; Polato, Nicholas; McClung, Anna; McCouch, Susan; Purugganan, Michael D.

    2006-01-01

    Rice (Oryza sativa) was cultivated by Asian Neolithic farmers >11,000 years ago, and different cultures have selected for divergent starch qualities in the rice grain during and after the domestication process. An intron 1 splice donor site mutation of the Waxy gene is responsible for the absence of amylose in glutinous rice varieties. This mutation appears to have also played an important role in the origin of low amylose, nonglutinous temperate japonica rice varieties, which form a primary component of Northeast Asian cuisines. Waxy DNA sequence analyses indicate that the splice donor mutation is prevalent in temperate japonica rice varieties, but rare or absent in tropical japonica, indica, aus, and aromatic varieties. Sequence analysis across a 500-kb genomic region centered on Waxy reveals patterns consistent with a selective sweep in the temperate japonicas associated with the mutation. The size of the selective sweep (>250 kb) indicates very strong selection in this region, with an inferred selection coefficient that is higher than similar estimates from maize domestication genes or wild species. These findings demonstrate that selection pressures associated with crop domestication regimes can exceed by one to two orders of magnitude those observed for genes under even strong selection in natural systems. PMID:16547098

  19. Molecular Breeding Strategy and Challenges Towards Improvement of Blast Disease Resistance in Rice Crop

    PubMed Central

    Ashkani, Sadegh; Rafii, Mohd Y.; Shabanimofrad, Mahmoodreza; Miah, Gous; Sahebi, Mahbod; Azizi, Parisa; Tanweer, Fatah A.; Akhtar, Mohd Sayeed; Nasehi, Abbas

    2015-01-01

    Rice is a staple and most important security food crop consumed by almost half of the world’s population. More rice production is needed due to the rapid population growth in the world. Rice blast caused by the fungus, Magnaporthe oryzae is one of the most destructive diseases of this crop in different part of the world. Breakdown of blast resistance is the major cause of yield instability in several rice growing areas. There is a need to develop strategies providing long-lasting disease resistance against a broad spectrum of pathogens, giving protection for a long time over a broad geographic area, promising for sustainable rice production in the future. So far, molecular breeding approaches involving DNA markers, such as QTL mapping, marker-aided selection, gene pyramiding, allele mining and genetic transformation have been used to develop new resistant rice cultivars. Such techniques now are used as a low-cost, high-throughput alternative to conventional methods allowing rapid introgression of disease resistance genes into susceptible varieties as well as the incorporation of multiple genes into individual lines for more durable blast resistance. The paper briefly reviewed the progress of studies on this aspect to provide the interest information for rice disease resistance breeding. This review includes examples of how advanced molecular method have been used in breeding programs for improving blast resistance. New information and knowledge gained from previous research on the recent strategy and challenges towards improvement of blast disease such as pyramiding disease resistance gene for creating new rice varieties with high resistance against multiple diseases will undoubtedly provide new insights into the rice disease control. PMID:26635817