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Sample records for local rice varieties

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

    USDA-ARS?s Scientific Manuscript database

    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. Four new rice varieties for specialty markets

    USDA-ARS?s Scientific Manuscript database

    Although conventional long grain rice varieties are grown on over 75% of the acreage in the US, there is interest in developing rice cultivars which possess specific qualities required for certain value-added markets. USDA ARS researchers at Beaumont, TX and Stuttgart, AR, in various collaborations ...

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

    USDA-ARS?s Scientific Manuscript database

    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, ...

  4. 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.

  5. [Terpenoids in root exudates of different allelopathic rice varieties].

    PubMed

    He, Haibin; He, Huaqin; Lin, Wenxiong; Chen, Xiangxu; Jia, Xiaoli; Xiong, Jun; Shen, Lihua; Liang, Yiyuan

    2005-04-01

    In this paper, a strong allelopathic rice variety PI312777 and a weak allelopathic rice variety Lemont were used as test materials, and the root exudates of two rice varieties grown in the media of sand and soil were respectively collected by using circulation system approach. The terpenoids in ether-extracts were detected by GC-MS, and characterized by spectrum database. The results showed that some terpenoids such as limonene oxide, limonene dioxide, carvone oxide, carveol, and cedrol were detected in the ether-extracts. Different rice varieties had the similar kinds of terpenoids, but their existing modes and quantities were different. The differences between different various cultural methods and between rice varieties were further discussed.

  6. Dynamic vapor sorption isotherms of medium grain rice varieties

    USDA-ARS?s Scientific Manuscript database

    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...

  7. Do rice varieties have differences in their plant mineral nutrition?

    USDA-ARS?s Scientific Manuscript database

    As a first step, in 2007 and 2008, preliminary trials in both flooded and unflooded conditions were conducted on 1,643 rice varieties from more than 114 countries. These trials, conducted at the Texas AgriLife Research and Extension Center at Beaumont, identified differences in the mineral nutritio...

  8. Genetic Diversity and Population Structure of Rice Varieties Cultivated in Temperate Regions.

    PubMed

    Reig-Valiente, Juan L; Viruel, Juan; Sales, Ester; Marqués, Luis; Terol, Javier; Gut, Marta; Derdak, Sophia; Talón, Manuel; Domingo, Concha

    2016-12-01

    After its domestication, rice cultivation expanded from tropical regions towards northern latitudes with temperate climate in a progressive process to overcome limiting photoperiod and temperature conditions. This process has originated a wide range of diversity that can be regarded as a valuable resource for crop improvement. In general, current rice breeding programs have to deal with a lack of both germplasm accessions specifically adapted to local agro-environmental conditions and adapted donors carrying desired agronomical traits. Comprehensive maps of genome variability and population structure would facilitate genome-wide association studies of complex traits, functional gene investigations and the selection of appropriate donors for breeding purposes. A collection of 217 rice varieties mainly cultivated in temperate regions was generated. The collection encompasses modern elite and old cultivars, as well as traditional landraces covering a wide genetic diversity available for rice breeders. Whole Genome Sequencing was performed on 14 cultivars representative of the collection and the genomic profiles of all cultivars were constructed using a panel of 2697 SNPs with wide coverage throughout the rice genome, obtained from the sequencing data. The population structure and genetic relationship analyses showed a strong substructure in the temperate rice population, predominantly based on grain type and the origin of the cultivars. Dendrogram also agrees population structure results. Based on SNP markers, we have elucidated the genetic relationship and the degree of genetic diversity among a collection of 217 temperate rice varieties possessing an enormous variety of agromorphological and physiological characters. Taken together, the data indicated the occurrence of relatively high gene flow and elevated rates of admixture between cultivars grown in remote regions, probably favoured by local breeding activities. The results of this study significantly expand the

  9. 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.

  10. 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.

  11. 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.

  12. Association of Commercial Rice Varieties with Weedy Rice Accessions (Oryza sativa complex) in Pulau Pinang’s Rice Granary Area

    PubMed Central

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

    2011-01-01

    Weedy rice (WR) is the most significant weed in direct-seeded fields. It has morphological characteristics similar to those of cultivated rice varieties. WR is more difficult to control than other weeds. We collected WR accessions from four sites within the Pulau Pinang rice growing areas. Thirty six different accessions were collected from each site: B, the northern site; P, the central site; A, the southern site; and N, the southwestern site. Wild rice (Oryza rufipogon), which grows in the sampled areas, was also collected together with four varieties (MR84, MR185, MR211 and MR219) that have been widely planted in these areas for a long period of time. The objective of this study was to compare the morphological characteristics of the WR accessions and cultivated rice. Twenty characteristics were observed for the comparison of WR accessions and rice cultivars. Morpho-matrix analyses allowed the specimens to be grouped to two main groups (A and B), based on a 95% dissimilarity matrix. Group A was subdivided into 7 subgroups consisting of a few WR accessions, wild rice and MR211 (control), and group B was subdivided to 10 subgroups consisting of other WR accessions and the 3 other control varieties. Dendrogram analysis indicated that the morphological traits used in this study were able to differentiate among the WR accessions and the cultivars, except for rice cultivar MR211 and WRA8, which grouped together in subgroup A2. STRUCTURE program analysis indicated that all individuals were distinguishable and were divided into 18 clusters. These results suggest that some genes of the WR accessions have been influenced by commercial varieties. The information gained from this study will be useful to develop rice weed management protocols and good agricultural practices to control WR in the future. PMID:24575213

  13. 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.

  14. [Relationships between allelopathic traits and agronomic characters of allelopathic rice varieties].

    PubMed

    Zhou, Shaochuan; Kong, Chuihua; Li, Hong; Lu, Decheng; Hu, Fei

    2005-04-01

    By using specific secondary metabolites as markers, this paper determined the allelopathic indices of nine allelopathic rice varieties widely cultivated in South China, and evaluated the main agronomic characters of these varieties and their weed-inhibiting effects in field. The correlations among allelopathic indices, agronomic characters and weed-inhibiting effects of test rice varieties were also analyzed. The results indicated that not all the rice varieties demonstrated their weed-inhibiting effects in field, and there were no relationships between allelopathic traits and main agronomic characters. However, the rice varieties with both allelopathic traits and competitive agronomic characters could significantly inhibit the weeds in field. The non-correlation between allelopathic traits and main agronomic characters of test rice varieties suggested that the transfer of allelopathic traits into rice varieties did not affect their agronomic characters, i.e., it's possible to breed allelopathic rice cultivars with any agronomic characters.

  15. Tocopherol and tocotrienol contents of different varieties of rice in Malaysia.

    PubMed

    Shammugasamy, Balakrishnan; Ramakrishnan, Yogeshini; Ghazali, Hasanah M; Muhammad, Kharidah

    2015-03-15

    The present study examined the contents of tocopherols and tocotrienols and their distribution in 58 different varieties of whole rice cultivated in Malaysia. The analytical method used was saponification of samples followed by dispersive liquid-liquid microextraction and reverse phase high-performance liquid chromatography. The total vitamin E contents of different varieties of whole rice ranged between 19.36 and 63.29 mg kg⁻¹. Contents of vitamin E isomers varied among rice varieties both within and between grain color groups. Black-pigmented rice showed significantly higher mean contents of α-tocopherol, β-tocopherol and α-tocotrienol than non-pigmented rice and red-pigmented rice. Red-pigmented rice had significantly lower mean contents of γ-tocotrienol and total vitamin E than non-pigmented rice. The mean contents of δ-tocotrienol and total vitamin E in non-pigmented rice, however, were similar to those in black-pigmented rice. γ-Tocotrienol was the predominant form of vitamin E isomer in all analyzed varieties. The Pearson correlations among vitamin E isomers and total vitamin E content of whole rice were also studied. This study provides information on vitamin E content of different rice varieties that would be beneficial for decision making in genetic breeding of bioactive compound-rich rice varieties. © 2014 Society of Chemical Industry.

  16. [CH4 emission features of leading super-rice varieties and their relationships with the varieties growth characteristics in Yangtze Delta of China].

    PubMed

    Yan, Xiao-Jun; Wang, Li-Li; Jiang, Yu; Deng, Ai-Xing; Tian, Yun-Lu; Zhang, Wei-Jian

    2013-09-01

    A pot experiment was conducted to study the CH4 emission features of fourteen leading super-rice varieties (six Japonica rice varieties and eight Indica hybrid rice varieties) and their relationships with the varieties growth characteristics in Yangtze Delta. Two distinct peaks of CH4 emission were detected during the entire growth period of the varieties, one peak occurred at full-tillering stage, and the other appeared at booting stage. The average total CH4 emission of Japonica rice varieties was 37.6% higher than that of the Indica hybrid rice varieties (P<0.01), and the differences in the CH4 emission between rice types occurred at the post-anthesis phase. For all the varieties, there was a significant positive correlation between the total CH4 emission and the maximum leaf area, but the correlations between the CH4 emission and the other growth characteristics varied with variety type. The total CH4 emission of Japonica rice varieties had a significant positive correlation with plant height, while the correlations between the total CH4 emission of Indica hybrid rice varieties and their plant height were not significant. The total CH4 emission of Indica hybrid rice varieties had significant negative correlations with the total aboveground biomass, grain yield, and harvest index, but the correlations were not significant for Japonica rice varieties. The lower CH4 emission of Indica hybrid rice varieties was likely due to their significantly higher root biomass, as compared with Japonica rice varieties.

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

    USDA-ARS?s Scientific Manuscript database

    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...

  18. Phytochemical profiles and iron chelating capability of rice varieties

    USDA-ARS?s Scientific Manuscript database

    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 ...

  19. 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

  20. 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

  1. 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.

  2. 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.

  3. 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

  4. Consumer Acceptance and Preference Study (CAPS) on brown and undermilled Indian rice varieties in Chennai, India.

    PubMed

    Sudha, Vasudevan; Spiegelman, Donna; Hong, Biling; Malik, Vasanti; Jones, Clara; Wedick, Nicole M; Hu, Frank B; Willett, Walter; Bai, Mookambika Ramya; Ponnalagu, Muthu Mariyammal; Arumugam, Kokila; Mohan, Viswanathan

    2013-01-01

    To study consumer acceptance of unmilled brown and undermilled rice among urban south Indians. Overweight and normal weight adults living in slum and nonslum residences in Chennai participated (n = 82). Bapatla (BPT) and Uma (red pigmented) rice varieties were chosen. These rice varieties were dehusked (unmilled, 0% polish) and further milled to 2.3% and 4.4% polishing (undermilled). Thus, 9 rice samples in both raw and parboiled forms were provided for consumer tasting over a period of 3 days. A 7-point hedonic scale was used to rate consumer preferences. A validated questionnaire was used to collect demographic, anthropometric, medical history, physical activity, dietary intake data, and willingness of the consumers to switch over to brown rice. Consumers reported that the color, appearance, texture, taste, and overall quality of the 4.4% polished rice was strongly preferred in both varieties and forms. Ratings for 0% polished (brown rice) were substantially lower than those of 2.3% polished rice, which were intermediate in ratings between 0% and 4.4% polishing. However, most of the consumers (93%) expressed a willingness to substitute brown or 2.3% polished rice, if affordable, after the taste tests and education on nutritional and health benefits of whole grains. Though most consumers preferred polished white rice, education regarding health benefits may help this population switch to brown or undermilled rice. Cooking quality and appearance of the grains were perceived as the most important factors to consider when purchasing rice among Chennai urban adults.

  5. Phytochemical profiles and antioxidant activity of brown rice varieties.

    PubMed

    Gong, Er Sheng; Luo, Shun Jing; Li, Tong; Liu, Cheng Mei; Zhang, Guo Wen; Chen, Jun; Zeng, Zi Cong; Liu, Rui Hai

    2017-07-15

    The phytochemical content and antioxidant activity of eight varieties of brown rice (BR) are reported. The total phenolic contents of BR ranged from 72.45 to 120.13mg of gallic acid equiv./100g. The phenolics from bound fraction contributed 40.6-50.2% of the total phenolic content. The total flavonoid contents of BR ranged from 75.90 to 112.03mg catechin equiv./100g. The flavonoids from the bound fraction contributed 26.9-48.2% of total flavonoids. Trans-ferulic acid was the predominant phenolic acid in BR. Total trans-ferulic acid content ranged from 161.42 to 374.81μg/100g. The percentage of trans-ferulic acid in bound fraction ranged from 96.4% to 99.2%. Only α- and γ-tocopherols and -tocotrienols were detected in BR with α-tocopherol and γ-tocotrienol being the predominant. The total peroxyl radical scavenging capacity (PSC) of BR ranged from 18.29 to 40.33mg vitamin C equiv./100g. The bound fraction contributed 67.2-77.2% of total PSC. Copyright © 2017 Elsevier Ltd. All rights reserved.

  6. 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.

  7. Nutritional and sensory profile of two Indian rice varieties with different degrees of polishing.

    PubMed

    Shobana, S; Malleshi, N G; Sudha, V; Spiegelman, D; Hong, B; Hu, F B; Willett, W C; Krishnaswamy, K; Mohan, V

    2011-12-01

    Traditional hand-pounded rice has been replaced today with highly polished white rice in the Asian Indian diets. The study aimed to evaluate the nutritional as well as the sensory differences between the brown (0% polish) and the rice milled to different degrees of polish (2.3, 4.4 and 8.0%). Bapatla and Uma (red pigmented) varieties in both raw and parboiled forms were used. The protein, fat, dietary fibre, γ-oryzanol, polyphenols, vitamin E, total antioxidant activity and free radical scavenging abilities of the brown rice decreased while the available carbohydrates increased with polishing. Sensory attributes of the cooked rice samples (whiteness, grain intactness, fluffiness, firmness, stickiness, chewiness and the cooked rice aroma) were evaluated by trained panelists. Scores for branny taste and chewiness decreased with polishing. On the whole, brown rice of both the varieties was readily accepted by the well-informed sensory trained panelists.

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

    USDA-ARS?s Scientific Manuscript database

    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...

  9. 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.

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

    USDA-ARS?s Scientific Manuscript database

    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...

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

    USDA-ARS?s Scientific Manuscript database

    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...

  12. Integrating choice of variety, soil amendments, and cover crops to optimize organic rice production

    USDA-ARS?s Scientific Manuscript database

    We have completed our first year of this project to determine the impact of winter cover crops, soil amendments, and rice varieties on organic rice production at Beaumont, TX. Two winter cover crops were established successfully and the amounts of dry biomass produced were 4,690 and 5,157 lb/acre f...

  13. 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.

  14. 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

  15. 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.

  16. Rice Varieties in Archaic East Asia: Reduction of Its Diversity from Past to Present Times.

    PubMed

    Kumagai, Masahiko; Kanehara, Masaaki; Shoda, Shin'ya; Fujita, Saburo; Onuki, Shizuo; Ueda, Shintaroh; Wang, Li

    2016-10-01

    The Asian cultivated rice, Oryza sativa, is one of the most important crops feeding more than a third of global population. In spite of the studies for several decades, the origin and domestication history of rice varietal groups, japonica and indica, have not been fully unveiled. Genetic information of ancient rice remains is essential for direct and exclusive insight into the domestication history of rice. We performed ancient DNA analysis of 950- to 2,800-year-old rice remains excavated from Japan and Korea. We found the presence of both japonica- and indica-type varieties in the Yayoi period and the middle ages of Japan and the middle part of Korea Peninsula 2,000 years ago. It is popularly considered that japonica has been exclusively cultivated in northern part of East Asia including Japan and Korea. Our result disclosed unexpectedly wide diversity of rice varieties in archaic East Asia. The present results from ancient rice DNA reveal an exclusive insight for the domestication history of rice which is not provided as far as contemporary rice. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  17. 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

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

    PubMed

    Pang, Yunlong; Ali, Jauhar; 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.

  19. 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.

  20. Assessment of the quality of bran and bran oil produced from some Egyptian rice varieties.

    PubMed

    Salem, Eglal G; El Hissewy, Ahmed; Agamy, Neveen F; Abd El Barry, Doaa

    2014-04-01

    Rice (Oryza sativa L.) is one of the leading food crops of the world, the staple food of over half the world's population. The bran, which is an important byproduct obtained during rice milling, constitutes about 1/10 of the weight of the rice grain. Rice bran is the outer brown layer including the rice germ that is removed during the milling process of brown grain. This milling byproduct is reported to be high in natural vitamins and minerals, particularly vitamin E. The present study was conducted to determine the chemical composition of bran and bran oil of 13 different rice varieties commonly produced in Egypt, to study the utilization of rice bran in bread production, and to assess the quality and acceptance of the rice bran edible oil produced. Rice bran was produced from 13 Egyptian varieties of recently harvested rice as well as from paddy rice stored for 1 year. The extracted bran was immediately stabilized then subjected to chemical analysis (such as moisture content, protein, fat, carbohydrates, fiber, and ash) as well as trace and heavy metals determination (P, K, Na, Ca, Fe, Zn, Cu, and Mg). Bread was produced by adding Giza172 rice bran at three different concentrations to wheat flour then subjected to chemical analysis, caloric content, and organoleptic examination. Bran oil was extracted from the different varieties of rice bran (recently harvested and stored) then subjected to chemical and organoleptic examinations as well as vitamin E and oryzanol determination. The percentage of rice bran of newly harvested Egyptian rice was 11.68% and was 10.97% in stored rice. The analysis showed mean values of 5.91 and 5.53% for moisture, 14.60 and 14.40% for crude protein, 14.83 and 15.20% for fat, 44.77 and 45.40% for carbohydrates, 6.55 and 7.06% for crude fiber, and 8.87 and 8.50% for ash for newly harvested and stored rice bran, respectively. Bread containing 15% rice bran showed the highest score percentages for organoleptic quality compared with the

  1. 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.

  2. Glycaemic index (GI) of an Indian branded thermally treated basmati rice variety: a multi centric study.

    PubMed

    Srinivasa, Dinesh; Raman, Abhi; Meena, P; Chitale, Geetanjali; Marwahat, Ankita; Jainani, Kiran J

    2013-10-01

    Glycaemic Index (GI) is the classification of carbohydrates based on their ability to raise blood glucose levels and evidence shows that its usage has beneficial health implications. Rice forms a part of the Indian staple diet and one of the major energy contributors. Hence, it is important to establish the Glycaemic Index (GI) value of rice. However, due to availability of different varieties of rice it is important first to identify a lower GI variety and to make it available to the Indian population. Subjecting rice to thermal processing is also known to reduce the GI of rice. An Indian thermally treated basmati rice variety was hypothesised to be low in GI. This multi centric study was conducted to test this hypothesis in healthy volunteers. In this study, out of 83 participants, data points of 70 healthy volunteers were taken into consideration for arriving at the final GI value. The study procedure was similar to the recommendations by FAO/WHO. A multi centric trial was conducted to nullify any regional or genetic variability. It was observed that reference glucose curve had the maximum average peak of 166.37 mg/dL while the basmati sample had a lower peak (136.22 mg/dL). The mean blood glucose incremental area under the curve for reference food was 5969.64 mins.mg/dL (SEM 95.94) and for rice it was 3267.81 mins. mg/dL (SEM 76.21). In this studyThe GI of Indian branded basmati rice was found to < 55 thus, placing it in lower GI category. The Indian basmati rice because of its lower GI can prove to be a healthier rice alternative.

  3. 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

  4. [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.

  5. 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.

  6. Phenolic profiles and antioxidant activity of black rice bran of different commercially available varieties.

    PubMed

    Zhang, Ming Wei; Zhang, Rui Feng; Zhang, Fang Xuan; Liu, Rui Hai

    2010-07-14

    Increased consumption of whole grains has been associated with reduced risk of developing major chronic diseases. These health benefits have been attributed in part to their unique phytochemicals. Previous studies on black rice mainly focused on anthocyanins. Little is known about the phytochemical profiles and antioxidant activities of different black rice varieties. The objective of this study was to determine the phytochemical profiles and antioxidant activity of rice bran samples from 12 diverse varieties of black rice. The free, bound, and total phenolic contents of black rice bran samples ranged from 2086 to 7043, from 221.2 to 382.7, and from 2365 to 7367 mg of gallic acid equiv/100 g of dry weight (DW), respectively. The percentage contribution of free phenolics to the total ranged from 88.2 to 95.6%. The average values of free, bound, and total phenolic contents of black rice bran were 8, 1.5, and 6 times higher than those of white rice bran, respectively (p < 0.05). The free, bound, and total flavonoid contents of black rice bran samples ranged from 3462 to 12061, from 126.7 to 386.9, and from 3596 to 12448 mg of catechin equiv/100 g of DW, respectively. The percentage contribution of free flavonoids to the total ranged from 96.3 to 97.6%. The average values of free, bound, and total flavonoid contents of black rice bran were 7.4, 1.9, and 6.7 times higher than those of white rice bran, respectively (p < 0.05). The free, bound, and total anthocyanin contents of black rice bran samples ranged from 1227 to 5096, from 4.89 to 8.23, and from 1231 to 5101 mg of cyanidin-3-glucoside equiv/100 g of DW, respectively. The percentage contribution of free anthocyanins to the total ranged from 99.5 to 99.9%. Cyanidin-3-glucoside, cyanidin-3-rutinoside, and peonidin-3-glucoside were detected in black rice bran samples and ranged from 736.6 to 2557, from 22.70 to 96.62, and from 100.7 to 534.2 mg/100 g of DW, respectively. The free, bound, and total antioxidant

  7. Effect of allelopathic rice varieties combined with cultural management options on paddy field weeds.

    PubMed

    Kong, Chui-Hua; Hu, Fei; Wang, Peng; Wu, Jing-Lun

    2008-03-01

    A number of techniques, including cultural management, allelopathy and bioherbicide, have been considered as alternatives for synthetic herbicides, but successful weed control will require the careful integration of these multiple techniques. This study was conducted to assess the use of allelopathic rice varieties in combination with cultural management options on paddy weeds, in order to develop an allelopathy-based technique to reduce herbicide use in paddies. The weed-suppressive effects of the rice varieties tested varied highly with allelopathic trait, planting pattern and cultural management including planting density, flooding depth and duration and supply of nitrogen. Allelopathic rice varieties PI312777 and Huagan-1 demonstrated much stronger weed suppression than the non-allelopathic variety Huajianxian under the same planting pattern and cultural management. Their weed-suppressive effect was increased with cultural management options. In particular, if integrated cultural management options of allelopathic rice varieties included a low-dose (bensulfuron-methyl, 25 g AI ha(-1), a third of the recommended dose) herbicide application, the emergence and growth of most weeds found in paddy fields was completely controlled. No grain yield reduction for allelopathic varieties occurred under integrated cultural management options, whereas with the non-allelopathic variety a reduction of up to 45-60% was measurable even with the low-dose herbicide application. The allelopathic potential of rice varieties will likely have a great impact on paddy weed control if integrated with cultural management options and application of low doses of herbicides. Therefore, it is feasible to reduce herbicide input in paddies if allelopathic rice is grown under integrated cultural management practices. (c) 2008 Society of Chemical Industry.

  8. 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.

  9. 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.

  10. 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.

  11. 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

  12. 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

  13. 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.

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

    USDA-ARS?s Scientific Manuscript database

    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. 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.

  16. 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.

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

    USDA-ARS?s Scientific Manuscript database

    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...

  18. Genetic diversity trend in Indian rice varieties: an analysis using SSR markers.

    PubMed

    Singh, Nivedita; Choudhury, Debjani Roy; Tiwari, Gunjan; Singh, Amit Kumar; Kumar, Sundeep; Srinivasan, Kalyani; Tyagi, R K; Sharma, A D; Singh, N K; Singh, Rakesh

    2016-09-05

    The knowledge of the extent and pattern of diversity in the crop species is a prerequisite for any crop improvement as it helps breeders in deciding suitable breeding strategies for their future improvement. Rice is the main staple crop in India with the large number of varieties released every year. Studies based on the small set of rice genotypes have reported a loss in genetic diversity especially after green revolution. However, a detailed study of the trend of diversity in Indian rice varieties is lacking. SSR markers have proven to be a marker of choice for studying the genetic diversity. Therefore, the present study was undertaken with the aim to characterize and assess trends of genetic diversity in a large set of Indian rice varieties (released between 1940-2013), conserved in the National Gene Bank of India using SSR markers. A set of 729 Indian rice varieties were genotyped using 36 HvSSR markers to assess the genetic diversity and genetic relationship. A total of 112 alleles was amplified with an average of 3.11 alleles per locus with mean Polymorphic Information Content (PIC) value of 0.29. Cluster analysis grouped these varieties into two clusters whereas the model based population structure divided them into three populations. AMOVA study based on hierarchical cluster and model based approach showed 3 % and 11 % variation between the populations, respectively. Decadal analysis for gene diversity and PIC showed increasing trend from 1940 to 2005, thereafter values for both the parameters showed decreasing trend between years 2006-2013. In contrast to this, allele number demonstrated increasing trend in these varieties released and notified between1940 to 1985, it remained nearly constant during 1986 to 2005 and again showed an increasing trend. Our results demonstrated that the Indian rice varieties harbors huge amount of genetic diversity. However, the trait based improvement program in the last decades forced breeders to rely on few parents, which

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

    USDA-ARS?s Scientific Manuscript database

    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 ...

  20. 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

  1. Aflatoxin contamination in stored rice variety PAU 201 collected from Punjab, India

    PubMed Central

    Siruguri, Vasanthi; Kumar, P Uday; Raghu, P.; Rao, M Vishnu Vardhana; Sesikeran, B.; Toteja, G. S.; Gupta, Priyanka; Rao, Spriha; Satyanarayana, K.; Katoch, V.M.; Bharaj, T.S.; Mangat, G.S.; Sharma, Neerja; Sandhu, J.S.; Bhargav, V.K.; Rani, Shobha

    2012-01-01

    Background & objectives: The present study was carried out on stored rice variety PAU 201 in Punjab that was not permitted for milling and public distribution due to the presence of damaged grains at levels exceeding the regulatory limits of 4.75 per cent. The aim of the study was to determine fungal and aflatoxin contamination in the rice samples to assess hazard from the presence of damaged grains. Presence of iron in discoloured rice grains was also assessed. Methods: Stored samples of paddy of PAU 201 rice variety were collected from six districts of Punjab, milled and analysed for presence of fungal and aflatoxin contamination. Scanning electron microscopy (SEM), energy dispersive X-ray (EDX) analysis and Prussian blue staining was used to determine fungal spores and presence of iron, respectively. Results: Aflatoxin analysis of rice samples indicated that none exceeded the Food Safety and Standards (Contaminants, Toxins and Residues) Regulations, 2011 tolerance limit of 30 μg/kg and majority of the samples had levels <15 μg/kg. The proportion of damaged grains exceeding the limit of 5 per cent was observed in 85.7 per cent of the samples. SEM and Prussian blue staining and EDX analysis of black tipped and pin point damaged rice grains did not show presence of fungal structures and presence of iron. Interpretation & conclusions: The results of the study indicated that the stored rice samples did not pose any health concern with respect to aflatoxin contamination as per the criteria laid down by the Food Safety and Standards Authority of India. PMID:22885269

  2. Aflatoxin contamination in stored rice variety PAU 201 collected from Punjab, India.

    PubMed

    Siruguri, Vasanthi; Kumar, P Uday; Raghu, P; Rao, M Vishnu Vardhana; Sesikeran, B; Toteja, G S; Gupta, Priyanka; Rao, Spriha; Satyanarayana, K; Katoch, V M; Bharaj, T S; Mangat, G S; Sharma, Neerja; Sandhu, J S; Bhargav, V K; Rani, Shobha

    2012-07-01

    The present study was carried out on stored rice variety PAU 201 in Punjab that was not permitted for milling and public distribution due to the presence of damaged grains at levels exceeding the regulatory limits of 4.75 per cent. The aim of the study was to determine fungal and aflatoxin contamination in the rice samples to assess hazard from the presence of damaged grains. Presence of iron in discoloured rice grains was also assessed. Stored samples of paddy of PAU 201 rice variety were collected from six districts of Punjab, milled and analysed for presence of fungal and aflatoxin contamination. Scanning electron microscopy (SEM), energy dispersive X-ray (EDX) analysis and Prussian blue staining was used to determine fungal spores and presence of iron, respectively. Aflatoxin analysis of rice samples indicated that none exceeded the Food Safety and Standards (Contaminants, Toxins and Residues) Regulations, 2011 tolerance limit of 30 μg/kg and majority of the samples had levels <15 μg/kg. The proportion of damaged grains exceeding the limit of 5 per cent was observed in 85.7 per cent of the samples. SEM and Prussian blue staining and EDX analysis of black tipped and pin point damaged rice grains did not show presence of fungal structures and presence of iron. The results of the study indicated that the stored rice samples did not pose any health concern with respect to aflatoxin contamination as per the criteria laid down by the Food Safety and Standards Authority of India.

  3. Effect of different cooking methods on glycaemic index of Indian and Pakistani basmati rice varieties.

    PubMed

    Gunathilaka, M D T L; Ekanayake, S

    2015-06-01

    Glycaemic index (GI) reflects the blood glucose response after ingestion of a 50 g digestible carbohydrate portion. Many factors affect the GI, including degree of starch gelatinization. The objective was to determine the GI and the effect of different cooking methods on GI of a Pakistani basmati rice (PBR) and an Indian basmati rice (IBR) frequently purchased by Sri Lankans. This was a crossover study. Participants were ten healthy individuals aged 20-30 years whose BMI range was 18.5-23.5 kgm(-2). Proximate composition, [carbohydrate, protein, fat, soluble dietary fibre (SDF), insoluble dietary fibre (IDF) and ash], amylose content and GI of the two rice varieties were determined by using standard methods. Rice was cooked separately in a rice cooker and a microwave by adding 1 cup of rice (110 g) and 1 cup of water (150 ml)). Glucose was used as the standard. GI values were expressed as the average value of 10 participants. Fat, total dietary fibre (TDF), SDF and IDF contents were significantly (p<0.05) higher in IBR when compared to PBR. The GI values of IBR and PBR cooked in a rice cooker (GI=54 SD=8; GI=64 SD=12) or microwave (GI=43 SD=28; GI=56 SD=12) belonged to low and medium GI categories respectively. A percentage reduction in GI values was seen in PBR (12.5%) and IBR (20.4%) when cooked in a microwave oven compared to a rice cooker. Irrespective of the method of cooking PBR had medium GI and IBR had low GI.

  4. The effect of alternate wetting and drying on methane fluxes on different varieties of European rice

    NASA Astrophysics Data System (ADS)

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

    2017-04-01

    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. The work presented here evaluated the impacts of AWD on the productivity and yield of twelve varieties of European rice, whilst simultaneously measuring CH4 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). Greenhouse gas fluxes were taken using the static chamber approach 11 times during the growing season between May and October 2015. Environmental variables (soil moisture, temperature, water table depth, water potential) were collected concomitantly. Above and belowground biomass were determined by destructively harvesting at the end of the growing season. Belowground biomass was estimated by manually extracting roots from 30 cm deep soil cores and aboveground biomass estimated by collecting and

  5. 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.

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

    SciTech Connect

    Kaur, Jaspreet Kumar, Anil

    2016-05-06

    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.

  7. Genetic Variation in Biomass Traits among 20 Diverse Rice Varieties1[W][OA

    PubMed Central

    Jahn, Courtney E.; Mckay, John K.; Mauleon, Ramil; Stephens, Janice; McNally, Kenneth L.; Bush, Daniel R.; Leung, Hei; Leach, Jan E.

    2011-01-01

    Biofuels provide a promising route of producing energy while reducing reliance on petroleum. Developing sustainable liquid fuel production from cellulosic feedstock is a major challenge and will require significant breeding efforts to maximize plant biomass production. Our approach to elucidating genes and genetic pathways that can be targeted for improving biomass production is to exploit the combination of genomic tools and genetic diversity in rice (Oryza sativa). In this study, we analyzed a diverse set of 20 recently resequenced rice varieties for variation in biomass traits at several different developmental stages. The traits included plant size and architecture, aboveground biomass, and underlying physiological processes. We found significant genetic variation among the 20 lines in all morphological and physiological traits. Although heritability estimates were significant for all traits, heritabilities were higher in traits relating to plant size and architecture than for physiological traits. Trait variation was largely explained by variety and breeding history (advanced versus landrace) but not by varietal groupings (indica, japonica, and aus). In the context of cellulosic biofuels development, cell wall composition varied significantly among varieties. Surprisingly, photosynthetic rates among the varieties were inversely correlated with biomass accumulation. Examining these data in an evolutionary context reveals that rice varieties have achieved high biomass production via independent developmental and physiological pathways, suggesting that there are multiple targets for biomass improvement. Future efforts to identify loci and networks underlying this functional variation will facilitate the improvement of biomass traits in other grasses being developed as energy crops. PMID:21062890

  8. Morpho-physiological analysis of tolerance to aluminum toxicity in rice varieties of North East India.

    PubMed

    Awasthi, Jay Prakash; Saha, Bedabrata; Regon, Preetom; Sahoo, Smita; Chowra, Umakanta; Pradhan, Amit; Roy, Anupam; Panda, Sanjib Kumar

    2017-01-01

    Aluminum (Al) is the third most abundant metal in earth crust, whose chemical form is mainly dependent on soil pH. The most toxic form of Al with respect to plants is Al3+, which exists in soil pH <5. Acidic soil significantly limits crop production mainly due to Al3+ toxicity worldwide, impacting approximately 50% of the world's arable land (in North-Eastern India 80% soil are acidic). Al3+ toxicity in plants ensues root growth inhibition leading to less nutrient and water uptake impacting crop productivity as a whole. Rice is one of the chief grains which constitutes the staple food of two-third of the world population including India and is not untouched by Al3+ toxicity. Al contamination is a critical constraint to plant production in agricultural soils of North East India. 24 indigenous Indica rice varieties (including Badshahbhog as tolerant check and Mashuri as sensitive check) were screened for Al stress tolerance in hydroponic plant growth system. Results show marked difference in growth parameters (relative growth rate, Root tolerance index, fresh and dry weight of root) of rice seedlings due to Al (100 μM) toxicity. Al3+ uptake and lipid peroxidation level also increased concomitantly under Al treatment. Histochemical assay were also performed to elucidate uptake of aluminum, loss of membrane integrity and lipid peroxidation, which were found to be more in sensitive genotypes at higher Al concentration. This study revealed that aluminum toxicity is a serious harmful problem for rice crop productivity in acid soil. Based on various parameters studied it's concluded that Disang is a comparatively tolerant variety whereas Joymati a sensitive variety. Western blot hybridization further strengthened the claim, as it demonstrated more accumulation of Glutathione reductase (GR) protein in Disang rice variety than Joymati under stressed condition. This study also observed that the emergence of lethal toxic symptoms occurs only after 48h irrespective of the dose

  9. 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

  10. 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

  11. 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

  12. Even minimal polishing of an Indian parboiled brown rice variety leads to increased glycemic responses.

    PubMed

    Shobana, Shanmugam; Lakshmipriya, Nagarajan; Bai, Mookambika Ramya; Gayathri, Rajagopal; Ruchi, Vaidya; Sudha, Vasudevan; Malleshi, Nagappa G; Krishnaswamy, Kamala; Henry, C-J K; Anjana, Ranjit Mohan; Unnikrishnan, Ranjit; Mohan, Viswanathan

    2017-01-01

    To evaluate the effect of polishing on the glycemic properties of Indian parboiled brown rice. We evaluated the effect of different degrees of polishing on the glycemic and insulinemic responses of Bapatla (BPT-5204), Indian parboiled Indica rice variety. Brown rice (BR), under milled rice (UMR) and white rice (WR) with 2.3% and 9.7% degree of polishing (DOP), respectively, were prepared and evaluated for the glycemic properties. Incremental Area Under the Curves (IAUC) were estimated for both glycemic index (GI) in 12 healthy participants (6 men, 6 women) and 24 hr glycemic response studies in 13 overweight participants (5 men, 8 women) using continuous glucose monitoring (CGM) system with ≈2000 kcal/day rice diets. Differences in pre and post meal insulin (Δ) were assessed. The GI of WR (GI=79.6) and UMR (GI=73) were significantly higher than BR (GI=57.6) (p<0.01). Similar results were obtained for 24 hr glycemic responses [IAUC: WR=58.4, UMR=55.5, BR=34.7 mg*5 min/dL, respectively]. The Δ Insulin responses were lower with BR meals compared with UMR and WR (p=0.025; p=0.003). Both UMR and WR had a high GI while BR had a medium GI. This could have influenced the 24 h glycaemic and insulinemic responses of BR which had the lowest responses as compared with UMR and WR, and the latter two had similar higher responses. Thus any degree of polishing leads to higher glycaemic responses.

  13. 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.

  14. 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.

  15. [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

  16. 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

  17. Resistant Starch: Variation among High Amylose Rice Varieties and Its Relationship with Apparent Amylose Content, Pasting Properties and Cooking Methods

    USDA-ARS?s Scientific Manuscript database

    Resistant starch (RS), which is not hydrolyzed in the small intestines, has proposed health benefits. We evaluated a set of 40 high amylose rice varieties for RS levels in cooked rice and approximately a 1.9-fold difference was found. The highest ones had more than two-fold greater RS concentration ...

  18. Drought susceptibility of modern rice varieties: an effect of linkage of drought tolerance with undesirable traits

    PubMed Central

    Vikram, Prashant; Swamy, B. P. Mallikarjuna; Dixit, Shalabh; Singh, Renu; Singh, Bikram P.; Miro, Berta; Kohli, Ajay; Henry, Amelia; Singh, N. K.; Kumar, Arvind

    2015-01-01

    Green Revolution (GR) rice varieties are high yielding but typically drought sensitive. This is partly due to the tight linkage between the loci governing plant height and drought tolerance. This linkage is illustrated here through characterization of qDTY1.1, a QTL for grain yield under drought that co-segregates with the GR gene sd1 for semi-dwarf plant height. We report that the loss of the qDTY1.1 allele during the GR was due to its tight linkage in repulsion with the sd1 allele. Other drought-yield QTLs (qDTY) also showed tight linkage with traits rejected in GR varieties. Genetic diversity analysis for 11 different qDTY regions grouped GR varieties separately from traditional drought-tolerant varieties, and showed lower frequency of drought tolerance alleles. The increased understanding and breaking of the linkage between drought tolerance and undesirable traits has led to the development of high-yielding drought-tolerant dwarf lines with positive qDTY alleles and provides new hope for extending the benefits of the GR to drought-prone rice-growing regions. PMID:26458744

  19. TNAURice: Database on rice varieties released from Tamil Nadu Agricultural University.

    PubMed

    Ramalingam, Jegadeesan; Arul, Loganathan; Sathishkumar, Natarajan; Vignesh, Dhandapani; Thiyagarajan, Katiannan; Samiyappan, Ramasamy

    2010-11-27

    WE DEVELOPED, TNAURICE: a database comprising of the rice varieties released from a public institution, Tamil Nadu Agricultural University (TNAU), Coimbatore, India. Backed by MS-SQL, and ASP-Net at the front end, this database provide information on both quantitative and qualitative descriptors of the rice varities inclusive of their parental details. Enabled by an user friendly search utility, the database can be effectively searched by the varietal descriptors, and the entire contents are navigable as well. The database comes handy to the plant breeders involved in the varietal improvement programs to decide on the choice of parental lines. TNAURice is available for public access at http://www.btistnau.org/germdefault.aspx.

  20. TNAURice: Database on rice varieties released from Tamil Nadu Agricultural University

    PubMed Central

    Ramalingam, Jegadeesan; Arul, Loganathan; Sathishkumar, Natarajan; Vignesh, Dhandapani; Thiyagarajan, Katiannan; Samiyappan, Ramasamy

    2010-01-01

    We developed, TNAURice: a database comprising of the rice varieties released from a public institution, Tamil Nadu Agricultural University (TNAU), Coimbatore, India. Backed by MS-SQL, and ASP-Net at the front end, this database provide information on both quantitative and qualitative descriptors of the rice varities inclusive of their parental details. Enabled by an user friendly search utility, the database can be effectively searched by the varietal descriptors, and the entire contents are navigable as well. The database comes handy to the plant breeders involved in the varietal improvement programs to decide on the choice of parental lines. TNAURice is available for public access at http://www.btistnau.org/germdefault.aspx. PMID:21364829

  1. 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.

  2. 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

  3. 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.

  4. 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

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. Identification of two phytotoxins, blumenol A and grasshopper ketone, in the allelopathic Japanese rice variety Awaakamai.

    PubMed

    Kato-Noguchi, Hisashi; Tamura, Kazuya; Sasaki, Hiroaki; Suenaga, Kiyotake

    2012-05-01

    Aqueous methanol extracts of the traditional rice (Oryza sativa) variety Awaakamai, which is known to have the greatest allelopathic activity among Japanese traditional rice varieties, inhibited the growth of roots and shoots of cress (Lepidium sativum), lettuce (Lactuca sativa), timothy (Phleum pratense), Digitaria sanguinalis, Lolium multiflorum and Echinochloa crus-galli. Increasing the extract concentration increased the inhibition, suggesting that the extract of Awaakamai contains growth inhibitory substances. The extract of Awaakamai was purified and two main growth inhibitory substances were isolated and determined by spectral data as blumenol A and grasshopper ketone. Blumenol A and grasshopper ketone, respectively, inhibited the growth of cress shoots and roots at concentrations greater than 10 and 30 μmol/L. The concentrations required for 50% growth inhibition on cress roots and shoots were 84 and 27 μmol/L, respectively, for blumenol A, and 185 and 76 μmol/L, respectively, for grasshopper ketone. These results suggest that blumenol A and grasshopper ketone may contribute to the growth inhibitory effect of Awaakamai and may play an important role in the allelopathy of Awaakamai. Copyright © 2012 Elsevier GmbH. All rights reserved.

  10. 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.

  11. 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.

  12. 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.

  13. 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

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

    USDA-ARS?s Scientific Manuscript database

    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...

  15. 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.

  16. The Inhibitory Effect of Grasshopper's Cyperus (Cyperus iria L.) on the Seedling Growth of Five Malaysian Rice Varieties.

    PubMed

    Ismail, B S; Siddique, Mohammed Abu Bakar

    2011-05-01

    Experiments were carried out in the laboratory and greenhouse to determine the growth inhibitory effects of Grassohopper's cyperus (Cyperus iria L.) on the seedlings of 5 Malaysian rice varieties namely MR211, MRQ74, MR220, MR84 and MR232. Three concentrations of the aqueous extract of the weed (12.5, 25.0 and 50.0 g/l) and weed debris (5, 10 and 20 g dry debris/1000 g soil) were used to test the allelopathic effect of C. iria on the growth of the rice plants. The weed leaf, stem and root extracts reduced the growth of the rice seedlings and showed selective activity in the varieties. The C. iria leaf and stem extracts showed comparatively higher growth inhibitory effects than those from the root. The weed extract caused more reduction in the root length of the rice plant compared to the shoot length. Among the rice varieties tested, MR232 was found to be more susceptible to the weed inhibitory effect. The leaf extract of C. iria at full strength caused root and shoot reduction of MR232 by 88.1% and 73.1% respectively (compared to the control). In most cases the fresh weight of the rice seedlings were more affected than the plant height. Weed debris caused significant reduction of leaf chlorophyll content in all the rice varieties tested with the exception of MR211. The chlorophyll content of MR232 was greatly affected by the weed debris which caused reduction of 36.4% compared to the control. The inhibitory effects of weed extracts and debris on rice growth parameters were found to be concentration dependent.

  17. 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.

  18. 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.

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

    PubMed Central

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

    2012-01-01

    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. PMID:22499169

  20. 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.

  1. 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.

  2. 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. Copyright © 2016 Elsevier Inc. All rights reserved.

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

    PubMed Central

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

    2016-01-01

    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 eleven seasonings to prepare two 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=1,025), 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=0.02, p=0.01; 1.31 and 1.23 servings/day in T2 and T3 versus 1.02 servings/day in T1, p<0.05) and rice (β=0.04, p=0.005) 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. PMID:27440532

  4. 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.

  5. Resistant starch: Variation among high amylose rice varieties and its relationship with apparent amylose content, pasting properties and cooking methods.

    PubMed

    Chen, Ming-Hsuan; Bergman, Christine J; McClung, Anna M; Everette, Jace D; Tabien, Rodante E

    2017-11-01

    Resistant starch (RS), which is not hydrolyzed in the small intestine, has proposed health benefits. We evaluated 40 high amylose rice varieties for RS content in cooked rice and a 1.9-fold difference was found. Some varieties had more than two-fold greater RS content than a US long-grain intermediate-amylose rice. The high amylose varieties were grouped into four classes according to paste viscosity and gelatinization temperature based on genetic variants of the Waxy and Starch Synthase IIa genes, respectively. RS content was not different between the four paste viscosity-gelatinization temperature classes. Multiple linear regression analysis showed that apparent amylose content and pasting temperature were strong predictors of RS within each class. Two cooking methods, fixed water-to-rice ratio/time and in excess-water/minimum-cook-time, were compared using six rice varieties that were extremes in RS in each of the genetic variant classes, no difference in RS content due to cooking method was observed. Published by Elsevier Ltd.

  6. Genetic signature of rice domestication shown by a variety of genes.

    PubMed

    Zhang, Yuanli; Wang, Jiao; Zhang, Xiaohui; Chen, Jian-Qun; Tian, Dacheng; Yang, Sihai

    2009-04-01

    Cultivated rice was domesticated from common wild rice. However, little is known about genetic adaptation under domestication. We investigated the nucleotide variation of both cultivated rice and its wild progenitors at 22 R-gene and 10 non-R-gene loci. A significant regression was observed between wild rice and rice cultivars in their polymorphic levels, particularly in their nonsynonymous substitutions (theta ( a )). Our data also showed that a similar proportion (approximately 60%) of nucleotide variation in wild rice was retained in cultivated rice in both R-genes and non-R-genes. Interestingly, the slope always was >1 and the intercept always >0 in linear regressions when a cultivar's polymorphism was x-axis. The slope and intercept values can provide a basis by which to estimate the founder effect and the strength of artificial direct selection. A larger founder effect than previously reported and a strong direct-selection effect were shown in rice genes. In addition, two-directional selection was commonly found in differentiated genes between indica and japonica rice subspecies. This kind of selection may explain the mosaic origins of indica and japonica rice subspecies. Furthermore, in most R-genes, no significant differentiation between cultivated and wild rice was detected. We found evidence for genetic introgression from wild rice, which may have played an important role during the domestication of rice R-genes.

  7. 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.

  8. 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

  9. 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.

  10. Environmental and physiological effects on grouping of drought-tolerant and susceptible rice varieties related to rice (Oryza sativa) root hydraulics under drought

    PubMed Central

    Henry, Amelia; Wehler, Regina; Grondin, Alexandre; Franke, Rochus; Quintana, Marinell

    2016-01-01

    Background and Aims Root hydraulic limitations (i.e. intra-plant restrictions to water movement) may be related to crop performance under drought, and groupings in the hydraulic function of drought-tolerant and drought-susceptible rice (Oryza sativa) varieties have been previously reported. This study aimed to better understand the environmental and physiological relationships with rice root hydraulics under drought. Methods Xylem sap bleeding rates in the field (gsap g–1 shoot) were measured on seasonal and diurnal time frames, during which time environmental conditions were monitored and physiological measurements were conducted. Complementary experiments on the effects of vapour pressure deficit (VPD) on root hydraulic conductivity and on transpiration rates of de-rooted tillers were conducted in growth chambers. Key Results The diurnal effects on bleeding rate were more closely related to irradiance than VPD, and VPD effects on root hydraulic conductivity measured on 21-day-old plants were due to effects on plant growth including root surface area, maximum root depth and root:shoot ratio. Leaf osmotic potential was related to the grouping of drought-tolerant and drought-susceptible varieties in rice root hydraulics, and these groupings were independent of differences in phenology. Low single-tiller bleeding rates were observed under high evapo-transpirational demand, higher bleeding rates were observed at more negative leaf osmotic potentials in drought-susceptible varieties, and drought-tolerant and susceptible varieties differed in the VPD-induced increase in transpiration rates of de-rooted tillers. Low root suberin amounts in some of the drought-susceptible varieties may have resulted in higher ion transport, as evidenced by higher sap K+ concentration and higher bleeding rates in those varieties. Conclusions These results provide evidence of the environmental effects on shoots that can influence root hydraulics. The consistent groupings of drought

  11. 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.

  12. 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.

  13. 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

  14. 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.

  15. 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.

  16. 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.

  17. Genome wide association analysis of cold tolerance at germination in temperate japonica rice (Oryza sativa L.) varieties

    PubMed Central

    Viruel, Juan; Domingo, Concha; Marqués, Luis

    2017-01-01

    A pool of 200 traditional, landraces and modern elite and old cultivars of rice, mainly japonica varieties adapted to temperate regions, have been used to perform a genome wide association study to detect chromosome regions associated to low temperature germination (LTG) regulation using a panel of 1672 SNP markers. Phenotyping was performed by determining growth rates when seeds were germinated at 25° and 15°C in order to separate the germination vigorousness from cold tolerance effects. As expected, the ability to produce viable seedlings varied widely among rice cultivars and also depended greatly on temperature. Furthermore, we observed a differential response during seed germination and in coleoptile elongation. Faster development at 15°C was observed in seeds from varieties traditionally used as cold tolerant parents by breeders, along with other potentially useful cultivars, mainly of Italian origin. When phenotypic data were combined with the panel of SNPs for japonica rice cultivars, significant associations were detected for 31 markers: 7 were related to growth rate at 25°C and 24 to growth rates at 15°. Among the latter, some chromosome regions were associated to LTG while others were related to coleoptile elongation. Individual effects of the associated markers were low, but by combining favourable alleles in a linear regression model we estimated that 27 loci significantly explained the observed phenotypic variation. From these, a core panel of 13 markers was selected and, furthermore, two wide regions of chromosomes 3 and 6 were consistently associated to rice LTG. Varieties with higher numbers of favourable alleles for the panels of associated markers significantly correlated with increased phenotypic values at both temperatures, thus corroborating the utility of the tagged markers for marker assisted selection (MAS) when breeding japonica rice for LTG. PMID:28817683

  18. Genome wide association analysis of cold tolerance at germination in temperate japonica rice (Oryza sativa L.) varieties.

    PubMed

    Sales, Ester; Viruel, Juan; Domingo, Concha; Marqués, Luis

    2017-01-01

    A pool of 200 traditional, landraces and modern elite and old cultivars of rice, mainly japonica varieties adapted to temperate regions, have been used to perform a genome wide association study to detect chromosome regions associated to low temperature germination (LTG) regulation using a panel of 1672 SNP markers. Phenotyping was performed by determining growth rates when seeds were germinated at 25° and 15°C in order to separate the germination vigorousness from cold tolerance effects. As expected, the ability to produce viable seedlings varied widely among rice cultivars and also depended greatly on temperature. Furthermore, we observed a differential response during seed germination and in coleoptile elongation. Faster development at 15°C was observed in seeds from varieties traditionally used as cold tolerant parents by breeders, along with other potentially useful cultivars, mainly of Italian origin. When phenotypic data were combined with the panel of SNPs for japonica rice cultivars, significant associations were detected for 31 markers: 7 were related to growth rate at 25°C and 24 to growth rates at 15°. Among the latter, some chromosome regions were associated to LTG while others were related to coleoptile elongation. Individual effects of the associated markers were low, but by combining favourable alleles in a linear regression model we estimated that 27 loci significantly explained the observed phenotypic variation. From these, a core panel of 13 markers was selected and, furthermore, two wide regions of chromosomes 3 and 6 were consistently associated to rice LTG. Varieties with higher numbers of favourable alleles for the panels of associated markers significantly correlated with increased phenotypic values at both temperatures, thus corroborating the utility of the tagged markers for marker assisted selection (MAS) when breeding japonica rice for LTG.

  19. Differences in glucose yield of residues from among varieties of rice, wheat, and sorghum after dilute acid pretreatment.

    PubMed

    Teramura, Hiroshi; Sasaki, Kengo; Kawaguchi, Hideo; Matsuda, Fumio; Kikuchi, Jun; Shirai, Tomokazu; Sazuka, Takashi; Yamasaki, Masanori; Takumi, Shigeo; Ogino, Chiaki; Kondo, Akihiko

    2017-08-01

    Bio-refinery processes require use of the most suitable lignocellulosic biomass for enzymatic saccharification and microbial fermentation. Glucose yield from biomass solid fractions obtained after dilute sulfuric acid (1%) pretreatment (at 180 °C) was investigated using 14, 8, and 16 varieties of rice, wheat, and sorghum, respectively. Biomass solid fractions of each crop showed similar cellulose content. However, glucose yield after enzymatic hydrolysis (cellulase loading at 6.6 filter paper unit/g-biomass) was different among the varieties of each crop, indicating genotypic differences for rice, wheat, and sorghum. Nuclear magnetic resonance method revealed that the high residual level of lignin aromatic regions decreased glucose yield from solid fraction of sorghum.

  20. Evaluating Crossbred Red Rice Variants for Postprandial Glucometabolic Responses: A Comparison with Commercial Varieties.

    PubMed

    Se, Chee-Hee; Chuah, Khun-Aik; Mishra, Ankitta; Wickneswari, Ratnam; Karupaiah, Tilakavati

    2016-05-20

    Consumption of white rice predisposes some Asian populations to increased risk of type 2 diabetes. We compared the postprandial glucometabolic responses to three newly-developed crossbred red rice variants (UKMRC9, UKMRC10, UKMRC11) against three selected commercial rice types (Thai red, Basmati white, Jasmine white) using 50-g carbohydrate equivalents provided to 12 normoglycaemic adults in a crossover design. Venous blood was drawn fasted and postprandially for three hours. Glycaemic (GI) and insulin (II) indices, incremental areas-under-the-curves for glucose and insulin (IAUCins), indices of insulin sensitivity and secretion, lactate and peptide hormones (motilin, neuropeptide-Y, orexin-A) were analyzed. The lowest to highest trends for GI and II were similar i.e., UKMRC9 < Basmati < Thai red < UKMRC10 < UKMRC11 < Jasmine. Postprandial insulinaemia and IAUCins of only UKMRC9 were significantly the lowest compared to Jasmine. Crude protein and fiber content correlated negatively with the GI values of the test rice. Although peptide hormones were not associated with GI and II characteristics of test rice, early and late phases of prandial neuropeptide-Y changes were negatively correlated with postprandial insulinaemia. This study indicated that only UKMRC9 among the new rice crossbreeds could serve as an alternative cereal option to improve diet quality of Asians with its lowest glycaemic and insulinaemic burden.

  1. Evaluating Crossbred Red Rice Variants for Postprandial Glucometabolic Responses: A Comparison with Commercial Varieties

    PubMed Central

    Se, Chee-Hee; Chuah, Khun-Aik; Mishra, Ankitta; Wickneswari, Ratnam; Karupaiah, Tilakavati

    2016-01-01

    Consumption of white rice predisposes some Asian populations to increased risk of type 2 diabetes. We compared the postprandial glucometabolic responses to three newly-developed crossbred red rice variants (UKMRC9, UKMRC10, UKMRC11) against three selected commercial rice types (Thai red, Basmati white, Jasmine white) using 50-g carbohydrate equivalents provided to 12 normoglycaemic adults in a crossover design. Venous blood was drawn fasted and postprandially for three hours. Glycaemic (GI) and insulin (II) indices, incremental areas-under-the-curves for glucose and insulin (IAUCins), indices of insulin sensitivity and secretion, lactate and peptide hormones (motilin, neuropeptide-Y, orexin-A) were analyzed. The lowest to highest trends for GI and II were similar i.e., UKMRC9 < Basmati < Thai red < UKMRC10 < UKMRC11 < Jasmine. Postprandial insulinaemia and IAUCins of only UKMRC9 were significantly the lowest compared to Jasmine. Crude protein and fiber content correlated negatively with the GI values of the test rice. Although peptide hormones were not associated with GI and II characteristics of test rice, early and late phases of prandial neuropeptide-Y changes were negatively correlated with postprandial insulinaemia. This study indicated that only UKMRC9 among the new rice crossbreeds could serve as an alternative cereal option to improve diet quality of Asians with its lowest glycaemic and insulinaemic burden. PMID:27213446

  2. 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.

  3. 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.

  4. Transgenerational variations in DNA methylation induced by drought stress in two rice varieties with distinguished difference to drought resistance.

    PubMed

    Zheng, Xiaoguo; Chen, Liang; 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.

  5. 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

  6. 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

  7. 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.

  8. 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

  9. 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

  10. 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.

  11. In vitro plant regeneration through anther culture of some Iranian local rice (Oryza sativa L.) cultivars.

    PubMed

    Talebi, Reza; Rahemi, Mohammad Reza; Arefi, Habibolah; Nourozi, Mohammad; Bagheri, Nadali

    2007-06-15

    In this study, effect of different genotypes, different callus induction and regeneration media were investigated using seven Iranian local rice. Anthers were cultured on N6, Fj and L8 media containing the same hormonal combination 3 mg L(-1) NAA, 0.5 mg L(-1) Kn and 0.5 mg L(-1) 2, 4-D and incubated at 25 +/- 1 degree C in dark for callus induction. All varieties in L8 medium, five varieties in Fj medium and six varieties in N6 medium produced highest percentage of callus. Calli induced in different induction media were transferred to SK 11 and N 19 medium and incubated at 25 +/- 1 degree C in light for plantlet regeneration. Among seven varieties upon transfer to SK 11 medium, highest percentage (40%) of green plants were produced in Hassani and in N 19 medium the highest percentage (15.78) of green plants and albino plants (21.05) were produced in Anbarbo. The finding in the present investigation showed that the successfully emberyogenesis and green plant regeneration in rice anther culture dependent on medium culture components and are affected by the genetic mack-up of the plants.

  12. 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...

  13. 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...

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

    USDA-ARS?s Scientific Manuscript database

    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...

  15. 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.

  16. Evaluation of arsenate content of rice and rice bran purchased from local markets in the People's Republic of China.

    PubMed

    Dai, Shouhui; Yang, Hui; Mao, Xuefei; Qiu, Jing; Liu, Quanji; Wang, Fuhua; Wang, Min

    2014-04-01

    In previous studies, inorganic arsenic and total arsenic concentrations in rice bran have been much higher than those in polished rice obtained from the same whole paddy rice. However, the arsenic species distribution between rice and bran is still unknown, especially for arsenite (AsIII) and arsenate (AsV). To characterize the arsenic species in rice and bran and explain the elevated concentrations of inorganic arsenic and total arsenic, four arsenic species, AsIII, AsV, dimethylarsinic acid, and monomethylarsonic acid, were evaluated. Rice and bran samples (n = 108) purchased from local markets in the People's Republic of China were analyzed using high-performance liquid chromatography with hydride generation and atomic fluorescence spectrometry and then microwave extraction. As expected, most of the arsenic was found in bran, with bran/rice ratios of 6.8 for total arsenic species and 6.4 for inorganic arsenic. Among four arsenic species, the maximum bran/rice ratio was 104.7 (335/3.2 μg kg(-1)) for AsV followed by 1.2 (69.2/56.1) for AsIII, 1.3 (6.7/5.2) for dimethylarsinic acid, and 4.0 (0.8/0.2) for monomethylarsonic acid. Thus, the large difference in arsenic concentration between rice and bran was mostly due to the difference in the AsV concentration, which account for 96 and 95 % of the difference for total arsenic species and inorganic arsenic, respectively. Therefore, the possibility of AsV contamination in rice bran and its by-products needs more study. This study is the first in which concentrations of AsIII and AsV in rice and bran have been documented, revealing that a higher percentage of AsV occurs in bran than in rice.

  17. 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.

  18. 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.

  19. 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

  20. 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.

  1. Marker-assisted introgression of broad-spectrum blast resistance genes into the cultivated MR219 rice variety.

    PubMed

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

    2017-07-01

    The rice cultivar MR219 is famous for its better yield and long and fine grain quality; however, it is susceptible to blast disease. The main objective of this study was to introgress blast resistance genes into MR219 through marker-assisted selection (MAS). The rice cultivar MR219 was used as the recurrent parent, and Pongsu Seribu 1 was used as the donor. Marker-assisted foreground selection was performed using RM6836 and RM8225 to identify plants possessing blast resistance genes. Seventy microsatellite markers were used to estimate recurrent parent genome (RPG) recovery. Our analysis led to the development of 13 improved blast resistant lines with Piz, Pi2 and Pi9 broad-spectrum blast resistance genes and an MR219 genetic background. The RPG recovery of the selected improved lines was up to 97.70% with an average value of 95.98%. Selected improved lines showed a resistance response against the most virulent blast pathogen pathotype, P7.2. The selected improved lines did not express any negative effect on agronomic traits in comparison with MR219. The research findings of this study will be a conducive approach for the application of different molecular techniques that may result in accelerating the development of new disease-resistant rice varieties, which in turn will match rising demand and food security worldwide. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

  2. 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

  3. 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

  4. Glycemic Index of a Novel High-Fiber White Rice Variety Developed in India--A Randomized Control Trial Study.

    PubMed

    Mohan, Viswanathan; Anjana, Ranjit Mohan; Gayathri, Rajgopal; Ramya Bai, Mookambika; Lakshmipriya, Nagrajan; Ruchi, Vaidya; Balasubramaniyam, K K; Jakir, M Mohamed; Shobana, Shanmugam; Unnikrishnan, Ranjit; Krishnaswamy, Kamala; Henry, Jeya Kumar; Sudha, Vasudevan

    2016-03-01

    White rice, a common Indian staple, has a high glycemic response and is associated with high risk of type 2 diabetes. The aim of this study was to compare the Glycemic Index (GI) of a newly developed high-fiber white rice (HFWR) with that of commercial white rice (WR). HFWR was developed using biochemical screening approaches and classical plant breeding techniques. The GI of HFWR was determined using a validated protocol in 30 healthy participants in the year 2013 and repeated in a subsample of 15 participants in the year 2014; the results were compared with the value for WR. The incremental area under the curve was calculated geometrically by applying the trapezoid rule for both reference food (glucose) and the test foods (HFWR and WR). Proximate principles along with dietary fiber, resistant starch, and amylose content were analyzed using standardized methods. The dietary fiber content of HFWR was fivefold higher (8.0 ± 0.1 vs. 1.58 ± 0.17 g%), resistant starch content was 6.5-fold higher (3.9 ± 0.2 vs. 0.6 ± 0.03 g%) (P < 0.001), and amylose content was significantly higher (32.8 ± 1.1 vs. 26.0 ± 0.2 g%) (P < 0.001), compared with WR. HFWR was found to be of medium GI (61.3 ± 2.8), whereas WR was of high GI (79.2 ± 4.8). Overall, HFWR had 23% lower GI compared with WR (P = 0.002). The new HFWR variety can be considered as a potentially healthier alternative to commercial WR in rice-eating populations, on account of its lower GI and high fiber content.

  5. Exogenous application of brassinosteroid offers tolerance to salinity by altering stress responses in rice variety Pusa Basmati-1.

    PubMed

    Sharma, Isha; Ching, Erwan; Saini, Shivani; Bhardwaj, Renu; Pati, Pratap Kumar

    2013-08-01

    Plant steroidal hormones, brassinosteroids, play a pivotal role in variety of plant developmental processes and adaptation to various environmental stresses. The present work investigates the response of various stress markers upon exogenous application of 24-epibrassinolide (EBL) on Pusa Basmati-1, a commercially important rice variety, under salt stress conditions. Rice seeds after treatment with different concentrations of NaCl alone or in combination with different concentrations of 24-epibrassinolide (EBL) were analysed for various growth parameters, protein, proline and malondialdehyde content (MDA) and antioxidant enzymes activities. The seedlings exposed to NaCl exhibited a significant decline in growth parameters and changes in the levels of antioxidant enzymes, however, treatment with EBL showed an improvement in growth, levels of protein and proline content and antioxidant enzymes activity. The enhanced levels of MDA content during salt stress in rice seedlings was decreased with EBL treatment. Further, the treatment with EBL increased the expression of various oxidative stress marker genes, although to different levels. Expression of various brassinosteroids (OsBRI1, OsDWF4) and salt (SalT) responsive genes, revealed the down regulation of OsDWF4 with application of EBL and upregulation of SalT in presence of salt stress thereby confirming the efficacy of the treatments. Interestingly, a significant down regulation of SalT gene was observed on application of EBL along with salt compared to salt treatment alone. On the other hand, the application of EBL alone and in combination with salt has resulted in upregulation of OsBRI1. Copyright © 2013 Elsevier Masson SAS. All rights reserved.

  6. Effects of acute salt stress on modulation of gene expression in a Malaysian salt-tolerant indigenous rice variety, Bajong.

    PubMed

    Yeo, Brandon Pei Hui; Bhave, Mrinal; Hwang, Siaw San

    2017-09-18

    The small genome size of rice relative to wheat and barley, together with its salt sensitivity, make it an ideal candidate for studies of salt stress response. Transcriptomics has emerged as a powerful technique to study salinity responses in many crop species. By identifying a large number of differentially expressed genes (DEGs) simultaneously after the stress induction, it can provide crucial insight into the immediate responses towards the stressor. In this study, a Malaysian salt-tolerant indigenous rice variety named Bajong and one commercial rice variety named MR219 were investigated for their performance in plant growth and ion accumulation properties after salt stress treatment. Bajong was further investigated for the changes in leaf's transcriptome after 6 h of stress treatment using 100 mM NaCl. Based on the results obtained, Bajong is found to be significantly more salt tolerant than MR219, showing better growth and a lower sodium ion accumulation after the stress treatment. Additionally, Bajong was analysed by transcriptomic sequencing, generating a total of 130 millions reads. The reads were assembled into de novo transcriptome and each transcript was annotated using several pre-existing databases. The transcriptomes of control and salt-stressed samples were then compared, leading to the discovery of 4096 DEGs. Based on the functional annotation results obtained, the enrichment factor of each functional group in DEGs was calculated in relation to the total reads obtained. It was found that the group with the highest gene modulation was involved in the secondary metabolite biosynthesis of plants, with approximately 2.5% increase in relation to the total reads obtained. This suggests an extensive transcriptional reprogramming of the secondary metabolic pathways after stress induction, which could be directly responsible for the salt tolerance capability of Bajong.

  7. 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.

  8. Local DNA hypomethylation activates genes in rice endosperm

    PubMed Central

    Zemach, Assaf; Kim, M. Yvonne; Silva, Pedro; Rodrigues, Jessica A.; Dotson, Bradley; Brooks, Matthew D.; Zilberman, Daniel

    2010-01-01

    Cytosine methylation silences transposable elements in plants, vertebrates, and fungi but also regulates gene expression. Plant methylation is catalyzed by three families of enzymes, each with a preferred sequence context: CG, CHG (H = A, C, or T), and CHH, with CHH methylation targeted by the RNAi pathway. Arabidopsis thaliana endosperm, a placenta-like tissue that nourishes the embryo, is globally hypomethylated in the CG context while retaining high non-CG methylation. Global methylation dynamics in seeds of cereal crops that provide the bulk of human nutrition remain unknown. Here, we show that rice endosperm DNA is hypomethylated in all sequence contexts. Non-CG methylation is reduced evenly across the genome, whereas CG hypomethylation is localized. CHH methylation of small transposable elements is increased in embryos, suggesting that endosperm demethylation enhances transposon silencing. Genes preferentially expressed in endosperm, including those coding for major storage proteins and starch synthesizing enzymes, are frequently hypomethylated in endosperm, indicating that DNA methylation is a crucial regulator of rice endosperm biogenesis. Our data show that genome-wide reshaping of seed DNA methylation is conserved among angiosperms and has a profound effect on gene expression in cereal crops. PMID:20937895

  9. 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.

  10. GNS4, a novel allele of DWARF11, regulates grain number and grain size in a high-yield rice variety.

    PubMed

    Zhou, Yong; Tao, Yajun; Zhu, Jinyan; Miao, Jun; Liu, Jun; Liu, Yanhua; Yi, Chuandeng; Yang, Zefeng; Gong, Zhiyun; Liang, Guohua

    2017-12-01

    Rice plays an extremely important role in food safety because it feeds more than half of the world's population. Rice grain yield depends on biomass and the harvest index. An important strategy to break through the rice grain yield ceiling is to increase the biological yield. Therefore, genes associated with organ size are important targets for rice breeding. We characterized a rice mutant gns4 (grain number and size on chromosome 4) with reduced organ size, fewer grains per panicle, and smaller grains compared with those of WT. Map-based cloning indicated that the GNS4 gene, encoding a cytochrome P450 protein, is a novel allele of DWARF11 (D11). A single nucleotide polymorphism (deletion) in the promoter region of GNS4 reduced its expression level in the mutant, leading to reduced grain number and smaller grains. Morphological and cellular analyses suggested that GNS4 positively regulates grain size by promoting cell elongation. Overexpression of GNS4 significantly increased organ size, 1000-grain weight, and panicle size, and subsequently enhanced grain yields in both the Nipponbare and Wuyunjing7 (a high-yielding cultivar) backgrounds. These results suggest that GNS4 is key target gene with possible applications in rice yield breeding. GNS4 was identified as a positive regulator of grain number and grain size in rice. Increasing the expression level of this gene in a high-yielding rice variety enhanced grain yield. GNS4 can be targeted in breeding programs to increase yields.

  11. 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

  12. Consumer motivations toward buying local rice: The case of northern Iranian consumers.

    PubMed

    Rahnama, Hassan

    2017-07-01

    This research had two purposes. The first aim was to identify Iranian and Non-Iranian rice consumers based on demographic characteristics and examine difference of these features with buying behaviors. The second purpose of study was to investigate consumer's motivation to buy local rice in Iran. The sample were 1500 people (men and women). The data was collected by using questionnaire based on a face-to-face survey. Chi-square, confirmatory factor analysis, and multiple linear regression were applied to assess collected data by a questionnaire survey. Regarding Iranian local rice buyers, 884 people buy local rice. Chi-square test showed that there is a significant difference between gender, having children, and marital status in buying local rice. Habitual Iranian local rice buyers include: female (51%), people who are more than 45 years old (51%), people with children (63%), people who are living urban (61%), married people (48%) and individuals that their monthly income is between 321.5 and 625 Dollars (53%). Regarding non-Iranian rice buyers, 616 people buy it. Also there is a significant difference between gender, location, marital status, and income in buying local rice. For considering consumers motivation toward buying local rice the econometrical model is used. Model had three aspects including; quality aspects (taste, good appearance), economic aspects (price, convenience, consumer's ethnocentrism), and safety aspects (health, not using pesticides and environment protection) and seven subset. The results of analysis indicated that quality aspects, economic aspects and safety aspects have positive effects on buying Iranian local rice. Also, indicative variables including; taste, good appearance, price, convenience, consumer's ethnocentrism, health, not using pesticides and environment have significant effects on buying it. Copyright © 2017 Elsevier Ltd. All rights reserved.

  13. 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.

  14. Differential responses of cell wall bound phenolic compounds in sensitive and tolerant varieties of rice in response to salinity.

    PubMed

    Gupta, Poulami; De, Bratati

    2017-09-14

    In plants, cell wall bound phenolics change in response to stress. The aim of the study was to investigate the effect of NaCl induced stress on wall bound phenolics in four rice varieties, of which two (Bhutnath, Nonabokra) were salt tolerant and two (MTU 7029, Sujala) were salt sensitive. After germination, seedlings were grown in hydroponic solution and subjected to salinity stress (25mM, 50mM, 100mM and 150mM NaCl) on day 12. Wall bound phenolic compounds were determined by GC-MS based metabolite analysis. Total seven wall bound phenols were identified from the leaf tissues and eight from the root tissues. Ferulic acid and 4-hydroxycinnamic acid were found in all the four varieties. After NaCl treatment, these two wall bound phenols increased in tolerant varieties only. Significant inverse correlation between leaf length and leaf fresh weight with wall bound ferulic acid and 4-hydroxycinnamic acid in Nonabokra suggests the positive role of these wall bound phenolics in salt tolerance.

  15. 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

  16. Plasma membrane-localized transporter for aluminum in rice

    PubMed Central

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

    2010-01-01

    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. PMID:20937890

  17. 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.

  18. Comparative Analysis of γ-Oryzanol, β-Glucan, Total Phenolic Content and Antioxidant Activity in Fermented Rice Bran of Different Varieties

    PubMed Central

    Jung, Tae-Dong; Shin, Gi-Hae; Kim, Jae-Min; Choi, Sun-Il; Lee, Jin-Ha; Lee, Sang Jong; Park, Seon Ju; Woo, Koan Sik; Oh, Sea Kwan; Lee, Ok-Hawn

    2017-01-01

    Rice bran, a by-product derived from processing rice, is a rich source of bioactive compounds. Recent studies have suggested that the fermentation can improve their biological activities. This study aimed to determined the level of γ-oryzanol, β-glucan and total phenol contents of fermented rice bran from 21 Korean varieties, as well as to evaluate their antioxidant activities. We also assessed the validation of the analytical method for determining γ-oryzanol content in fermented rice brans. Among the fermented rice brans, the Haedam rice bran contained the highest level of total phenol content (156.08 mg gallic acid equivalents/g), DPPH (2,2-diphenyl-1-picrylhydrazyl) radical scavenging activity (71.30%) and ORAC (Oxygen radical absorbance capacity) value (1101.31 μM trolox equivalents/g). Furthermore, the fermented Migwang rice bran showed the highest level of γ-oryzanol content (294.77 ± 6.74 mg/100 g). PMID:28587204

  19. 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. Copyright © 2014 Elsevier B.V. All rights

  20. 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

  1. 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.

  2. 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

  3. Effect of Rates and Timing of Midseason Nitrogen Applications on Performance of Short-season Rice Varieties, 1964-1965

    Treesearch

    John L. Sims; V. L. Hall; T. H. Johnston

    1967-01-01

    Research conducted in Arkansas has shown the value of splitting nitrogen applications made to rice and the importance of proper timing of applications near midseason. Results of these studies recently were presented and references to the world literature on timing of nitrogen applications to rice were reviewed.

  4. 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. Copyright © 2014 Elsevier Ltd. All rights reserved.

  5. 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

  6. 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.

  7. 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

  8. Genomic variation associated with local adaptation of weedy rice during de-domestication

    PubMed Central

    Qiu, Jie; Zhou, Yongjun; Mao, Lingfeng; Ye, Chuyu; Wang, Weidi; Zhang, Jianping; Yu, Yongyi; Fu, Fei; Wang, Yunfei; Qian, Feijian; Qi, Ting; Wu, Sanling; Sultana, Most Humaira; Cao, Ya-Nan; Wang, Yu; Timko, Michael P.; Ge, Song; Fan, Longjiang; Lu, Yongliang

    2017-01-01

    De-domestication is a unique evolutionary process by which domesticated crops are converted into ‘wild predecessor like' forms. Weedy rice (Oryza sativa f. spontanea) is an excellent model to dissect the molecular processes underlying de-domestication. Here, we analyse the genomes of 155 weedy and 76 locally cultivated rice accessions from four representative regions in China that were sequenced to an average 18.2 × coverage. Phylogenetic and demographic analyses indicate that Chinese weedy rice was de-domesticated independently from cultivated rice and experienced a strong genetic bottleneck. Although evolving from multiple origins, critical genes underlying convergent evolution of different weedy types can be found. Allele frequency analyses suggest that standing variations and new mutations contribute differently to japonica and indica weedy rice. We identify a Mb-scale genomic region present in weedy rice but not cultivated rice genomes that shows evidence of balancing selection, thereby suggesting that there might be more complexity inherent to the process of de-domestication. PMID:28537247

  9. Effect of nano packaging on preservation quality of Nanjing 9108 rice variety at high temperature and humidity.

    PubMed

    Wang, Fan; Hu, Qiuhui; Mugambi Mariga, Alfred; Cao, Chongjiang; Yang, Wenjian

    2018-01-15

    A nano packaging material containing nano Ag, nano TiO2, nano attapulgite and SiO2 was prepared, and its impact on quality of Nanjing 9108 rice at 37°C and 85% relative humidity was studied. Effects of the packaging on ambient gases and chromatic aberration of rice were determined. Moreover, oxidation level, molds growth and flavor of rice were also analyzed. Results showed that nano packaging material had antimicrobial effects and maintained low O2 and high CO2 content in the packages. The packages thereby inhibited the growth of molds and the production of fatty acids, restrained the increase of lipase activity, and reduced the oxidation of fats and proteins. As a result, the production of yellow and white-belly rice were inhibited. Furthermore, the color and flavor of rice were maintained. Therefore, the nano-packing material could be applied for preservation of rice to improve preservation quality. Copyright © 2017 Elsevier Ltd. All rights reserved.

  10. 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.

  11. 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.

  12. 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

  13. 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.

  14. Localization Accuracy and Immobilization Effectiveness of a Stereotactic Body Frame for a Variety of Treatment Sites

    SciTech Connect

    Foster, Ryan; Meyer, Jeffrey; Iyengar, Puneeth; Pistenmaa, David; Timmerman, Robert; Choy, Hak; Solberg, Timothy

    2013-12-01

    Purpose: The purpose of this study was to analyze the pretreatment setup errors and intrafraction motion using cone beam computed tomography (CBCT) for stereotactic body radiation therapy patients immobilized and localized with a stereotactic body frame for a variety of treatment sites. Methods and Materials: Localization errors were recorded for patients receiving SBRT for 141 lung, 29 liver, 48 prostate, and 45 spine tumors representing 1005 total localization sessions. All patients were treated in a stereotactic body frame with a large custom-molded vacuum pillow. Patients were first localized to the frame using tattoos placed during simulation. Subsequently, the frame was aligned to the room lasers according to the stereotactic coordinates determined from the treatment plan. Every patient received a pretreatment and an intrafraction CBCT. Abdominal compression was used for all liver patients and for approximately 40% of the lung patients to reduce tumor motion due to respiration. Results: The mean ± standard deviation pretreatment setup errors from all localizations were −2.44 ± 3.85, 1.31 ± 5.84, and 0.11 ± 3.76 mm in the anteroposterior, superoinferior, and lateral directions, respectively. The mean pretreatment localization results among all treatment sites were not significantly different (F test, P<.05). For all treatment sites, the mean ± standard deviation intrafraction shifts were 0.33 ± 1.34, 0.15 ± 1.45, and −0.02 ± 1.17 mm in the anteroposterior, superoinferior, and lateral directions, respectively. The mean unidimensional intrafraction shifts were statistically different for several of the comparisons (P<.05) as assessed by the Tukey-Kramer test. Conclusions: Despite the varied tumor locations, the pretreatment mean localization errors for all sites were found to be consistent among the treatment sites and not significantly different, indicating that the body frame is a suitable immobilization and localization device for a variety of

  15. 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

    USDA-ARS?s Scientific Manuscript database

    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...

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

    USDA-ARS?s Scientific Manuscript database

    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...

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

    USDA-ARS?s Scientific Manuscript database

    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...

  18. 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

  19. 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

  20. The knockdown of OsVIT2 and MIT affects iron localization in rice seed.

    PubMed

    Bashir, Khurram; Takahashi, Ryuichi; Akhtar, Shamim; Ishimaru, Yasuhiro; Nakanishi, Hiromi; Nishizawa, Naoko K

    2013-11-20

    The mechanism of iron (Fe) uptake in plants has been extensively characterized, but little is known about how Fe transport to different subcellular compartments affects Fe localization in rice seed. Here, we discuss the characterization of a rice vacuolar Fe transporter 2 (OsVIT2) T-DNA insertion line (osvit2) and report that the knockdown of OsVIT2 and mitochondrial Fe transporter (MIT) expression affects seed Fe localization. osvit2 plants accumulated less Fe in their shoots when grown under normal or excess Fe conditions, while the accumulation of Fe was comparable to that in wild-type (WT) plants under Fe-deficient conditions. The accumulation of zinc, copper, and manganese also changed significantly in the shoots of osvit2 plants. The growth of osvit2 plants was also slow compared to that of WT plants. The concentration of Fe increased in osvit2 polished seeds. Previously, we reported that the expression of OsVIT2 was higher in MIT knockdown (mit-2) plants, and in this study, the accumulation of Fe in mit-2 seeds decreased significantly. These results suggest that vacuolar Fe trafficking is important for plant Fe homeostasis and distribution, especially in plants grown in the presence of excess Fe. Moreover, changes in the expression of OsVIT2 and MIT affect the concentration and localization of metals in brown rice as well as in polished rice seeds.

  1. 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.

  2. 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

  3. 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

  4. 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.

  5. 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.

  6. An ethnobotanical study of traditional rice landraces (Oryza sativa L.) used for medical treatment in selected local communities of the Philippines.

    PubMed

    Cabanting, Rosa Mia F; Perez, Loida M

    2016-12-24

    Rice (Oryza sativa L.) remains as one the most important staple food of the Philippines with an overabundance of varieties and gastronomic use. Despite this, no published comprehensive ethnobotanical information exists for the exclusive subject on Philippine traditional rice varieties and their ethnomedicinal value. To identify and collect traditional rice landrace with ethnomedicinal application from local communities of the Philippines; and document the application, traditional preparation and administration of these plants. The ethnobotanical study was performed in nine areas distributed across four provinces: Palawan, Zamboanga del Norte, Zamboanga del Sur and North Cotabato for a period of two years (2014-2015). A total of 39 key informants were identified and interviewed using semi-structured interviews and informal discussion. Descriptive statistics was used to analyze and organize the collected information from the surveys. Nineteen (19) traditional rice were identified for the native treatment and control of 22 community health concerns. Predominant use of the plants collected were for the treatment of some types of nutritional disorders (18%), digestive system disorders (18%), ill-defined symptoms (13%); viral infections (13%); and several cultural diseases and disorders (11%). Grains were the most frequently used plant part and oral administration was the most preferred mode of treatment. This study is the first to formally confirm that certain traditional rice have a role in the healthcare system of selected local communities in the Philippines. The novel findings open a paradigm for scientists towards therapeutic investigations and development of probable high value products from the highlighted landrace. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  7. 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.

  8. 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.

  9. Rice ascorbate peroxidase gene family encodes functionally diverse isoforms localized in different subcellular compartments.

    PubMed

    Teixeira, Felipe Karam; Menezes-Benavente, Larissa; Galvão, Vinícius Costa; Margis, Rogério; Margis-Pinheiro, Márcia

    2006-07-01

    Aerobic organisms evolved a complex antioxidant system, which protect the cells against oxidative damage caused by partially reduced oxygen intermediates, also known as reactive oxygen species. In plants, ascorbate peroxidases (EC, 1.11.1.11) catalyze the conversion of H(2)O(2) to H(2)O, using ascorbate as the specific electron donor in this enzymatic reaction. Previously, eight APx genes were identified in the rice (Oryza sativa L.) genome through in silico analysis: two cytosolic isoforms, two putative peroxisomal isoforms, and four putative chloroplastic ones. Using gene-specific probes, we confirmed the presence of the eight APx genes in the rice genome by Southern blot hybridization. Transcript accumulation analysis showed specific expression patterns for each member of the APx family according to developmental stage and in response to salt stress, revealing the complexity of the antioxidant system in plants. Finally, the subcellular localization of rice APx isoforms was determined using GFP-fusion proteins in BY-2 tobacco cells. In agreement with the initial prediction, OSAPX3 was localized in the peroxisomes. On the other hand, the OSAPX6-GFP fusion protein was found in mitochondria of the BY-2 cells, in contrast to the chloroplastic location predicted by sequence analysis. Our findings reveal the functional diversity of the rice APx genes and suggest complementation and coordination of the antioxidant defenses in different cellular compartments during development and abiotic stress.

  10. 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.

  11. 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

  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

    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.

  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 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

  14. 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.…

  15. 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.…

  16. Variation in Maltese English: The Interplay of the Local and the Global in an Emerging Postcolonial Variety

    ERIC Educational Resources Information Center

    Bonnici, Lisa Marie

    2010-01-01

    In our current era of increased globalization, constraints on language variation in postcolonial English varieties are multifaceted. Local and global language ideologies collide and multiple sources of influence converge in present-day patterns of linguistic variation in emerging English varieties. While research into the structure and…

  17. 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.

  18. 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.

  19. 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

  20. 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.

  1. 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

  2. Different Localization Patterns of Anthocyanin Species in the Pericarp of Black Rice Revealed by Imaging Mass Spectrometry

    PubMed Central

    Yoshimura, Yukihiro; Zaima, Nobuhiro; Moriyama, Tatsuya; Kawamura, Yukio

    2012-01-01

    Black rice (Oryza sativa L. Japonica) contains high levels of anthocyanins in the pericarp and is considered an effective health-promoting food. Several studies have identified the molecular species of anthocyanins in black rice, but information about the localization of each anthocyanin species is limited because methodologies for investigating the localization such as determining specific antibodies to anthocyanin, have not yet been developed Matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI-IMS) is a suitable tool for investigating the localization of metabolites. In this study, we identified 7 species of anthocyanin monoglycosides and 2 species of anthocyanin diglycosides in crude extracts from black rice by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) analysis. We also analyzed black rice sections by MALDI-IMS and found 2 additional species of anthocyanin pentosides and revealed different localization patterns of anthocyanin species composed of different sugar moieties. Anthocyanin species composed of a pentose moiety (cyanidin-3-O-pentoside and petunidin-3-O-pentoside) were localized in the entire pericarp, whereas anthocyanin species composed of a hexose moiety (cyanidin-3-O-hexoside and peonidin-3-O-hexoside) were focally localized in the dorsal pericarp. These results indicate that anthocyanin species composed of different sugar moieties exhibit different localization patterns in the pericarp of black rice. This is the first detailed investigation into the localization of molecular species of anthocyanins by MALDI-IMS. PMID:22363605

  3. Characterization of a rice variety with high hydraulic conductance and identification of the chromosome region responsible using chromosome segment substitution lines

    PubMed Central

    Adachi, Shunsuke; Tsuru, Yukiko; Kondo, Motohiko; Yamamoto, Toshio; Arai-Sanoh, Yumiko; Ando, Tsuyu; Ookawa, Taiichiro; Yano, Masahiro; Hirasawa, Tadashi

    2010-01-01

    Background and Aims The rate of photosynthesis in paddy rice often decreases at noon on sunny days because of water stress, even under submerged conditions. Maintenance of higher rates of photosynthesis during the day might improve both yield and dry matter production in paddy rice. A high-yielding indica variety, ‘Habataki’, maintains a high rate of leaf photosynthesis during the daytime because of the higher hydraulic conductance from roots to leaves than in the standard japonica variety ‘Sasanishiki’. This research was conducted to characterize the trait responsible for the higher hydraulic conductance in ‘Habataki’ and identified a chromosome region for the high hydraulic conductance. Methods Hydraulic conductance to passive water transport and to osmotic water transport was determined for plants under intense transpiration and for plants without transpiration, respectively. The varietal difference in hydraulic conductance was examined with respect to root surface area and hydraulic conductivity (hydraulic conductance per root surface area, Lp). To identify the chromosome region responsible for higher hydraulic conductance, chromosome segment substitution lines (CSSLs) derived from a cross between ‘Sasanishiki’ and ‘Habataki’ were used. Key Results The significantly higher hydraulic conductance resulted from the larger root surface area not from Lp in ‘Habataki’. A chromosome region associated with the elevated hydraulic conductance was detected between RM3916 and RM2431 on the long arm of chromosome 4. The CSSL, in which this region was substituted with the ‘Habataki’ chromosome segment in the ‘Sasanishiki’ background, had a larger root mass than ‘Sasanishiki’. Conclusions The trait for increasing plant hydraulic conductance and, therefore, maintaining the higher rate of leaf photosynthesis under the conditions of intense transpiration in ‘Habataki’ was identified, and it was estimated that there is at least one

  4. Characterization of a rice variety with high hydraulic conductance and identification of the chromosome region responsible using chromosome segment substitution lines.

    PubMed

    Adachi, Shunsuke; Tsuru, Yukiko; Kondo, Motohiko; Yamamoto, Toshio; Arai-Sanoh, Yumiko; Ando, Tsuyu; Ookawa, Taiichiro; Yano, Masahiro; Hirasawa, Tadashi

    2010-11-01

    The rate of photosynthesis in paddy rice often decreases at noon on sunny days because of water stress, even under submerged conditions. Maintenance of higher rates of photosynthesis during the day might improve both yield and dry matter production in paddy rice. A high-yielding indica variety, 'Habataki', maintains a high rate of leaf photosynthesis during the daytime because of the higher hydraulic conductance from roots to leaves than in the standard japonica variety 'Sasanishiki'. This research was conducted to characterize the trait responsible for the higher hydraulic conductance in 'Habataki' and identified a chromosome region for the high hydraulic conductance. Hydraulic conductance to passive water transport and to osmotic water transport was determined for plants under intense transpiration and for plants without transpiration, respectively. The varietal difference in hydraulic conductance was examined with respect to root surface area and hydraulic conductivity (hydraulic conductance per root surface area, L(p)). To identify the chromosome region responsible for higher hydraulic conductance, chromosome segment substitution lines (CSSLs) derived from a cross between 'Sasanishiki' and 'Habataki' were used. The significantly higher hydraulic conductance resulted from the larger root surface area not from L(p) in 'Habataki'. A chromosome region associated with the elevated hydraulic conductance was detected between RM3916 and RM2431 on the long arm of chromosome 4. The CSSL, in which this region was substituted with the 'Habataki' chromosome segment in the 'Sasanishiki' background, had a larger root mass than 'Sasanishiki'. The trait for increasing plant hydraulic conductance and, therefore, maintaining the higher rate of leaf photosynthesis under the conditions of intense transpiration in 'Habataki' was identified, and it was estimated that there is at least one chromosome region for the trait located on chromosome 4.

  5. 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.

  6. 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.

  7. 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

  8. 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

  9. 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.

  10. An efficient and reproducible method for regeneration of whole plants from mature seeds of a high yielding Indica rice (Oryza sativa L.) variety PAU 201.

    PubMed

    Wani, Shabir H; Sanghera, Gulzar S; Gosal, Satbir S

    2011-07-01

    Tissue culture is one of the tools necessary for genetic engineering and many other breeding programs. Moreover, selection of high regenerating rice varieties is a pre-requisite for success in rice biotechnology. In this report we established a reproducible plant regeneration system through somatic embryogenesis. The explants used for regeneration were embryogenic calli derived from mature seeds cultured on callus induction media. For callus induction mature seeds were cultured on MS medium containing 30 g/l sucrose combined with 560 mg/l proline and 1.5-3.5 mg/l 2,4-D and 0.5-1.5 mg/l Kin. For plant regeneration, embryogenic calli were transferred to MS medium containing 30 g/l sucrose, supplemented with 1.0-3.0 mg/l BAP, 0.5-1.5 mg/l Kin and 0.5-1.5 mg/l NAA. The highest frequency of callus induction (44.4%) was observed on the MS medium supplemented with 2.5 mg/l 2,4-D, 0.5 mg/l Kin, 560 mg/l proline and 30 g/l sucrose. The highest frequency of shoot regeneration (42.5%) was observed on the MS medium supplemented with 2.0 mg/l BAP, 0.5 mg/l NAA and 0.5 mg/l Kin. The plantlets were hardened and transferred to soil in earthen pots. The developed method was highly reproducible. The in vitro developed plants showed normal growth and flowering under glasshouse conditions. Copyright © 2011 Elsevier B.V. All rights reserved.

  11. 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…

  12. 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.

    PubMed

    Chen, Ming-Hsuan; McClung, Anna M; Bergman, Christine J

    2016-09-01

    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 this germplasm collection are provided along with data of total flavonoid and total phenolic contents, oxygen radical absorbance capacity and total proanthocyanidin contents. The contents and proportions of individual oligomers, from degree of polymerization of monomers to 14-mers, and polymers in bran of these 32 rice varieties are presented (DOI: http://dx.doi.org/10.1016/j.foodchem.2016.04.004) [1].

  13. 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.

  14. Change in Localizations of Arsenic in Rice Grains After Cooking with High Arsenic Waters - µXRF and XANES studies

    NASA Astrophysics Data System (ADS)

    Datta, S.; Ryan, B.; Kumar, N.; Bortz, T.; Bolen, Z. T.

    2016-12-01

    Threats of Arsenic (As) through food uptake, via consumption of rice, is a potential pathway that presents a concern not only for the millions of inhabitants who reside in river valleys and irrigate their soil with contaminated water, but the global rice market as well. This study focuses on high As rice from India and Bangladesh grown in such soils, and the effect of boiling rice with As-contaminated water in preparation for dietary intake. Husked and unhusked rice grains were boiled with >500 µg/L As-bearing water from the field to simulate local cooking methods. The resulting cooked water was analyzed using iCAP low limit detection via ICP-MS to understand the changes in dissolved elemental concentrations before and after cooking, and HPLC was introduced to measure for changes in As speciation in the waters. Using spectroscopic methods such as µXRF mapping associated with µXANES, distribution/localization and speciation changes of As in rice grains were identified. Further, with Linear Combination Fitting (LCF) of XANES spectra utilizing relevant reference compounds (As-S, AsIII, AsV, MMA and DMA), organic and inorganic As species were able to be mapped within rice grains. The results for uncooked/raw grains showed that predominantly As-S combined with AsIII and AsV accounted for 90% of speciation in most samples, localized in areas such as the outer aleurone layer. When analyzing cooked rice grains, the speciation appears to be an unidentified As species while the best LCF shows between 63-93% of As as MMA. Arsenic was found less localized throughout the cooked grains but rather heterogeneously distributed when compared to the uncooked/raw samples. The analyses of boiled/cooked water resulted in a significant decrease in dissolved As post-cooking (90%), but a subsequent increase in elements such as K, La, Li, Mo, Na, Ni, and Zr was observed; As-V was shown to be the main in-As species in the cooked water. The impact that this study portrays is consuming rice

  15. [Study on the global and local calibration methods of tryptophan content in rice by near infrared reflectance spectroscopy].

    PubMed

    Zhang, Bin; Zhang, Da-Peng; Zhang, Wen-Bin; Wang, Ke-Min; Li, Guan; Yao, Ya-Zhen; Wu, Jian-Guo; Shi, Chun-Hai

    2011-01-01

    Tryptophan is one of the essential amino acids in human, and also considered as an important limiting amino acid in rice. Alkali hydrolysis method was used to determine the tryptophan content of 272 representative samples selected from the 1 256 samples in four years. Based on the milled rice flour spectroscopy, by comparing the prediction abilities of the equations with global calibrations and local calibration, the global calibration method with MPLS and the local calibration method were better than others. Their calibration models could be introduced to application because of low standard errors of prediction for both methods (0.007%) and high coefficients of determination (87.1% and 87.4%, respectively). Furthermore, the prediction ability of the equation based on the brown rice spectroscopy could be still used for determination application though their effects were worse than that of the milled rice flour spectroscopy. It was concluded that the equation could be directly used to estimate the content of tryptophan in milled rice, and the technology of near infrared reflectance spectroscopy developed in this study could be applied in selecting breeding materials for higher tryptophan content and in quality control during rice processing.

  16. 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.

  17. Transgenics of an elite indica rice variety Pusa Basmati 1 harbouring the codA gene are highly tolerant to salt stress.

    PubMed

    Mohanty, A; Kathuria, H; Ferjani, A; Sakamoto, A; Mohanty, P; Murata, N; Tyagi, A K

    2002-12-01

    Transgenic lines of indica rice were generated by Agrobacterium-mediated transformation with the choline oxidase ( codA) gene from Arthrobacter globiformis. Choline oxidase catalyses conversion of choline to glycine betaine. Glycine betaine is known to provide tolerance against a variety of stresses. Molecular analyses of seven independent transgenic lines as performed by Southern, Northern and Western hybridization revealed integration and expression of the transgene as well as inheritance in the progeny plants. A good correlation was observed between levels of mRNA and protein accumulation, and a significant amount of choline oxidase product, i.e. glycine betaine, accumulated in R0 as well as R1 plants. Mendelian as well as non-Mendelian segregation patterns were obtained in the progeny plants. Challenge studies performed with R1 plants by exposure to salt stress (0.15 M NaCl) for 1 week, followed by a recovery period, revealed that in some cases more than 50% of the transgenic plants could survive salt stress and set seed whereas wild-type plants failed to recover.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. Comparative Transcriptome Analyses of Gene Expression Changes Triggered by Rhizoctonia solani AG1 IA Infection in Resistant and Susceptible Rice Varieties

    PubMed Central

    Zhang, Jinfeng; Chen, Lei; Fu, Chenglin; Wang, Lingxia; Liu, Huainian; Cheng, Yuanzhi; Li, Shuangcheng; Deng, Qiming; Wang, Shiquan; Zhu, Jun; Liang, Yueyang; Li, Ping; Zheng, Aiping

    2017-01-01

    Rice sheath blight, caused by Rhizoctonia solani, is one of the most devastating diseases for stable rice production in most rice-growing regions of the world. Currently, studies of the molecular mechanism of rice sheath blight resistance are scarce. Here, we used an RNA-seq approach to analyze the gene expression changes induced by the AG1 IA strain of R. solani in rice at 12, 24, 36, 48, and 72 h. By comparing the transcriptomes of TeQing (a moderately resistant cultivar) and Lemont (a susceptible cultivar) leaves, variable transcriptional responses under control and infection conditions were revealed. From these data, 4,802 differentially expressed genes (DEGs) were identified. Gene ontology and pathway enrichment analyses suggested that most DEGs and related metabolic pathways in both rice genotypes were common and spanned most biological activities after AG1 IA inoculation. The main difference between the resistant and susceptible plants was a difference in the timing of the response to AG1 IA infection. Photosynthesis, photorespiration, and jasmonic acid and phenylpropanoid metabolism play important roles in disease resistance, and the relative response of disease resistance-related pathways in TeQing leaves was more rapid than that of Lemont leaves at 12 h. Here, the transcription data include the most comprehensive list of genes and pathway candidates induced by AG1 IA that is available for rice and will serve as a resource for future studies into the molecular mechanisms of the responses of rice to AG1 IA. PMID:28861102

  3. 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

  4. 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.

  5. 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.

  6. Flavonoid composition and antioxidant activities of Chinese local pummelo (Citrus grandis Osbeck.) varieties.

    PubMed

    Xi, Wanpeng; Fang, Bo; Zhao, Qiyang; Jiao, Bining; Zhou, Zhiqin

    2014-10-15

    China is one of the most important diversity centres of the genus Citrus L. and is particularly rich in pummelo germplasm. In this study, the flavonoids in the peels and pulps of 28 Chinese local pummelos and four grapefruits were determined by optimised Ultra Performance Liquid Chromatography (UPLC), and their antioxidant capacities were evaluated using 2,2-diphenyl-1-picrylhydrazyl radicals (DPPH), ferric reducing/antioxidant power (FRAP) and superoxide anion methods. We found that naringin was the predominant flavonoid in pummelo, while naringin and neohesperidin were the predominant flavonoids in grapefruit. The fruit peels of Citrus paradisi cvs. Rio Red and Cocktail had the highest contents of naringin (9871.69mg/kg FW) and neohesperidin (7011.15mg/kg FW), respectively. Overall, C. paradisi cvs. Cocktail, Rio Red and Changshanhuyou, Citrus grandis cvs. 28-19, Chandler, and Hongxinyou contained more flavonoids and exhibited higher antioxidant capacities and are potentially good sources of phytochemicals and natural antioxidants. Copyright © 2014 Elsevier Ltd. All rights reserved.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. A resistance locus in the American heirloom rice variety Carolina Gold Select is triggered by TAL effectors with diverse predicted targets and is effective against African strains of Xanthomonas oryzae pv. oryzicola

    PubMed Central

    Triplett, Lindsay R.; Cohen, Stephen P.; Heffelfinger, Christopher; Schmidt, Clarice L.; Huerta, Alejandra; Tekete, Cheick; Verdier, Valerie; Bogdanove, Adam J.; Leach, Jan E.

    2016-01-01

    Summary The rice pathogens Xanthomonas oryzae pathovar (pv.) oryzae and pv. oryzicola produce numerous transcription activator-like (TAL) effectors that increase bacterial virulence by activating expression of host susceptibility genes. Rice resistance mechanisms against TAL effectors include polymorphisms that prevent effector binding to susceptibility gene promoters, or that allow effector activation of resistance genes. This study identifies, in the heirloom variety Carolina Gold Select, a third mechanism of rice resistance involving TAL effectors. This resistance manifests through strong suppression of disease development in response to diverse TAL effectors from both X. oryzae pathovars. The resistance can be triggered by an effector with only 3.5 central repeats, is independent of the composition of the repeat variable diresidues that determine TAL effector binding specificity, and is independent of the transcriptional activation domain. We determined that the resistance is conferred by a single dominant locus, designated Xo1, that maps to a 1.09 Mbp fragment on chromosome 4. The Xo1 interval also confers complete resistance to the strains in the African clade of X. oryzae pv. oryzicola, representing the first dominant resistance locus against bacterial leaf streak in rice. The strong phenotypic similarity between the TAL effector triggered resistance conferred by Xo1 and that conferred by the tomato resistance gene Bs4 suggests that monocots and dicots share an ancient or convergently evolved mechanism to recognize analogous TAL effector epitopes. PMID:27197779

  12. 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...

  13. 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...

  14. 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.

  15. 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

  16. 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

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

    PubMed

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

    2013-12-01

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

  18. Exogenous Proline and Glycine Betaine Mediated Upregulation of Antioxidant Defense and Glyoxalase Systems Provides Better Protection against Salt-Induced Oxidative Stress in Two Rice (Oryza sativa L.) Varieties

    PubMed Central

    Hasanuzzaman, Mirza; Alam, Md. Mahabub; Rahman, Anisur; Hasanuzzaman, Md.; Nahar, Kamrun; Fujita, Masayuki

    2014-01-01

    The present study investigates the roles of exogenous proline (Pro, 5 mM) and glycine betaine (GB, 5 mM) in improving salt stress tolerance in salt sensitive (BRRI dhan49) and salt tolerant (BRRI dhan54) rice (Oryza sativa L.) varieties. Salt stresses (150 and 300 mM NaCl for 48 h) significantly reduced leaf relative water (RWC) and chlorophyll (chl) content and increased endogenous Pro and increased lipid peroxidation and H2O2 levels. Ascorbate (AsA), glutathione (GSH) and GSH/GSSG, ascorbate peroxidae (APX), monodehydroascorbate reductase (MDHAR), dehydroascorbate reductase (DHAR), glutathione reductase (GR), glutathione peroxidase (GPX), catalase (CAT), and glyoxalase I (Gly I) activities were reduced in sensitive variety and these were increased in tolerant variety due to salt stress. The glyoxalase II (Gly II), glutathione S-transferase (GST), and superoxide dismutase (SOD) activities were increased in both cultivars by salt stress. Exogenous Pro and GB application with salt stress improved physiological parameters and reduced oxidative damage in both cultivars where BRRI dhan54 showed better tolerance. The result suggests that exogenous application of Pro and GB increased rice seedlings' tolerance to salt-induced oxidative damage by upregulating their antioxidant defense system where these protectants rendered better performance to BRRI dhan54 and Pro can be considered as better protectant than GB. PMID:24991566

  19. 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. © The Author 2015. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please email: journals.permissions@oup.com.

  20. 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

  1. 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.

  2. 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

  3. 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

  4. 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.

  5. 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

  6. 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.

  7. 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.

  8. P1-independent replication and local movement of Rice yellow mottle virus in host and non-host plant species.

    PubMed

    Nummert, Grete; Sõmera, Merike; Uffert, Gabriela; Abner, Erik; Truve, Erkki

    2017-02-01

    Sobemovirus P1 protein, characterized previously as a suppressor of posttranscriptional gene silencing, is required for systemic virus spread and infection in plants. Mutations in the ORF1 initiation codon do not affect viral replication indicating P1 is not necessary for this process. Wild type, recombinant and P1 deletion mutants of Cocksfoot mottle virus and Rice yellow mottle virus were used to infect oat, rice, wheat, barley, Arabidopsis thaliana and Nicotiana benthamiana plants. Wild type RYMV, RYMV without P1 and RYMV with CfMV P1 were detected in inoculated leaves of all tested plant species. We found that RYMV does not need P1 for replication and for local movement neither in host nor non-host species tested in this study. However, it is crucial for successful systemic spread of the virus in its host plant rice. Moreover, adding CfMV P1 into RYMV genome did not help it to overcome restriction to the inoculated leaf. Copyright © 2016 Elsevier Inc. All rights reserved.

  9. 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.

  10. 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.

  11. "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.

  12. "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.

  13. Aflatoxin (B1 , B2 , G1 , and G2 ) contamination in rice of Mexico and Spain, from local sources or imported.

    PubMed

    Suárez-Bonnet, Elena; Carvajal, Magda; Méndez-Ramírez, Ignacio; Castillo-Urueta, Pável; Cortés-Eslava, Josefina; Gómez-Arroyo, Sandra; Melero-Vara, José María

    2013-11-01

    Rice is an important cereal but it is often contaminated with aflatoxins (AFs). The purpose of this study was to identify and quantify AF (B1 , B2 , G1 , and G2 ) in 67 rice samples cultivated in Mexico and Spain, and from imported crops collected in 2008 and 2009. The methodology was validated, the rice samples were concentrated and purified with immunoaffinity columns and were quantified by high-pressure liquid chromatography (HPLC). The average total AF (AFt) in the Spanish rice was 37.3 μg/kg, the range was from 1.6 to 1383 μg/kg, the most contaminated samples being from San Juan de Aznalfarache, Sevilla (AFt = 138.6 μg/kg), from Tortosa, Tarragona (AFt = 104.6 μg/kg), and Calasparra, Murcia (AFt = 103.9 μg/kg). The rice imported from France to Spain had AFt of 26.6 μg/kg and from Pakistan AFt of 18.4 μg/kg, showing less AF contamination than the local one. The rice which originated from Mexico contained (AFt = 16.9 μg/kg), and those imported from the United States (AFt = 14.4 μg/kg) and Uruguay (AFt = 15.6 μg/kg). The imported rice had better quality in terms of the presence of AFs.

  14. [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.

  15. 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

  16. 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.

  17. 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

  18. Characterization of RNA binding protein RBP-P reveals a possible role in rice glutelin gene expression and RNA localization.

    PubMed

    Doroshenk, Kelly A; Tian, Li; Crofts, Andrew J; Kumamaru, Toshihiro; Okita, Thomas W

    2014-07-01

    RNA binding proteins (RBPs) play an important role in mRNA metabolism including synthesis, maturation, transport, localization, and stability. In developing rice seeds, RNAs that code for the major storage proteins are transported to specific domains of the cortical endoplasmic reticulum (ER) by a regulated mechanism requiring RNA cis-localization elements, or zipcodes. Putative trans-acting RBPs that recognize prolamine RNA zipcodes required for restricted localization to protein body-ER have previously been identified. Here, we describe the identification of RBP-P using a Northwestern blot approach as an RBP that recognizes and binds to glutelin zipcode RNA, which is required for proper RNA localization to cisternal-ER. RBP-P protein expression coincides with that of glutelin during seed maturation and is localized to both the nucleus and cytosol. RNA-immunoprecipitation and subsequent RT-PCR analysis further demonstrated that RBP-P interacts with glutelin RNAs. In vitro RNA-protein UV-crosslinking assays showed that recombinant RBP-P binds strongly to glutelin mRNA, and in particular, 3' UTR and zipcode RNA. RBP-P also exhibited strong binding activity to a glutelin intron sequence, suggesting that RBP-P might participate in mRNA splicing. Overall, these results support a multifunctional role for RBP-P in glutelin mRNA metabolism, perhaps in nuclear pre-mRNA splicing and cytosolic localization to the cisternal-ER.

  19. 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.

  20. 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.

  1. 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.

  2. 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

  3. Over-expression of Arabidopsis thaliana SFD1/GLY1, the gene encoding plastid localized glycerol-3-phosphate dehydrogenase, increases plastidic lipid content in transgenic rice plants

    PubMed Central

    Siddiqui, Adnan; Singh, Subaran; Banday, Zeeshan Zahoor; Nandi, Ashis Kumar

    2016-01-01

    Lipids are the major constituents of all membranous structures in plants. Plants possess two pathways for lipid biosynthesis: the prokaryotic pathway (i.e., plastidic pathway) and the eukaryotic pathway (i.e., endoplasmic-reticulum (ER) pathway). Whereas some plants synthesize galactolipids from diacylglycerol assembled in the plastid, others, including rice, derive their galactolipids from diacylglycerols assembled by the eukaryotic pathway. Arabidopsis thaliana glycerol-3-phosphate dehydrogenase (G3pDH), coded by SUPPRESSOR OF FATTY ACID DESATURASE 1 (SFD1; alias GLY1) gene, catalyzes the formation of glycerol 3-phosphate (G3p), the backbone of many membrane lipids. Here SFD1 was introduced to rice as a transgene. Arabidopsis SFD1 localizes in rice plastids and its over-expression increases plastidic membrane lipid content in transgenic rice plants without any major impact on ER lipids. The results suggest that over-expression of plastidic G3pDH enhances biosynthesis of plastid-localized lipids in rice. Lipid composition in the transgenic plants is consistent with increased phosphatidylglycerol synthesis in the plastid and increased galactolipid synthesis from diacylglycerol produced via the ER pathway. The transgenic plants show a higher photosynthetic assimilation rate, suggesting a possible application of this finding in crop improvement. PMID:26747130

  4. Over-expression of Arabidopsis thaliana SFD1/GLY1, the gene encoding plastid localized glycerol-3-phosphate dehydrogenase, increases plastidic lipid content in transgenic rice plants.

    PubMed

    Singh, Vijayata; Singh, Praveen Kumar; Siddiqui, Adnan; Singh, Subaran; Banday, Zeeshan Zahoor; Nandi, Ashis Kumar

    2016-03-01

    Lipids are the major constituents of all membranous structures in plants. Plants possess two pathways for lipid biosynthesis: the prokaryotic pathway (i.e., plastidic pathway) and the eukaryotic pathway (i.e., endoplasmic-reticulum (ER) pathway). Whereas some plants synthesize galactolipids from diacylglycerol assembled in the plastid, others, including rice, derive their galactolipids from diacylglycerols assembled by the eukaryotic pathway. Arabidopsis thaliana glycerol-3-phosphate dehydrogenase (G3pDH), coded by SUPPRESSOR OF FATTY ACID DESATURASE 1 (SFD1; alias GLY1) gene, catalyzes the formation of glycerol 3-phosphate (G3p), the backbone of many membrane lipids. Here SFD1 was introduced to rice as a transgene. Arabidopsis SFD1 localizes in rice plastids and its over-expression increases plastidic membrane lipid content in transgenic rice plants without any major impact on ER lipids. The results suggest that over-expression of plastidic G3pDH enhances biosynthesis of plastid-localized lipids in rice. Lipid composition in the transgenic plants is consistent with increased phosphatidylglycerol synthesis in the plastid and increased galactolipid synthesis from diacylglycerol produced via the ER pathway. The transgenic plants show a higher photosynthetic assimilation rate, suggesting a possible application of this finding in crop improvement.

  5. Proteolytic activity, mycotoxins and andrastin A in Penicillium roqueforti strains isolated from Cabrales, Valdeón and Bejes-Tresviso local varieties of blue-veined cheeses.

    PubMed

    Fernández-Bodega, M A; Mauriz, E; Gómez, A; Martín, J F

    2009-11-30

    High quality local varieties of blue-veined cheese are made in the villages of the valleys of Cabrales, Valdeón and Bejes-Tresviso in North Spain. Penicillium roqueforti strains have been isolated from each of those blue cheeses and compared with the collection strain P. roqueforti CECT 2905 (ATCC 10110) and a strain 'Valdeón-industrial' used for large scale production of Valdeón cheese. Using molecular genetics techniques and 5.8S and 18S rRNAs and the D1-D2 regions of 28S rRNA all strains were identified as authentic P. roqueforti. These strains from local varieties of blue cheese could be distinguished from the Valdeón-industrial strain and the control strain CECT 2905 by the mitochondrial DNA restriction pattern. The industrial strain showed high levels of aspartylprotease AspA, whereas the culture collection strain showed barely detectable levels of this enzyme, as shown by proteolysis tests and by immunodetection with anti-AspA antibodies. The lipolytic activity was similar in the strains isolated from the three types of local blue cheeses. The strains isolated from the local varieties of the blue cheese produced moderate levels of PR toxin, whereas the Valdeón-industrial strains showed a higher content of this mycotoxin. All strains (except the control strain CECT 2905) showed similar levels of roquefortine C. The antitumoral compound andrastin A was produced by all strains at different levels. P. roqueforti CECT 2905 showed high ability to synthesize this compound. Andrastin A was present in all industrial and local varieties of blue cheese. The content of andrastin A was similar to that of other well-known blue cheeses from France and Denmark.

  6. Developing and delivering biofortified Rice to the consumer

    USDA-ARS?s Scientific Manuscript database

    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...

  7. 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.

  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. 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.

  10. 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

  11. 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.

  12. 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

  13. 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.

  14. 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

  15. Mutation of the rice XA21 predicted nuclear localization sequence does not affect resistance to Xanthomonas oryzae pv. oryzae

    DOE PAGES

    Wei, Tong; Chen, Tsung-Chi; Ho, Yuen Ting; ...

    2016-10-05

    Background: The rice receptor kinase XA21 confers robust resistance to the bacterial pathogenXanthomonas oryzae pv.oryzae(Xoo). We previously reported that XA21 is cleaved in transgenic plants overexpressing XA21 with a GFP tag (Ubi-XA21-GFP) and that the released C-terminal domain is localized to the nucleus. XA21 carries a predicted nuclear localization sequence (NLS) that directs the C-terminal domain to the nucleus in transient assays, whereas alanine substitutions in the NLS disrupt the nuclear localization. Methods: To determine if the predicted NLS is required for XA21-mediated immunityin planta, we generated transgenic plants overexpressing an XA21 variant carrying the NLS with the same alaninemore » substitutions (Ubi-XA21nls-GFP). Results: Ubi- XA21nls-GFP plants displayed slightly longer lesion lengths, higherXoo bacterial populations after inoculation and lower levels of reactive oxygen species production compared with the Ubi- XA21-GFP control plants. However, the Ubi- XA21nls-GFP plants express lower levels of protein than that observed inUbi- XA21-GFP. Discussion: These results demonstrate that the predicted NLS is not required for XA21-mediated immunity.« less

  16. 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

  17. The strategies of local farmers' water management and the eco-hydrological effects of irrigation-drainage engineering systems in world heritage of Honghe Hani Rice Terraces

    NASA Astrophysics Data System (ADS)

    Gao, Xuan

    2017-04-01

    Terraces are built in mountainous regions to provide larger area for cultivation,in which the hydrological and geomorphological processes are impacted by local farmers' water management strategies and are modified by manmade irrigation-drainage engineering systems.The Honghe Hani Rice Terraces is a 1300a history of traditional agricultural landscape that was inscribed in the 2013 World Heritage List.The local farmers had developed systematic water management strategies and built perfect irrigation-drainage engineering systems to adapt the local rainfall pattern and rice farming activities.Through field investigation,interviews,combined with Geographic Information Systems,Remote Sensing images and Global Positioning Systems technology,the water management strategies as well as the irrigation-drainage systems and their impacts on eco-hydrological process were studied,the results indicate:Firstly,the local people created and maintained an unique woodcarving allocating management system of irrigating water over hundreds years,which aids distributing water and natural nutrition to each terrace field evenly,and regularly according to cultivation schedule.Secondly,the management of local people play an essential role in effective irrigation-drainage engineering system.A ditch leader takes charge of managing the ditch of their village,keeping ample amount of irrigation water,repairing broken parts of ditches,dealing with unfair water using issues,and so on.Meanwhile,some traditional leaders of minority also take part in.Thus, this traditional way of irrigation-drainage engineering has bringed Hani people around 1300 years of rice harvest for its eco-hydrological effects.Lastly we discuss the future of Honghe Hani Rice Terraces,the traditional cultivation pattern has been influenced by the rapid development of modern civilization,in which some related changes such as the new equipment of county roads and plastic channels and the water overusing by tourism are not totally

  18. Iron absorption from brown rice/brown rice-based meal and milled rice/milled rice-based meal.

    PubMed

    Trinidad, Trinidad P; Mallillin, Aida C; Sagum, Rosario S; Briones, Dave P; Encabo, Rosario R; Juliano, Bienvenido O

    2009-12-01

    Milled rice is the staple food among Filipinos and is mostly consumed three times a day. Rice as a source of iron could therefore have an important role in the existing 37% prevalence of iron-deficiency anemia in the country. Previous iron absorption studies in Filipinos from rice and rice-based meals were carried out on milled rice but no research was done on brown rice of the same variety. This leads to the hypothesis that brown rice may be better than milled rice in terms of iron content. To determine iron absorption from brown rice and brown rice-based meal, and from milled rice and milled rice-based meal of the same variety. The rice variety used in the study was F(2) seeds of PSB Rc72H. Iron absorption from brown/milled rice and brown/milled rice-based meals was determined in 12 healthy human subjects from the incorporation of radioisotopes of iron into erythrocytes 14 days after administration of the labeled rice/rice-based meals. The above samples were also analyzed for nutrient content, including dietary fiber, and iron. The iron content of brown rice was significantly higher (1.1 +/- 0.1 mg/100 g) than that of milled rice (0.6 +/- 0.1 mg/100 g). Brown rice has significantly greater amounts of total dietary fiber (5.4 +/- 0.4%) than milled rice (1.7 +/- 0.2%; P < 0.05). Both tannic acid and phytic acid contents in brown rice (56.9 +/- 3.2 mg/100 g and 290.1 +/- 18.0 mg/100 g, respectively) were significantly higher than those of milled rice (21.3 +/- 2.3 mg/100 g and 84.0 +/- 12.4 mg/100 g, respectively; P<0.05). The amount of iron absorbed from brown rice (0.13 +/- 0.02 mg) did not differ significantly from that from milled rice (0.14 +/- 0.02 mg). However, the amount from brown rice-based meal (0.36 +/- 0.04 mg) differed significantly from that from brown rice (P<0.05) as well as that from milled rice-based meal (0.35 +/- 0.03 mg) from that from milled rice (P<0.05). Moreover, brown rice-based meal did not differ significantly from milled rice-based meal

  19. 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.

  20. 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

  1. Citizen earthquake alert using near real time PGA estimation from a local array combining a variety of accelerometric instruments

    NASA Astrophysics Data System (ADS)

    Melis, Nikolaos S.; Konstantinou, Konstantinos; Kalogeras, Ioannis; Sokos, Efthimios; Tselentis, G.-Akis

    2017-04-01

    It is of a great importance to assess rapidly the intensity of a felt event in a highly populated environment. Rapid and reliable information plays a key role to decision making responses, by performing correctly the first steps after a felt ground shaking. Thus, it is important to accurately respond to urgent societal demand using reliable information. A strong motion array is under deployment and trial operation in the area of Patras, Greece. It combines: (a) standard accelerometric stations operated by the National Observatory of Athens, Institute of Geodynamics (NOA), (b) QCN-type USB MEMS acceleration sensors deployed in schools and (c) P-alert MEMS acceleration devices deployed in public sector buildings as well as in private dwellings. The array intends to cover the whole city of Patras and the populated suburbs. All instruments are operating in near real time and they are linked to a combined Earthworm - SeisComP3 server at NOA, Athens. Rapid intensity estimation can be also performed by the P-alert accelerometers locally, but the performance of a near real time intensity estimation system is under operation at NOA. The procedure is based on observing the maximum PGA value at each instrument and empirically estimate the corresponding intensity. The values are also fed to a SeisComP3 based ShakeMap procedure that is served at NOA and uses the scwfparam module of SeisComP3. Earthquake activity has been recorded so far from the western Corinth Gulf, the Ionian Islands and Achaia-Elia area, western Peloponnesus. The first phase involves correlation tests of collocated instruments and assessment of their performance to low intensity as well as to strongly felt events in the Patras city area. Steps of expanding the array are also under consideration, in order to cover the wider area of northwestern Peloponnesus and Ionian islands.

  2. 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

  3. Impaired function of the tonoplast-localized sucrose transporter in rice, OsSUT2, limits the transport of vacuolar reserve sucrose and affects plant growth.

    PubMed

    Eom, Joon-Seob; Cho, Jung-Il; Reinders, Anke; Lee, Sang-Won; Yoo, Youngchul; Tuan, Pham Quoc; Choi, Sang-Bong; Bang, Geul; Park, Youn-Il; Cho, Man-Ho; Bhoo, Seong Hee; An, Gynheung; Hahn, Tae-Ryong; Ward, John M; Jeon, Jong-Seong

    2011-09-01

    Physiological functions of sucrose (Suc) transporters (SUTs) localized to the tonoplast in higher plants are poorly understood. We here report the isolation and characterization of a mutation in the rice (Oryza sativa) OsSUT2 gene. Expression of OsSUT2-green fluorescent protein in rice revealed that OsSUT2 localizes to the tonoplast. Analysis of the OsSUT2 promoter::β-glucuronidase transgenic rice indicated that this gene is highly expressed in leaf mesophyll cells, emerging lateral roots, pedicels of fertilized spikelets, and cross cell layers of seed coats. Results of Suc transport assays in yeast were consistent with a H(+)-Suc symport mechanism, suggesting that OsSUT2 functions in Suc uptake from the vacuole. The ossut2 mutant exhibited a growth retardation phenotype with a significant reduction in tiller number, plant height, 1,000-grain weight, and root dry weight compared with the controls, the wild type, and complemented transgenic lines. Analysis of primary carbon metabolites revealed that ossut2 accumulated more Suc, glucose, and fructose in the leaves than the controls. Further sugar export analysis of detached leaves indicated that ossut2 had a significantly decreased sugar export ability compared with the controls. These results suggest that OsSUT2 is involved in Suc transport across the tonoplast from the vacuole lumen to the cytosol in rice, playing an essential role in sugar export from the source leaves to sink organs.

  4. 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.

  5. Weed control in rice with metham-sodium.

    PubMed

    Sparacino, A C; Ferro, R; Riva, N; Ditto, D; Tano, F; Croce, G; Rabasse, J M

    2006-01-01

    Metam-sodium is a soil fumigant with herbicidal properties. A field experiment was conducted in 2000 at Copiano (Pavia, Italy) to determine the efficacy of three rates of metam-sodium (300, 450 and 600 l/ha) at three different planting times (5, 12 and 18 days after chemical treatments) for the control of weeds in rice cultivation. The study mainly focused on the control of red rice (Oryza sativa var. selvatica), a weed which is worldwide distributed in rice fields and difficult to eradicate Test design was a split-plot with four replications. The main plot size was 13, 5 by 15 m and the subplot size was 13, 5 by 5 m. The chemical treatments were carried out as pre-sowing. Two days after chemical treatments, all field plots were flooded with 10 cm of water as practiced locally. An early variety of rice (Loto) was sown at 150 kg/ha. Weed control was visually evaluated as a percentage of ground covering by all weeds and by each weed individually at three, four and five weeks after treatments. Observations were made also on rice selectivity, and rice grain yield was assessed at the end. Metam-sodium did not injure the rice plants. Metam-sodium at 450 l/ha controlled 100%, 97% and 92% of red rice at the first, second and third observations, respectively. Good results were also obtained with metam-sodium at 300 and 600 l/ha, which controlled 94 to 82% of red rice during the season. Echinochloa crus-galli was better controlled with the higher rates of metam-sodium, particularly in the early part of the season. Metam-sodium did not show enough efficacy in this study against Heteranthera reniformis, Bulboschoenus maritimus and Lindernia spp. The best rice grain yield was obtained with all rates of metam-sodium, when rice was sown 5 days after treatment.

  6. Variation in arsenic bioavailability in rice genotypes using swine model: An animal study.

    PubMed

    Islam, Shofiqul; Rahman, Mohammad Mahmudur; Duan, Luchun; Islam, M R; Kuchel, Tim; Naidu, Ravi

    2017-12-01

    An in vivo assay using swine was used to measure the absolute bioavailability (AB) of As from cooked rice of twelve genotypes commonly grown in Bangladesh. An assessment of both total As in rice and its bioavailability is crucial for estimating human exposure following dietary intake by the local community. Average As concentrations in each rice genotype ranged from 108±4μg/kg to 580±6μg/kg. Arsenic speciation shows that most of the rice genotype contains 73 to 100% inorganic As. Swine were administered with As orally and via intravenous method, i.e. injection and fed certain common Bangladeshi rice genotypes (cooked). Swine blood As levels were measured to calculate As bioavailability from rice. Pilot studies shows that for As(III) and As(V), 90.8±12.4% and 85.0±19.2% of the administered oral dose was absorbed from the gastrointestinal tract whereas organic As was poorly absorbed resulting in low bioavailability values 20.2±2.6% (MMA) to 31.2±3.4% (DMA), respectively. These studies demonstrates that rice genotypic characters influenced As bioavailability in rice grown in As-contaminated areas and the bioavailability varied between 25% and 94%. Arsenic in salt tolerant rice genotypes Binadhan-10 and BRRI dhan47 as well as brown rice genotypes Kheali Boro and Local Boro has lower bioavailability (<50%) compared to other rice genotypes. The most commonly cultivated and consumed variety (BRRI dhan28) has As bioavailability of 70%, which poses a significant risk to consumers. Calculation of maximum tolerable daily intake (MTDI) for humans due to consumption of rice based on bioavailability data was higher than those calculated based on inorganic and organic As concentration in rice genotypes. Copyright © 2017 Elsevier B.V. All rights reserved.

  7. 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. © 2013 John Wiley & Sons Ltd.

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

    USDA-ARS?s Scientific Manuscript database

    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...

  9. 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

  10. 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

  11. 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.

  12. Surface Variety

    NASA Image and Video Library

    2015-09-10

    Mosaic of high-resolution images of Pluto, sent back from NASA's New Horizons spacecraft from Sept. 5 to 7, 2015. The image is dominated by the informally-named icy plain Sputnik Planum, the smooth, bright region across the center. This image also features a tremendous variety of other landscapes surrounding Sputnik. The smallest visible features are 0.5 miles (0.8 kilometers) in size, and the mosaic covers a region roughly 1,000 miles (1600 kilometers) wide. The image was taken as New Horizons flew past Pluto on July 14, 2015, from a distance of 50,000 miles (80,000 kilometers). http://photojournal.jpl.nasa.gov/catalog/PIA19936

  13. Surface Variety

    NASA Image and Video Library

    2015-09-10

    Mosaic of high-resolution images of Pluto, transmitted by NASA's New Horizons spacecraft from Sept. 5 to 7, 2015. The image is dominated by the informally-named icy plain Sputnik Planum, the smooth, bright region across the center. This image also features a tremendous variety of other landscapes surrounding Sputnik. The smallest visible features are 0.5 miles (0.8 kilometers) in size, and the mosaic covers a region roughly 1,000 miles (1,600 kilometers) wide. The image was taken as New Horizons flew past Pluto on July 14, 2015, from a distance of 50,000 miles (80,000 kilometers). The two white rectangles show the locations of the two closeup views by New Horizons, released separately. http://photojournal.jpl.nasa.gov/catalog/PIA19935

  14. Communities of endophytic microorganisms in different developmental stages from a local variety as well as transgenic and conventional isogenic hybrids of maize.

    PubMed

    da Silva, Kelly Justin; de Armas, Rafael Dutra; Soares, Cláudio Roberto F S; Ogliari, Juliana Bernardi

    2016-11-01

    The diversity of endophytic microorganisms may change due to the genotype of the host plant and its phenological stage. In this study we evaluated the effect of phenological stage, transgenes and genetic composition of maize on endophytic bacterial and fungal communities. The maize populations were composed of a local variety named Rosado (RS) and three isogenic hybrids. One isogenic hybrid was not genetically modified (NGM). Another hybrid (Hx) contained the transgenes cry1F and pat (T1507 event), which provide resistance to insects of the order Lepidoptera and tolerance to the glufosinate-ammonium herbicide, respectively. The third hybrid (Hxrr) contained the transgene cp4 epsps (NK603 event) combined with the transgenes cry1F and pat (T1507 event), which allow tolerance to the Roundup Ready herbicide, besides the characteristics of Hx. Evaluation of the foliar tissue was done through PCR-DGGE analysis, with specific primers for bacteria and fungi within four phenological stages of maize. The endophytic bacteria were only clustered by phenological stages; the structure of the fungal community was clustered by maize genotypes in each phenological stage. The fungal community from the local variety RS was different from the three hybrids (NGM, Hx and Hxrr) within the four evaluated stages. In the reproductive stage, the fungal community from the two transgenic hybrids (Hx and Hxrr) were separated, and the Hxrr was different from NGM, in the two field experiments. This research study showed that the genetic composition of the maize populations, especially the presence of transgenes, is the determining factor for the changes detected in the endophytic fungal community of maize leaves.

  15. 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.

  16. 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.

  17. 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

  18. 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

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

    PubMed

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

    2014-01-01

    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. 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). 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. 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.

  20. 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.

  1. 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.

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

    USDA-ARS?s Scientific Manuscript database

    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 ...

  3. 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.

  4. 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.

  5. 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

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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

  11. Plasma Membrane Localization Is Essential for Oryza sativa Pto-Interacting Protein 1a-Mediated Negative Regulation of Immune Signaling in Rice1[W][OPEN

    PubMed Central

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

    2014-01-01

    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. PMID:24958714

  12. 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.

  13. 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).

  14. 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.

  15. 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.

  16. 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

  17. 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

    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.

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

    PubMed

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

    2006-01-01

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

  19. Exploring Japan through Rice.

    ERIC Educational Resources Information Center

    Wojtan, Linda S.

    1998-01-01

    Explores the role of rice in Japanese culture by presenting historical background and teaching activities in a variety of categories, such as language, sociology, history, and contemporary politics. Suggests teachers create cross-cultural comparisons; for example, the role of corn in the United States. Provides a list of teacher resources. (CMK)

  20. 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.

  1. Mercury pollution in two typical areas in Guizhou province, China and its neurotoxic effects in the brains of rats fed with local polluted rice.

    PubMed

    Cheng, Jinping; Yuan, Tao; Wang, Wenhua; Jia, Jinping; Lin, Xueyu; Qu, Liya; Ding, Zhenhua

    2006-12-01

    Guizhou province, which located in southwestern of China, is an important mercury (Hg) production center. This study was to investigate the environmental levels and ecological effects of mercury in two typical Hg polluted areas in Guizhou province. In addition, to improve the understanding of the neurotoxic effects of Hg, a rats based laboratory study was also carried out in this study. Samples of water, soil, plants, crops and animals collected from Wanshan mercury mine area, Guzhou province, were analyzed by mercury analyzer. The effects of Hg contaminated rice on the expression of c-jun mRNA in rat's brain and the expression of c-JUN protein in cortex, hippocampus were observed using reverse transcription polymerase chain reaction (RT-PCR) and immunocytochemical methods. The results showed that the mercury contents in most environmental samples of aquatics, soil, atmosphere and the biomass of corn, plant and animals, were higher than the national standard and the corresponding data from unpolluted area. It was found mercury pollutions were significant in soil and air. In the laboratory study, the expression of c-jun mRNA and its protein was significantly induced by Hg polluted rice collected from local area. Selenium could reduce the Hg accumulation in the body and had antagonist effect on Hg in terms of the expression of c-jun mRNA and c-JUN protein. The environmental data and Hg levels in different creatures collected in this study will facilitate the environmental and ecological risk assessment of Hg in the polluted areas. It was urged to be alert of mental health problem in human beings when any kind of Hg-polluted food was taken. More efforts should be performed to protect the local ecosystem and human health in the mercury polluted area of Wanshan, Guizhou province of China.

  2. 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.

  3. 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.

  4. Mutation of the rice XA21 predicted nuclear localization sequence does not affect resistance to Xanthomonas oryzae pv. oryzae

    SciTech Connect

    Wei, Tong; Chen, Tsung-Chi; Ho, Yuen Ting; Ronald, Pamela C.

    2016-10-05

    Background: The rice receptor kinase XA21 confers robust resistance to the bacterial pathogenXanthomonas oryzae pv.oryzae(Xoo). We previously reported that XA21 is cleaved in transgenic plants overexpressing XA21 with a GFP tag (Ubi-XA21-GFP) and that the released C-terminal domain is localized to the nucleus. XA21 carries a predicted nuclear localization sequence (NLS) that directs the C-terminal domain to the nucleus in transient assays, whereas alanine substitutions in the NLS disrupt the nuclear localization. Methods: To determine if the predicted NLS is required for XA21-mediated immunityin planta, we generated transgenic plants overexpressing an XA21 variant carrying the NLS with the same alanine substitutions (Ubi-XA21nls-GFP). Results: Ubi- XA21nls-GFP plants displayed slightly longer lesion lengths, higherXoo bacterial populations after inoculation and lower levels of reactive oxygen species production compared with the Ubi- XA21-GFP control plants. However, the Ubi- XA21nls-GFP plants express lower levels of protein than that observed inUbi- XA21-GFP. Discussion: These results demonstrate that the predicted NLS is not required for XA21-mediated immunity.

  5. 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.

  6. 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

  7. 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.

  8. 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.

  9. Potential of rice stubble as a reservoir of bradyrhizobial inoculum in rice-legume crop rotation.

    PubMed

    Piromyou, Pongdet; Greetatorn, Teerana; Teamtisong, Kamonluck; Tittabutr, Panlada; Boonkerd, Nantakorn; Teaumroong, Neung

    2017-09-15

    Bradyrhizobium encompasses a variety of bacteria that can live in symbiotic and endophytic associations with leguminous and non-leguminous plants such as rice. Therefore, it can be expected that rice endophytic bradyrhizobia can be applied in the rice-legume crop rotation system. Some endophytic bradyrhizobial strains were isolated from rice (Oryza sativa L.) tissues. The rice biomass could be enhanced when supplying KNO3, NH4NO3, or urea with bradyrhizobial strain inoculation, especially strain SUTN9-2. In contrast, the strains which suppressed rice growth were photosynthetic bradyrhizobia and also found to produce nitric oxide (NO) in the rice root. The expression of genes involved in NO production was conducted using qRT-PCR technique. The nirK gene expression level of SUT-PR48 with nitrate was higher than that of norB gene. In contrast, the inoculation of SUTN9-2 resulted in a lower expression of nirK gene when compared with norB gene. These results suggest that SUT-PR48 may accumulate NO more than SUTN9-2 does. Furthermore, the nifH expression of SUTN9-2 was induced in treatment without nitrogen supplementation in endophytic association with rice. The IAA and ACC deaminase produced in planta by SUTN9-2 were also detected. Enumeration of rice endophytic bradyrhizobia from rice tissues revealed that SUTN9-2 still persisted in rice tissues until rice-harvesting season. The mung bean (Vigna radiata) can be nodulated after rice stubbles were decomposed. Therefore, it is possible that rice stubbles can be used as inoculum in the rice-legume crop rotation system under both low- and high-organic matter soil condition.Importance This study shows that some rice endophytic bradyrhizobia could perform IAA production, and ACC deaminase activity together with nitrogen fixation ability during symbiosis inside rice tissues. These characteristics may play an important role in rice growth promotion by endophytic bradyrhizobium. However, the NO producing strains should be of

  10. 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

  11. Processes underpinning development and maintenance of diversity in rice in West Africa: evidence from combining morphological and molecular markers.

    PubMed

    Mokuwa, Alfred; Nuijten, Edwin; Okry, Florent; Teeken, Béla; 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

  12. Influence of ethnic traditional cultures on genetic diversity of rice landraces under on-farm conservation in southwest China.

    PubMed

    Wang, Yanjie; Wang, Yanli; Sun, Xiaodong; Caiji, Zhuoma; Yang, Jingbiao; Cui, Di; Cao, Guilan; Ma, Xiaoding; Han, Bing; Xue, Dayuan; Han, Longzhi

    2016-10-27

    Crop genetic resources are important components of biodiversity. However, with the large-scale promotion of mono-cropping, genetic diversity has largely been lost. Ex-situ conservation approaches were widely used to protect traditional crop varieties worldwide. However, this method fails to maintain the dynamic evolutionary processes of crop genetic resources in their original habitats, leading to genetic diversity reduction and even loss of the capacity of resistance to new diseases and pests. Therefore, on-farm conservation has been considered a crucial complement to ex-situ conservation. This study aimed at clarifying the genetic diversity differences between ex-situ conservation and on-farm conservation and to exploring the influence of traditional cultures on genetic diversity of rice landraces under on-farm conservation. The conservation status of rice landrace varieties, including Indica and Japonica, non-glutinous rice (Oryza sativa) and glutinous rice (Oryza sativa var. glutinosa Matsum), was obtained through ethno-biology investigation method in 12 villages of ethnic groups from Guizhou, Yunnan and Guangxi provinces of China. The genetic diversity between 24 pairs of the same rice landraces from different times were compared using simple sequence repeat (SSR) molecular markers technology. The landrace paris studied were collected in 1980 and maintained ex-situ, while 2014 samples were collected on-farm in southwest of China. The results showed that many varieties of rice landraces have been preserved on-farm by local farmers for hundreds or thousands of years. The number of alleles (Na), effective number of alleles (Ne), Nei genetic diversity index (He) and Shannon information index (I) of rice landraces were significantly higher by 12.3-30.4 % under on-farm conservation than under ex-situ conservation. Compared with the ex-situ conservation approach, rice landraces under on-farm conservation programs had more alleles and higher genetic diversity. In

  13. Determination of sockage for accurate rough rice quality assessment

    USDA-ARS?s Scientific Manuscript database

    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...

  14. The Puzzle of Italian Rice Origin and Evolution: Determining Genetic Divergence and Affinity of Rice Germplasm from Italy and Asia

    PubMed Central

    Jiang, Zhuxi; Basso, Barbara; Sala, Francesco; Spada, Alberto; Grassi, Fabrizio; Lu, Bao-Rong

    2013-01-01

    The characterization of genetic divergence and relationships of a set of germplasm is essential for its efficient applications in crop breeding and understanding of the origin/evolution of crop varieties from a given geographical region. As the largest rice producing country in Europe, Italy holds rice germplasm with abundant genetic diversity. Although Italian rice varieties and the traditional ones in particular have played important roles in rice production and breeding, knowledge concerning the origin and evolution of Italian traditional varieties is still limited. To solve the puzzle of Italian rice origin, we characterized genetic divergence and relationships of 348 rice varieties from Italy and Asia based on the polymorphisms of microsatellite fingerprints. We also included common wild rice O. rufipogon as a reference in the characterization. Results indicated relatively rich genetic diversity (He = 0.63-0.65) in Italian rice varieties. Further analyses revealed a close genetic relationship of the Italian traditional varieties with those from northern China, which provides strong genetic evidence for tracing the possible origin of early established rice varieties in Italy. These findings have significant implications for the rice breeding programs, in which appropriate germplasm can be selected from a given region and utilized for transferring unique genetic traits based on its genetic diversity and evolutionary relationships. PMID:24265814

  15. (/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.

  16. 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.

  17. 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.

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

    USDA-ARS?s Scientific Manuscript database

    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...

  19. 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.

  20. 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.

  1. 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.

  2. Ethylene-Inhibited Jasmonic Acid Biosynthesis Promotes Mesocotyl/Coleoptile Elongation of Etiolated Rice Seedlings[OPEN

    PubMed Central

    Xiong, Qing; Ma, Biao; Lu, Xiang; Huang, Yi-Hua; He, Si-Jie; Yang, Chao; Yin, Cui-Cui; Zhou, Yang; Wang, Wen-Sheng; Li, Zhi-Kang; Chen, Shou-Yi

    2017-01-01

    Elongation of the mesocotyl and coleoptile facilitates the emergence of rice (Oryza sativa) seedlings from soil and is affected by various genetic and environment factors. The regulatory mechanism underlying this process remains largely unclear. Here, we examined the regulation of mesocotyl and coleoptile growth by characterizing a gaoyao1 (gy1) mutant that exhibits a longer mesocotyl and longer coleoptile than its original variety of rice. GY1 was identified through map-based cloning and encodes a PLA1-type phospholipase that localizes in chloroplasts. GY1 functions at the initial step of jasmonic acid (JA) biosynthesis to repress mesocotyl and coleoptile elongation in etiolated rice seedlings. Ethylene inhibits the expression of GY1 and other genes in the JA biosynthesis pathway to reduce JA levels and enhance mesocotyl and coleoptile growth by promoting cell elongation. Genetically, GY1 acts downstream of the OsEIN2-mediated ethylene signaling pathway to regulate mesocotyl/coleoptile growth. Through analysis of the resequencing data from 3000 rice accessions, we identified a single natural variation of the GY1 gene, GY1376T, which contributes to mesocotyl elongation in rice varieties. Our study reveals novel insights into the regulatory mechanism of mesocotyl/coleoptile elongation and should have practical applications in rice breeding programs. PMID:28465411

  3. 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

  4. Breeding of commercially acceptable allelopathic rice cultivars in China.

    PubMed

    Kong, Chui-Hua; Chen, Xiong-Hui; Hu, Fei; Zhang, Song-Zhu

    2011-09-01

    One promising area of paddy weed control is the potential for exploiting the weed-suppressing ability of rice. This study was conducted to develop commercially acceptable allelopathic rice cultivars using crosses between allelopathic rice variety PI312777 and commercial Chinese cultivars (N2S, N9S, Huahui354, Peiai64S and Tehuazhan35), and to assess their weed suppression and grain yield in paddy fields in relation to their parents. There was a positive dominance in the crosses Huahui354 × PI312777 and N2S × PI312777 but recessive or negative dominance in N9S × PI312777, Peiai64S × PI312777 and Tehuazhan35 × PI312777. Huahui354 × PI312777 and N2S × PI312777 showed stronger weed suppression than their parents and other crosses. Finally, an F8 line with an appearance close to Huahui354 and a magnitude of weed suppression close to PI312777 was obtained from Huahui354 × PI312777. This line, named Huagan-3, was released as a first commercially acceptable allelopathic rice cultivar in China. The grain yield and quality of Huagan-3 met the commercial standard of the local rice industry. Huagan-3 greatly suppressed paddy weeds, although suppression was influenced by year-to-year variation and plant density. There was no certain yield reduction in Huagan-3 even under a slight infestation of barnyard grass in paddy fields. The successful breeding of Huagan-3 with high yield and strong weed suppression may be incorporated into present rice production systems to minimise the amount of herbicide used. Copyright © 2011 Society of Chemical Industry.

  5. 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.

  6. 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

  7. 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.

  8. 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.

  9. 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.

  10. Iron Biofortification of Myanmar Rice

    PubMed Central

    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. PMID:23750162

  11. Investigations of methane emissions from rice cultivation in Indian context.

    PubMed

    Anand, Shalini; Dahiya, R P; Talyan, Vikash; Vrat, Prem

    2005-05-01

    The increasing demand of the growing population requires enhancement in the production of rice. This has a direct bearing on the global environment since the rice cultivation is one of the major contributors to the methane emissions. As the rice cultivation is intensified with the current practices and technologies, the methane fluxes from paddy fields will substantially rise. Improved high yielding rice varieties together with efficient cultivation techniques will certainly contribute to the curtailment of the methane emission fluxes. In this paper, the system dynamic approach is used for estimating the methane emissions from rice fields in India till the year 2020. Mitigation options studied for curtailing the methane emissions include rice production management, use of low methane emitting varieties of rice, water management and fertilizer amendment. The model is validated quantitatively and sensitivity tests are carried out to examine the robustness of the model.

  12. Effects of fresh cassava tops on rumen environment parameters, thyroid gland hormones and liver enzymes of local yellow cattle fed urea-treated fresh rice straw.

    PubMed

    Khang, D N; Wiktorsson, H

    2004-11-01

    In a 4 x 4 Latin square design study, four rumen-cannulated local yellow cattle, average weight 330 kg, were fed urea-treated fresh rice straw (UFRS) ad libitum and given 1 kg cassava root meal daily as basal diet in each 30-day trial period. Four treatment levels of crude protein of fresh cassava tops (FCT) were supplied: 0 (FCT0), 50 (FCT50), 100 (FCT100) and 150 g (FCT150) crude protein per 100 kg body weight. The results showed a continuous decrease in dry matter intake (DMI) of UFRS with increasing level of FCT supplementation (p<0.001). Total DMI for treatments FCT150, FCT100, FCT50 and FCT0 were 2.66, 2.42, 2.23 and 2.05 kg dry matter per 100 kg live weight per day, respectively. Increasing levels of FCT supplementation increased the concentration of total volatile fatty acids (p<0.05) and ammonia (p<0.001) and resulted in a decrease in pH (p<0.05). Rumen protozoa population varied widely but was significantly lower with increasing FCT supplementation (p<0.001), while rumen bacteria population was higher (p<0.05). Overall, average plasma triiodothyronine and thyroxine concentrations in the four groups were respectively 1.36, 0.94, 0.91, 0.80 ng/ml (p<0.01) and 60.9, 48.7, 45.2, 42.5 ng/ml (p<0.001). There were non-significant differences in alanine aminotransferase and aspartate aminotransferase concentrations among the treatments.

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

    PubMed Central

    2014-01-01

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

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

    PubMed

    Kim, HyunJung; Jeong, Eung Gi; Ahn, Sang-Nag; Doyle, Jeffrey; Singh, Namrata; Greenberg, Anthony J; Won, Yong Jae; McCouch, Susan R

    2014-01-01

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

  15. [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.

  16. 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.

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

    USDA-ARS?s Scientific Manuscript database

    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...

  18. A comprehensive catalog of the lysine-acetylation targets in rice (Oryza sativa) based on proteomic analyses.

    PubMed

    Xiong, Yehui; Peng, Xiaojun; Cheng, Zhongyi; Liu, Wende; Wang, Guo-Liang

    2016-04-14

    Lysine acetylation is a dynamic and reversible post-translational modification that plays an important role in the gene transcription regulation. Here, we report high quality proteome-scale data for lysine-acetylation (Kac) sites and Kac proteins in rice (Oryza sativa). A total of 1337 Kac sites in 716 Kac proteins with diverse biological functions and subcellular localizations were identified in rice seedlings. About 42% of the sites were predicted to be localized in the chloroplast. Seven putative acetylation motifs were detected. Phenylalanine, located in both the upstream and downstream of the Kac sites, is the most conserved amino acid surrounding the regions. In addition, protein interaction network analysis revealed that a variety of signaling pathways are modulated by protein acetylation. KEGG pathway category enrichment analysis indicated that glyoxylate and dicarboxylate metabolism, carbon metabolism, and photosynthesis pathways are significantly enriched. Our results provide an in-depth understanding of the acetylome in rice seedlings, and the method described here will facilitate the systematic study of how Kac functions in growth, development, and abiotic and biotic stress responses in rice and other plants. Rice is one of the most important crops consumption and is a model monocot for research. In this study, we combined a highly sensitive immune-affinity purification method (used pan anti-acetyl-lysine antibody conjugated agarose for immunoaffinity acetylated peptide enrichment) with high-resolution LC-MS/MS. In total, we identified 1337 Kac sites on 716 Kac proteins in rice cells. Bioinformatic analysis of the acetylome revealed that the acetylated proteins are involved in a variety of cellular functions and have diverse subcellular localizations. We also identified seven putative acetylation motifs in the acetylated proteins of rice. In addition, protein interaction network analysis revealed that a variety of signaling pathways were modulated by

  19. 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.

  20. 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.

  1. 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.

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

    USDA-ARS?s Scientific Manuscript database

    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...

  3. 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.

  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. Peanut variety tests

    USDA-ARS?s Scientific Manuscript database

    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...

  6. Peanut Variety Tests

    USDA-ARS?s Scientific Manuscript database

    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...

  7. Peanut variety tests

    USDA-ARS?s Scientific Manuscript database

    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...

  8. Peanut variety tests

    USDA-ARS?s Scientific Manuscript database

    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...

  9. 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,…

  10. 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…

  11. 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

  12. 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. Copyright © 2013 Elsevier Ltd. All rights reserved.

  13. Global Expression Profiling of Low Temperature Induced Genes in the Chilling Tolerant Japonica Rice Jumli Marshi

    PubMed Central

    Chawade, Aakash; Lindlöf, Angelica; Olsson, Björn; Olsson, Olof

    2013-01-01

    Low temperature is a key factor that limits growth and productivity of many important agronomical crops worldwide. Rice (Oryza sativa L.) is negatively affected already at temperatures below +10°C and is therefore denoted as chilling sensitive. However, chilling tolerant rice cultivars exist and can be commercially cultivated at altitudes up to 3,050 meters with temperatures reaching as low as +4°C. In this work, the global transcriptional response to cold stress (+4°C) was studied in the Nepalese highland variety Jumli Marshi (spp. japonica) and 4,636 genes were identified as significantly differentially expressed within 24 hours of cold stress. Comparison with previously published microarray data from one chilling tolerant and two sensitive rice cultivars identified 182 genes differentially expressed (DE) upon cold stress in all four rice cultivars and 511 genes DE only in the chilling tolerant rice. Promoter analysis of the 182 genes suggests a complex cross-talk between ABRE and CBF regulons. Promoter analysis of the 511 genes identified over-represented ABRE motifs but not DRE motifs, suggesting a role for ABA signaling in cold tolerance. Moreover, 2,101 genes were DE in Jumli Marshi alone. By chromosomal localization analysis, 473 of these cold responsive genes were located within 13 different QTLs previously identified as cold associated. PMID:24349120

  14. 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.

  15. YSL16 Is a Phloem-Localized Transporter of the Copper-Nicotianamine Complex That Is Responsible for Copper Distribution in Rice[C][W

    PubMed Central

    Zheng, Luqing; Yamaji, Naoki; Yokosho, Kengo; Ma, Jian Feng

    2012-01-01

    Cu is an essential element for plant growth, but the molecular mechanisms of its distribution and redistribution within the plants are unknown. Here, we report that Yellow stripe-like16 (YSL16) is involved in Cu distribution and redistribution in rice (Oryza sativa). Rice YSL16 was expressed in the roots, leaves, and unelongated nodes at the vegetative growth stage and highly expressed in the upper nodes at the reproductive stage. YSL16 was expressed at the phloem of nodes and vascular tissues of leaves. Knockout of this gene resulted in a higher Cu concentration in the older leaves but a lower concentration in the younger leaves at the vegetative stage. At the reproductive stage, a higher Cu concentration was found in the flag leaf and husk, but less Cu was present in the brown rice, resulting in a significant reduction in fertility in the knockout line. Isotope labeling experiments with 65Cu showed that the mutant lost the ability to transport Cu-nicotianamine from older to younger leaves and from the flag leaf to the panicle. Rice YSL16 transported the Cu-nicotianamine complex in yeast. Taken together, our results indicate that Os-YSL16 is a Cu-nicotianamine transporter that is required for delivering Cu to the developing young tissues and seeds through phloem transport. PMID:23012434

  16. 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.

  17. 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.

  18. 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.

  19. Introgression and selection shaping the genome and adaptive loci of weedy rice in northern China.

    PubMed

    Sun, Jian; Qian, Qian; Ma, Dian-Rong; Xu, Zheng-Jin; Liu, Dan; Du, Hong-Bo; Chen, Wen-Fu

    2013-01-01

    As a weed of rice paddy fields, weedy rice has spread worldwide. In northern China, the expansion of weedy rice has been rapid over the past two decades. Its evolutionary history and adaptive mechanisms are poorly understood. Evolutionary relationships between northern weedy rice and rice cultivars were analyzed using presumed neutral markers sampled across the rice genome. Genes involved in rice domestication were evaluated for their potential roles in weedy rice adaptation. Seed longevity, a critical trait of weedy rice, was examined in an F(2) population derived from a cross between weedy rice and a rice cultivar to evaluate weedy rice adaptation and the potential effect of candidate genes. Weedy rice in northern China was not derived directly from closely related wild Oryza species or from the introgression of indica subspecies. Introgression with local cultivars, coupled with selection that maintained weedy identity, shaped the evolution of weedy rice in northern China. Weedy rice is a unique system with which to investigate how weedy plants adapt to an agricultural environment. Our finding that extensive introgression from local cultivars, combined with the continuing ability to maintain weedy genes, is characteristic of weedy rice in northern China provides a clue for the field control of weedy rice. © 2012 The Authors. New Phytologist © 2012 New Phytologist Trust.

  20. 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.

  1. Rice growth adapting to deepwater.

    PubMed

    Hattori, Yoko; Nagai, Keisuke; Ashikari, Motoyuki

    2011-02-01

    Flooding is one of the most hazardous natural disasters, and there are several levels of flooding. Recently, research on flood-tolerant rice plants revealed that some rice varieties have evolved to overcome two different flood types, 'flash flood' and 'deepwater flood', using two different mechanisms, and their molecular mechanisms were determined. During flash flooding, the tolerant plants that are fully submerged for a few weeks stop elongating and thus avoid energy consumption that will be needed to restart growth when the water recedes. On the contrary, during deepwater flooding, with water depth up to several meters for several months, the deepwater-flood-tolerant rice plants promote elongation of internodes to keep the foliage above the water surface and thus allow respiration and photosynthesis. Copyright © 2010 Elsevier Ltd. All rights reserved.

  2. 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.

  3. Ontogenetic changes in vitamin C in selected rice varieties

    USDA-ARS?s Scientific Manuscript database

    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...

  4. Population structure in Japanese rice population

    PubMed Central

    Yamasaki, Masanori; Ideta, Osamu

    2013-01-01

    It is essential to elucidate genetic diversity and relationships among even related individuals and populations for plant breeding and genetic analysis. Since Japanese rice breeding has improved agronomic traits such as yield and eating quality, modern Japanese rice cultivars originated from narrow genetic resource and closely related. To resolve the population structure and genetic diversity in Japanese rice population, we used a total of 706 alleles detected by 134 simple sequence repeat markers in a total of 114 cultivars composed of 94 improved varieties and 20 landraces, which are representative and important for Japanese rice breeding. The landraces exhibit greater gene diversity than improved lines, suggesting that landraces can provide additional genetic diversity for future breeding. Model-based Bayesian clustering analysis revealed six subgroups and admixture situation in the cultivars, showing good agreement with pedigree information. This method could be superior to phylogenetic method in classifying a related population. The leading Japanese rice cultivar, Koshihikari is unique due to the specific genome constitution. We defined Japanese rice diverse sets that capture the maximum number of alleles for given sample sizes. These sets are useful for a variety of genetic application in Japanese rice cultivars. PMID:23641181

  5. 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.

  6. 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.

  7. Genetic diversity and origin of weedy rice (Oryza sativa f. spontanea) populations found in North-eastern China revealed by simple sequence repeat (SSR) markers.

    PubMed

    Cao, Qianjin; Lu, Bao-Rong; Xia, Hui; Rong, Jun; Sala, Francesco; Spada, Alberto; Grassi, Fabrizio

    2006-12-01

    Weedy rice (Oryza sativa f. spontanea) is one of the most notorious weeds occurring in rice-planting areas worldwide. The objectives of this study are to determine the genetic diversity and differentiation of weedy rice populations from Liaoning Province in North-eastern China and to explore the possible origin of these weedy populations by comparing their genetic relationships with rice varieties (O. sativa) and wild rice (O. rufipogon) from different sources. Simple sequence repeat (SSR) markers were used to estimate the genetic diversity of 30 weedy rice populations from Liaoning, each containing about 30 individuals, selected rice varieties and wild O. rufipogon. Genetic differentiation and the relationships of weedy rice populations were analysed using cluster analysis (UPGMA) and principle component analysis (PCA). The overall genetic diversity of weedy rice populations from Liaoning was relatively high (H(e) = 0.313, I = 0.572), with about 35 % of the genetic variation found among regions. The Liaoning weedy rice populations were closely related to rice varieties from Liaoning and japonica varieties from other regions but distantly related to indica rice varieties and wild O. rufipogon. Weedy rice populations from Liaoning are considerably variable genetically and most probably originated from Liaoning rice varieties by mutation and intervarietal hybrids. Recent changes in farming practices and cultivation methods along with less weed management may have promoted the re-emergence and divergence of weedy rice in North-eastern China.

  8. 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.

  9. 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.

  10. 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.

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

    USDA-ARS?s Scientific Manuscript database

    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...

  12. Algebraic Legendrian Varieties

    NASA Astrophysics Data System (ADS)

    Buczyński, Jarosław

    2008-05-01

    Real Legendrian subvarieties are classical objects of differential geometry and classical mechanics and they have been studied since antiquity. However, complex Legendrian subvarieties are much more rigid and have more exceptional properties. The most remarkable case is the Legendrian subvarieties of projective space and prior to the author's research only few smooth examples of these were known. The first series of results of this thesis is related to the automorphism group of any Legendrian subvariety in any projective contact manifold. The connected component of this group (under suitable minor assumptions) is completely determined by the sections of the distinguished line bundle on the contact manifold vanishing on the Legendrian variety. Moreover its action preserves the contact structure. The second series of results is devoted to finding new examples of smooth Legendrian subvarieties of projective space. The contribution of this thesis is in three steps: First we find an example of a smooth toric surface. Next we find a smooth quasihomogeneous Fano 8-fold that admits a Legendrian embedding. Finally, we realise that both of these are special cases of a very general construction: a general hyperplane section of a smooth Legendrian variety, after a suitable projection, is a smooth Legendrian variety of smaller dimension. By applying this result to known examples and decomposable Legendrian varieties, we construct infinitely many new examples in every dimension, with various Picard rank, canonical degree, Kodaira dimension and other invariants.

  13. Moisture diffusivity in rice components during absorption and desorption

    USDA-ARS?s Scientific Manuscript database

    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...

  14. Volatile profiles of aromatic and non-aromatic rice

    USDA-ARS?s Scientific Manuscript database

    Rice is enjoyed by many people as a staple food because of its flavor and texture. Some scented varieties command a premium in the marketplace because of their distinctive aroma and flavor. The compound most commonly associated with the popcorn or nutty scent of aromatic rice is 2-acetyl-1-pyrroline...

  15. 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

  16. 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.

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

    USDA-ARS?s Scientific Manuscript database

    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...

  18. 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.

  19. 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.

  20. Quantitation of tocotrienol and tocopherol in various rice brans.

    PubMed

    Sookwong, Phumon; Nakagawa, Kiyotaka; Murata, Kazamasa; Kojima, Yoichiro; Miyazawa, Teruo

    2007-01-24

    Rice bran is abundant in bioactive compounds including tocotrienol (T3, unsaturated vitamin E). T3 has been reported about its potential functionalities (i.e., antiangiogenic effect), so much attention has been paid on usability of rice bran T3. Hence, we developed a rapid screening method for T3-rich rice bran by one-step equilibrium direct solvent extraction followed by normal phase high-performance liquid chromatography (HPLC). The method gave high-extraction rate of rice bran T3 and tocopherol (above 90%), and the determination of vitamin E by HPLC was completed within 15 min. Using the method, an average of total T3 content in 109 kinds of rice bran samples was 830 mug/g dry wt. Kouchi-Akamai, Joushuu, and Wataribune were found as the T3-rich rice bran varieties (1350-1430 microg T3/g dry wt). According to T3 ratio against total vitamin E (wt %), the average ratio was 61%. Hirayama, Moritawase, and Kaneko were found as the varieties having the highest T3 ratio (80-86%). Since T3 content in Koshihikari rice bran (the leading variety in Japan) was a little above the average, we cross-fertilized Koshihikari with T3-rich varieties and found that T3 content or ratio in F1 was improved compared with Koshihikari. The varieties found rich in T3 could be used for nutraceutical purpose.

  1. 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.

  2. 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

  3. 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. © 2013 Published by Elsevier Inc.

  4. A natural rice rhizospheric bacterium abates arsenic accumulation in rice (Oryza sativa L.).

    PubMed

    Lakshmanan, Venkatachalam; Shantharaj, Deepak; Li, Gang; Seyfferth, Angelia L; Janine Sherrier, D; Bais, Harsh P

    2015-10-01

    A natural rice rhizospheric isolate abates arsenic uptake in rice by increasing Fe plaque formation on rice roots. Rice (Oryza sativa L.) is the staple food for over half of the world's population, but its quality and yield are impacted by arsenic (As) in some regions of the world. Bacterial inoculants may be able to mitigate the negative impacts of arsenic assimilation in rice, and we identified a nonpathogenic, naturally occurring rice rhizospheric bacterium that decreases As accumulation in rice shoots in laboratory experiments. We isolated several proteobacterial strains from a rice rhizosphere that promote rice growth and enhance the oxidizing environment surrounding rice root. One Pantoea sp. strain (EA106) also demonstrated increased iron (Fe)-siderophore in culture. We evaluated EA106's ability to impact rice growth in the presence of arsenic, by inoculation of plants with EA106 (or control), subsequently grew the plants in As-supplemented medium, and quantified the resulting plant biomass, Fe and As concentrations, localization of Fe and As, and Fe plaque formation in EA106-treated and control plants. These results show that both arsenic and iron concentrations in rice can be altered by inoculation with the soil microbe EA106. The enhanced accumulation of Fe in the roots and in root plaques suggests that EA106 inoculation improves Fe uptake by the root and promotes the formation of a more oxidative environment in the rhizosphere, thereby allowing more expansive plaque formation. Therefore, this microbe may have the potential to increase food quality through a reduction in accumulation of toxic As species within the aerial portions of the plant.

  5. 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.

  6. 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

  7. 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

  8. 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.

  9. 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.

  10. 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

  11. 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.

  12. 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.

  13. 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.

  14. Compartmentation and dynamics of flavone metabolism in dry and germinated rice seeds.

    PubMed

    Galland, Marc; Boutet-Mercey, Stéphanie; Lounifi, Imen; Godin, Béatrice; Balzergue, Sandrine; Grandjean, Olivier; Morin, Halima; Perreau, François; Debeaujon, Isabelle; Rajjou, Loïc

    2014-09-01

    Among secondary metabolites, flavonoids are particularly important for the plant life cycle and could be beneficial for human health. The study of Arabidopsis thaliana transparent testa mutants showed that seed flavonoids are important for environmental adaptation, reactive oxygen species homeostasis, dormancy and longevity. Compared with Arabidopsis and maize (Zea mays L.), far less research has been conducted on rice (Oryza sativa L.) particularly for cultivars with non-pigmented seeds. In this study, we describe the localization, nature and relative abundance of flavonoids in mature and germinated non-pigmented Nipponbare seeds using a combination of confocal microscopy, mass spectrometry and gene expression analysis. The mature seed exclusively accumulates flavones mostly in the embryo and to a lesser extent in the pericarp/testa. Due to the variety of flavone conjugation patterns, 21 different flavones were identified, including sulfated flavones never mentioned before in cereals. Schaftoside (apigenin-6-C-glucoside-8-C-arabinoside) and its two isomers represent nearly 50% of all rice seed flavones and are the only flavonoids accumulated in the pericarp/testa seed compartment. These 21 conjugated flavones showed a very stable profile during rice seed germination sensu stricto, while expression of key flavone synthesis genes strongly increases before the completion of germination. We discuss the potential roles of these rice seed flavones in a seed biology context. © The Author 2014. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please email: journals.permissions@oup.com.

  15. 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. © 2014 American Society of Plant Biologists. All Rights Reserved.

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

    PubMed

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

    2015-05-01

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

  17. A Class II small heat shock protein OsHsp18.0 plays positive roles in both biotic and abiotic defense responses in rice.

    PubMed

    Kuang, Jie; Liu, Jianzhong; Mei, Jun; Wang, Changchun; Hu, Haitao; Zhang, Yanjun; Sun, Meihao; Ning, Xi; Xiao, Langtao; Yang, Ling

    2017-09-12

    Bacterial blight caused by Xanthomonas oryzae pv. oryzae (Xoo) is one of the most devastating diseases of rice. However, the molecular mechanism underpinning the Xoo resistance of rice is still not fully understood. Here, we report that a class II small heat shock protein gene, OsHsp18.0, whose expression was differentially induced between a resistant and a susceptible variety in response to Xoo infection, plays positive roles in both biotic and abiotic resistance. The molecular chaperone activity of OsHsp18.0 was confirmed by a bacterium-expressed glutathione S-transferase fusion protein. Overexpression of OsHsp18.0 in a susceptible rice variety significantly enhanced its resistance to multiple Xoo strains, whereas silencing of OsHsp18.0 in a resistant variety drastically increased its susceptibility. The enhanced Xoo resistance in OsHsp18.0-overexpressing lines was positively correlated with the sensitized salicylic acid-dependent defense responses. In addition to disease resistance, the OsHsp18.0 overexpressing and silencing lines exhibited enhanced and reduced tolerance, respectively, to heat and salt treatments. The subcellular localization study revealed that the green fluorescent protein-OsHsp18.0 was enriched on the nuclear envelope, suggesting a potential role of OsHsp18.0 in the nucleo-cytoplasmic trafficking. Together, our results reveal that the rice OsHsp18.0 is a positive regulator in both biotic and abiotic defense responses.

  18. [Biological characters of the different varieties for Luffa cylindrica].

    PubMed

    Yang, Y; Ma, X; Wu, W; Guo, P

    1999-04-01

    The yield of Luffa cylindrica cultivated in Taiyuan of Shanxi Province, which introduced from Zhejiang Province, was obviously high than that of local variety. The paper reported the biological characters of the two varieties.

  19. [Rice breeding by space technology].

    PubMed

    Li, Yuan-xiang; Li, Jin-guo; Liu, Han-dong; Jiang, Xing-cun; Hua, Yu-jian; Zhou, Huo-liang; Che, Xin-ming

    2002-07-01

    In order to inquire into the influences of space conditions on rice breeding,the dry seeds of 12 rice varieties were carried by recoverable satellite. After recovery,these seeds were showed in the yield, the inheritance and variation of the characters of their progenies were observed and analysed. The results showed that the characters of the progenies mutated under space conditions segregated and varied in many aspects and directions,and the segregated and varied characters were heritable. These progenies posoessed significant transgressive inheritance, a plenty of variation types and variation was characterized by short breeding period. The results in this study indicated that space technology breeding could be developed and used as a new method of mutation breeding.

  20. 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.

  1. Neck blast disease influences grain yield and quality traits of aromatic rice.

    PubMed

    Khan, Mohammad Ashik Iqbal; Bhuiyan, Md Rejwan; Hossain, Md Shahadat; Sen, Partha Pratim; Ara, Anjuman; Siddique, Md Abubakar; Ali, Md Ansar

    2014-11-01

    A critical investigation was conducted to find out the effect of neck blast disease on yield-contributing characters, and seed quality traits of aromatic rice in Bangladesh. Both healthy and neck-blast-infected panicles of three aromatic rice cultivars (high-yielding and local) were collected and investigated at Plant Pathology Division, Bangladesh Rice Research Institute (BRRI), Gazipur, Bangladesh. All of the tested varieties were highly susceptible to neck blast disease under natural conditions, though no leaf blast symptoms appear on leaves. Neck blast disease increased grain sterility percentages, reduced grain size, yield and quality traits of seeds. The degrees of yield and seed quality reduction depended on disease severity and variety's genetic make-up. Unfilled grains were the main source of seed-borne pathogen, especially for blast in the seed lot. Transmission of blast pathogen from neck (panicle base) to seed was very poor. These findings are important, especially concerning the seed certification programme in which seed lots are certified on the basis of field inspection. Finally, controlled experiments are needed to draw more critical conclusions. Copyright © 2014 Académie des sciences. Published by Elsevier SAS. All rights reserved.

  2. Identification of Rice Transcription Factors Associated with Drought Tolerance Using the Ecotilling Method

    PubMed Central

    Yu, Shunwu; Liao, Fengxian; Wang, Feiming; Wen, Weiwei; Li, Jiajia; Mei, Hanwei; Luo, Lijun

    2012-01-01

    The drought tolerance (DT) of plants is a complex quantitative trait. Under natural and artificial selection, drought tolerance represents the crop survival ability and production capacity under drought conditions (Luo, 2010). To understand the regulation mechanism of varied drought tolerance among rice genotypes, 95 diverse rice landraces or varieties were evaluated within a field screen facility based on the ‘line–source soil moisture gradient’, and their resistance varied from extremely resistant to sensitive. The method of Ecotype Targeting Induced Local Lesions in Genomes (Ecotilling) was used to analyze the diversity in the promoters of 24 transcription factor families. The bands separated by electrophoresis using Ecotilling were converted into molecular markers. STRUCTURE analysis revealed a value of K = 2, namely, the population with two subgroups (i.e., indica and japonica), which coincided very well with the UPGMA clusters (NTSYS-pc software) using distance-based analysis and InDel markers. Then the association analysis between the promoter diversity of these transcription factors and the DT index/level of each variety was performed. The results showed that three genes were associated with the DT index and that five genes were associated with the DT level. The sequences of these associated genes are complex and variable, especially at approximately 1000 bp upstream of the transcription initiation sites. The study illuminated that association analysis aimed at Ecotilling diversity of natural groups could facilitate the isolation of rice genes related to complex quantitative traits. PMID:22348023

  3. Rice bran fermented with saccharomyces boulardii generates novel metabolite profiles with bioactivity.

    PubMed

    Ryan, Elizabeth P; Heuberger, Adam L; Weir, Tiffany L; Barnett, Brittany; Broeckling, Corey D; Prenni, Jessica E

    2011-03-09

    Emerging evidence supporting chronic disease fighting properties of rice bran has advanced the development of stabilized rice bran for human use as a functional food and dietary supplement. A global and targeted metabolomic investigation of stabilized rice bran fermented with Saccharomyces boulardii was performed in three rice varieties. Metabolites from S. boulardii-fermented rice bran were detected by gas chromatography-mass spectrometry (GC-MS) and assessed for bioactivity compared to nonfermented rice bran in normal and malignant lymphocytes. Global metabolite profiling revealed significant differences in the metabolome that led to discovery of candidate compounds modulated by S. boulardii fermentation. Fermented rice bran extracts from three rice varieties reduced growth of human B lymphomas compared to each variety's nonfermented control and revealed that fermentation differentially altered bioactive compounds. These data support that integration of global and targeted metabolite analysis can be utilized for assessing health properties of rice bran phytochemicals that are enhanced by yeast fermentation and that differ across rice varieties.

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

    USDA-ARS?s Scientific Manuscript database

    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...

  5. 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.

  6. 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).

  7. 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.

  8. Rice Production and Marketing.

    ERIC Educational Resources Information Center

    Briers, Gary; Lee, Jasper S.

    This guide contains lesson plans for use in secondary programs of agricultural education in geographical areas in which rice is produced. Six units and 13 problem areas are organized into teaching plans that cover the broad nature of rice production. The six units are: (1) determining the importance and history of rice production; (2) determining…

  9. 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

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

    PubMed

    Koga, Nobuhisa; Tajima, Ryosuke

    2011-03-01

    To establish energetically and environmentally viable paddy rice-based bioethanol production systems in northern Japan, it is important to implement appropriately selected agronomic practice options during the rice cultivation step. In this context, effects of rice variety (conventional vs. high-yielding) and rice straw management (return to vs. removal from the paddy field) on energy inputs from fuels and consumption of materials, greenhouse gas emissions (fuel and material consumption-derived CO(2) emissions as well as paddy soil CH(4) and N(2)O emissions) and ethanol yields were assessed. The estimated ethanol yield from the high-yielding rice variety, "Kita-aoba" was 2.94 kL ha(-1), a 32% increase from the conventional rice variety, "Kirara 397". Under conventional rice production in northern Japan (conventional rice variety and straw returned to the paddy), raising seedlings, mechanical field operations, transportation of harvested unhulled brown rice and consumption of materials (seeds, fertilizers, biocides and agricultural machinery) amounted to 28.5 GJ ha(-1) in energy inputs. The total energy input was increased by 14% by using the high-yielding variety and straw removal, owing to increased requirements for fuels in harvesting and transporting harvested rice as well as in collecting, loading and transporting rice straw. In terms of energy efficiency, the variation among rice variety and straw management scenarios regarding rice varieties and rice straw management was small (28.5-32.6 GJ ha(-1) or 10.1-14.0 MJ L(-1)). Meanwhile, CO(2)-equivalent greenhouse gas emissions varied considerably from scenario to scenario, as straw management had significant impacts on CH(4) emissions from paddy soils. When rice straw was incorporated into the soil, total CO(2)-equivalent greenhouse gas emissions for "Kirara 397" and "Kita-aoba" were 25.5 and 28.2 Mg CO(2) ha(-1), respectively; however, these emissions were reduced notably for the two varieties when rice straw

  11. 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%.

  12. 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

  13. 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.

  14. 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.

  15. Evaluation of Rice Resistance to Southern Rice Black-Streaked Dwarf Virus and Rice Ragged Stunt Virus through Combined Field Tests, Quantitative Real-Time PCR, and Proteome Analysis.

    PubMed

    Wang, Zhenchao; Yu, Lu; Jin, Linhong; Wang, Wenli; Zhao, Qi; Ran, Longlu; Li, Xiangyang; Chen, Zhuo; Guo, Rong; Wei, Yongtian; Yang, Zhongcheng; Liu, Enlong; Hu, Deyu; Song, Baoan

    2017-02-22

    Diseases caused by southern rice black-streaked dwarf virus (SRBSDV) and rice ragged stunt virus (RRSV) considerably decrease grain yield. Therefore, determining rice cultivars with high resistance to SRBSDV and RRSV is necessary. In this study, rice cultivars with high resistance to SRBSDV and RRSV were evaluated through field trials in Shidian and Mangshi county, Yunnan province, China. SYBR Green I-based quantitative real-time polymerase chain reaction (qRT-PCR) analysis was used to quantitatively detect virus gene expression levels in different rice varieties. The following parameters were applied to evaluate rice resistance: acre yield (A.Y.), incidence of infected plants (I.I.P.), virus load (V.L.), disease index (D.I.), and insect quantity (I.Q.) per 100 clusters. Zhongzheyou1 (Z1) and Liangyou2186 (L2186) were considered the most suitable varieties with integrated higher A.Y., lower I.I.P., V.L., D.I. and I.Q. In order to investigate the mechanism of rice resistance, comparative label-free shotgun liquid chromatography tandem-mass spectrometry (LC-MS/MS) proteomic approaches were applied to comprehensively describe the proteomics of rice varieties' SRBSDV tolerance. Systemic acquired resistance (SAR)-related proteins in Z1 and L2186 may result in the superior resistance of these varieties compared with Fengyouxiangzhan (FYXZ).

  16. Rice Bran Fermented with Saccharomyces boulardii Generates Novel Metabolite Profiles with Bioactivity

    PubMed Central

    2011-01-01

    Emerging evidence supporting chronic disease fighting properties of rice bran has advanced the development of stabilized rice bran for human use as a functional food and dietary supplement. A global and targeted metabolomic investigation of stabilized rice bran fermented with Saccharomyces boulardii was performed in three rice varieties. Metabolites from S. boulardii-fermented rice bran were detected by gas chromatography−mass spectrometry (GC−MS) and assessed for bioactivity compared to nonfermented rice bran in normal and malignant lymphocytes. Global metabolite profiling revealed significant differences in the metabolome that led to discovery of candidate compounds modulated by S. boulardii fermentation. Fermented rice bran extracts from three rice varieties reduced growth of human B lymphomas compared to each variety’s nonfermented control and revealed that fermentation differentially altered bioactive compounds. These data support that integration of global and targeted metabolite analysis can be utilized for assessing health properties of rice bran phytochemicals that are enhanced by yeast fermentation and that differ across rice varieties. PMID:21306106

  17. 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

  18. 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.

  19. 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

    2017-02-01

    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. © The Author 2017. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please email: journals.permissions@oup.com.

  20. 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.

  1. 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