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Sample records for cultivars oryza sativa

  1. Contrasting physiological responses by cultivars of Oryza sativa and O. glaberrima to prolonged submergence

    PubMed Central

    Sakagami, Jun-Ichi; Joho, Yukiko; Ito, Osamu

    2009-01-01

    Background and Aims Oryza glaberrima is widely grown in flood-prone areas of African river basins and is subject to prolonged periods of annual submergence. The effects of submergence on shoot elongation, shoot biomass, leaf area and CO2 uptake were studied and compared with those of O. sativa. Methods A wide selection of lines of O. sativa and O. glaberrima, including some classified as submergence tolerant, were compared in field and pot experiments. Plants were submerged completely for 31 d in a field experiment, and partially or completely for 37 d in a pot experiment in a growth chamber. Key Results Leaf elongation and growth in shoot biomass during complete submergence in the field were significantly greater in O. glaberrima than in O. sativa. So-called submergence-tolerant cultivars of O. sativa were unable to survive prolonged complete submergence for 31–37 d. This indicates that the mechanism of suppressed leaf elongation that confers increased survival of short-term submergence is inadequate for surviving long periods underwater. The O. sativa deepwater cultivar ‘Nylon’ and the ‘Yélé1A’ cultivar of O. glaberrima succeeded in emerging above the floodwater. This resulted in greatly increased shoot length, shoot biomass and leaf area, in association with an increased net assimilation rate compared with the lowland-adapted O. sativa ‘Banjoulou’. Conclusions The superior tolerance of deepwater O. sativa and O. glaberrima genotypes to prolonged complete submergence appears to be due to their greater photosynthetic capacity developed by leaves newly emerged above the floodwater. Vigorous upward leaf elongation during prolonged submergence is therefore critical for ensuring shoot emergence from water, leaf area extension above the water surface and a subsequent strong increase in shoot biomass. PMID:18940851

  2. Cultivar variability of iron uptake mechanisms in rice (Oryza sativa L.).

    PubMed

    Pereira, Margarida P; Santos, Carla; Gomes, Ana; Vasconcelos, Marta W

    2014-12-01

    Rice (Oryza sativa L.) is the most important staple food in the world. It is rich in genetic diversity and can grow in a wide range of environments. Iron (Fe) deficiency is a major abiotic stress in crop production and in aerobic soils, where Fe forms insoluble complexes, and is not readily available for uptake. To cope with Fe deficiency, plants developed mechanisms for Fe uptake, and although rice was described as a Strategy II plant, recent evidence suggests that it is capable of utilizing mechanisms from both Strategies. The main objective of this work was to compare two cultivars, Bico Branco (japonica) and Nipponbare (tropical japonica), to understand if the regulation of Fe uptake mechanisms could be cultivar (cv.)dependent. Plants of both cultivars were grown under Fe-deficient and -sufficient conditions and physiological and molecular responses to Fe deficiency were evaluated. Bico Branco cv. developed more leaf chlorosis and was more susceptible to Fe deficiency, retaining more nutrients in roots, than Nipponbare cv., which translocated more nutrients to shoots. Nipponbare cv. presented higher levels of Fe reductase activity, which was significantly up-regulated by Fe deficiency, and had higher expression levels of the Strategy I-OsFRO2 gene in roots, while Bico Branco cv. induced more genes involved in Strategy II.These new findings show that rice cultivars have different responses to Fe deficiency and that the induction of Strategy I or II may be rice cultivar-dependent, although the utilization of the reduction mechanisms seems to be an ubiquitous advantage.

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

    PubMed

    Lu, Ying; Dong, Fei; Deacon, Claire; Chen, Huo-Jun; Raab, Andrea; Meharg, Andrew A

    2010-05-01

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

  4. Combined herbicide and saline stress differentially modulates hormonal regulation and antioxidant defense system in Oryza sativa cultivars.

    PubMed

    Islam, Faisal; Ali, Basharat; Wang, Jian; Farooq, Muhammad A; Gill, Rafaqat A; Ali, Shafaqat; Wang, Danying; Zhou, Weijun

    2016-10-01

    Plants are simultaneously exposed to a combination of biotic and abiotic stresses in field conditions. Crops respond to the combined stress in a unique way which cannot be understood by extrapolating the results of individual stress. In the present study, effects of individual and combined stress of herbicide (2,4-dichlorophenoxyacetic acid) and salinity (NaCl) on two Oryza sativa cultivars (ZJ 88 and XS 134) were investigated. Both herbicide and saline stress affected the plant growth differentially and produced oxidative stress in rice cultivars. Interestingly, the combination of herbicide and salinity showed a significant protection to both rice cultivars by reducing ROS (H2O2, O2(-)) and lipid peroxidation through modulation of enzymatic (SOD, POD, CAT and APX) and non-enzymatic (TSP, sugars, phenolic and proline) antioxidants. In addition, active regulation of transcript levels of genes encoding Na(+) and K(+) (OsHKT1;5, OsLti6a,b, OsHKT2;1, OsSOS1, OsCNGC1, OsNHX1 and OsAKT1) transporter proteins reduced sodium and enhanced potassium accumulation under combined stress, resulted a better growth and ionic homeostasis in both rice cultivars. The production of ABA and IAA was significantly higher in cultivar XS 134 compared to cultivar ZJ 88 under control conditions. However, combined herbicide and saline stress enhanced the accumulation of phytohormones (IAA and ABA) and transcription of ethylene in cultivar ZJ 88, which might be one of the factors responsible for poor salt tolerance in sensitive cultivar. These findings indicated that herbicide application under saline stress confers tolerance to salinity in rice cultivars, likely by reducing oxidative damage, modulating mineral absorption, upgradation of antioxidant defense and by dynamic regulation of key genes involved in Na(+) and K(+) homeostasis in plants.

  5. Morphological and biochemical responses of Oryza sativa L. (cultivar MR219) to ion beam irradiation*

    PubMed Central

    Ling, Anna Pick Kiong; Ung, Ying Chian; Hussein, Sobri; Harun, Abdul Rahim; Tanaka, Atsushi; Yoshihiro, Hase

    2013-01-01

    Objective: Heavy ion beam, which has emerged as a new mutagen in the mutation breeding of crops and ornamental plants, is expected to result in the induction of novel mutations. This study investigates the morphological and biochemical responses of Oryza sativa toward different doses of carbon ion beam irradiation. Methods: In this study, the dry seeds of O. sativa were irradiated at 0, 20, 40, 60, 80, 100, and 120 Gy, followed by in-vitro germination under controlled conditions. Morphological and biochemical studies were conducted to investigate the morphological and physiological responses of O. sativa towards ion beam irradiation. Results: The study demonstrated that low doses (10 Gy) of ion beam have a stimulating effect on the height, root length, and fresh weight of the plantlets but not on the number of leaves. Meanwhile, doses higher than 10 Gy caused reductions in all the morphological parameters studied as compared to the control samples. The highest total soluble protein content [(2.11±0.47) mg/g FW] was observed in plantlets irradiated at 20 Gy. All irradiated plantlets were found to have 0.85% to 58.32% higher specific activity of peroxidase as compared to the control samples. The present study also revealed that low doses of ion beam (10 and 20 Gy) had negligible effect on the total chlorophyll content of O. sativa plantlets while 40 Gy had a stimulating effect on the chlorophyll content. Plantlets irradiated between 40 to 120 Gy were shown to be 0.38% to 9.98% higher in total soluble nitrogen content which, however, was not significantly different from the control samples. Conclusions: Carbon ion beam irradiation administered at low to moderate doses of 10 to 40 Gy may induce O. sativa mutants with superior characteristics. PMID:24302713

  6. Expression of drought tolerance genes in tropical upland rice cultivars (Oryza sativa).

    PubMed

    Silveira, R D D; Abreu, F R M; Mamidi, S; McClean, P E; Vianello, R P; Lanna, A C; Carneiro, N P; Brondani, C

    2015-07-27

    Gene expression related to drought response in the leaf tissues of two Brazilian upland cultivars, the drought-tolerant Douradão and the drought-sensitive Primavera, was analyzed. RNA-seq identified 27,618 transcripts in the Douradão cultivar, with 24,090 (87.2%) homologous to the rice database, and 27,221 transcripts in the Primavera cultivar, with 23,663 (86.9%) homologous to the rice database. Gene-expression analysis between control and water-deficient treatments revealed 493 and 1154 differentially expressed genes in Douradão and Primavera cultivars, respectively. Genes exclusively expressed under drought were identified for Douradão, including two genes of particular interest coding for the protein peroxidase precursor, which is involved in three distinct metabolic pathways. Comparisons between the two drought-exposed cultivars revealed 2314 genes were differentially expressed (978 upregulated, 1336 downregulated in Douradão). Six genes distributed across 4 different transcription factor families (bHLH, MYB, NAC, and WRKY) were identified, all of which were upregulated in Douradão compared to Primavera during drought. Most of the genes identified in Douradão activate metabolic pathways responsible for production of secondary metabolites and genes coding for enzymatically active signaling receptors. Quantitative PCR validation showed that most gene expression was in agreement with computational prediction of these transcripts. The transcripts identified here will define molecular markers for identification of Cis-acting elements to search for allelic variants of these genes through analysis of polymorphic SNPs in GenBank accessions of upland rice, aiming to develop cultivars with the best combination of these alleles, resulting in materials with high yield potential in the event of drought during the reproductive phase.

  7. A comparison of nitrate transport in four different rice (Oryza sativa L.) cultivars.

    PubMed

    Fan, Xiaorong; Shen, Qirong; Ma, Zhengqiang; Zhu, Huilan; Yin, Xiaoming; Miller, Anthony J

    2005-09-01

    As rice can use both nitrate (NO(3)(-)) and ammonium (NH(4)(+)), we have tested the hypothesis that the shift in the pattern of cultivars grown in Jiangsu Province reflects the ability of the plants to exploit NO(3)(-) as a nitrogen (N) source. Four rice cultivars were grown in solution culture for comparison of their growth on NO(3)(-) and NH(4)(+) nitrogen sources. All four types of rice, Xian You 63 (XY63), Yang Dao 6 (YD), Nong Keng 57 (NK) and Si You 917 (SY917), grew well and produced similar amounts of shoot biomass with 1 mmol/L NH(4)(+) as the only N source. However, the roots of NK were significantly smaller in comparison with the other cultivars. When supplied with 1 mmol/L NO(3)(-), YD produced the greatest biomass; while NK achieved the lowest growth among the four cultivars. Electrophysiological measurements on root rhizodermal cells showed that the NO(3)(-)-elicited changes in membrane potential (Delta E(m)) of these four rice cultivars were significantly different when exposed to low external NO(3)(-) (<1 mmol/L); while they were very similar at high external NO(3)(-) (10 mmol/L). The root cell membrane potentials of YD and XY63 were more responsive to low external NO(3)(-) than those of NK and SY917. The Delta E(m) values for YD and XY63 rhizodermal cells were almost the same at both 0.1 mmol/L and 1 mmol/L NO(3)(-); while for the NK and SY917 the values became larger as the external NO(3)(-) increased. For YD cultivar, Delta E(m) was measured over a range of NO(3)(-) concentrations and a Michaelis-Menten fit to the data gave aK(m) value of 0.17 mmol/L. Net N(3)(-) uptake depletion kinetics were also compared and for some cultivars (YD and XY63) a single-phase uptake system with first order kinetics best fitted the data; while other cultivars (ND and SY917) showed a better fit to two uptake systems. These uptake systems had two affinity ranges: one had a similar K(m) in all the cultivars (0.2 mmol/L); the other much higher affinity system (0

  8. A comparison of nitrate transport in four different rice (Oryza sativa L.) cultivars.

    PubMed

    Fan, Xiaorong; Shen, Qirong; Ma, Zhengqiang; Zhu, Huilan; Yin, Xiaoming; Miller, Anthony J

    2005-12-01

    As rice can use both nitrate (NO3-) and ammonium (NH4+), we have tested the hypothesis that the shift in the pattern of cultivars grown in Jiangsu Province reflects the ability of the plants to exploit NO3- as a nitrogen (N) source. Four rice cultivars were grown in solution culture for comparison of their growth on NO3- and NH4+ nitrogen sources. All four types of rice, Xian You 63 (XY63), Yang Dao 6 (YD), Nong Keng 57 (NK) and Si You 917 (SY917), grew well and produced similar amounts of shoot biomass with 1 mmol/L NH4+ as the only N source. However, the roots of NK were significantly smaller in comparison with the other cultivars. When supplied with 1 mmol/L NO3-, YD produced the greatest biomass; while NK achieved the lowest growth among the four cultivars. Electrophysiological measurements on root rhizodermal cells showed that the NO3- -elicited changes in membrane potential (deltaEm) of these four rice cultivars were significantly different when exposed to low external NO3- (<1 mmol/L); while they were very similar at high external NO3- (10 mmol/L). The root cell membrane potentials of YD and XY63 were more responsive to low external NO3- than those of NK and SY917. The deltaEm values for YD and XY63 rhizodermal cells were almost the same at both 0.1 mmol/L and 1 mmol/L NO3-; while for the NK and SY917 the values became larger as the external NO3- increased. For YD cultivar, deltaEm was measured over a range of NO3- concentrations and a Michaelis-Menten fit to the data gave a Km value of 0.17 mmol/L. Net NO3- uptake depletion kinetics were also compared and for some cultivars (YD and XY63) a single-phase uptake system with first order kinetics best fitted the data; while other cultivars (ND and SY917) showed a better fit to two uptake systems. These uptake systems had two affinity ranges: one had a similar Km in all the cultivars (0.2 mmol/L); the other much higher affinity system (0.03 mmol/L) was only present in NK and SY917. The expression pattern of

  9. A (1)H HR-MAS NMR-Based Metabolomic Study for Metabolic Characterization of Rice Grain from Various Oryza sativa L. Cultivars.

    PubMed

    Song, Eun-Hye; Kim, Hyun-Ju; Jeong, Jaesik; Chung, Hyun-Jung; Kim, Han-Yong; Bang, Eunjung; Hong, Young-Shick

    2016-04-20

    Rice grain metabolites are important for better understanding of the plant physiology of various rice cultivars and thus for developing rice cultivars aimed at providing diverse processed products. However, the variation of global metabolites in rice grains has rarely been explored. Here, we report the identification of intra- or intercellular metabolites in rice (Oryza sativa L.) grain powder using a (1)H high-resolution magic angle spinning (HR-MAS) NMR-based metabolomic approach. Compared with nonwaxy rice cultivars, marked accumulation of lipid metabolites such as fatty acids, phospholipids, and glycerophosphocholine in the grains of waxy rice cultivars demonstrated the distinct metabolic regulation and adaptation of each cultivar for effective growth during future germination, which may be reflected by high levels of glutamate, aspartate, asparagine, alanine, and sucrose. Therefore, this study provides important insights into the metabolic variations of diverse rice cultivars and their associations with environmental conditions and genetic backgrounds, with the aim of facilitating efficient development and the improvement of rice grain quality through inbreeding with genetic or chemical modification and mutation.

  10. Genotypic variation in the uptake, accumulation, and translocation of di-(2-ethylhexyl) phthalate by twenty cultivars of rice (Oryza sativa L.).

    PubMed

    Cai, Quan-Ying; Xiao, Pei-Yun; Chen, Tong; Lü, Huixiong; Zhao, Hai-Ming; Zeng, Qiao-Yun; Li, Yan-Wen; Li, Hui; Xiang, Lei; Mo, Ce-Hui

    2015-06-01

    Agricultural soil in China contains high levels of di-(2-ethylhexyl) phthalate (DEHP), especially in paddy-field soil of Guangdong province of China, but the accumulation and translocation of DEHP by rice (Oryza sativa L.) remains unknown. In the present study, twenty rice cultivars were cultivated in paddy soil spiked with DEHP, and variations in DEHP accumulation and translocation among various cultivars were investigated. Our results showed that DEHP concentrations in roots and shoots of different rice cultivars at four growth stages (i.e., ripening, tillering, jointing, and flowering stages) varied greatly from 0.26 to 11.8 mg/kg (dry weight, dw) and 0.40 to 7.58 mg/kg (dw), respectively. No obvious change over time was observed. The greatest variation in DEHP concentrations among the rice cultivars occurred at ripening stage, whereas the lowest variation at flowering stage. During ripening stage, the largest variation in DEHP concentrations among cultivars were observed in stems (varying from 0.35 to 13.2 mg/kg), whereas the least one was observed in roots (ranging from 1.01 to 5.72 mg/kg). Significant differences in DEHP concentrations in the roots, stems, leaves and grains of most rice cultivars were found. The translocation factors of DEHP from roots to stems or stems to leaves were higher than those from shoots to grains. Overall, cultivars Tianfengyou 316, Wuyou 308, and Peizataifeng, which contained low levels of DEHP in grains but high levels in shoots, were ideal cultivars for simultaneous production of safe food and phytoremediation of contaminated soil.

  11. Heat and chilling induced disruption of redox homeostasis and its regulation by hydrogen peroxide in germinating rice seeds (Oryza sativa L., Cultivar Ratna).

    PubMed

    Bhattacharjee, Soumen

    2013-04-01

    Extremes of temperature (both heat and chilling) during early inbibitional phase of germination caused disruption of redox-homeostasis by increasing accumulation of reactive oxygen species (superoxide and hydrogen peroxide) and significant reduction of antioxidative defense (assessed in terms of total thiol content and activities of superoxide dismutase, catalase, ascorbate peroxidase and glutathione reductase) in germinating tissues of rice (Oryza sativa L., cultivar Ratna). Imbibitional heat and chilling stress also induced oxidative damage to newly assembled membrane system by aggravating membrane lipid peroxidation and protein oxidation [measured in terms of thiobarbituric acid reactive substances (TBARS), free carbonyl content (C = O groups) and membrane protein thiol level (MPTL)]. Treatment with standardized low titer hydrogen peroxide during early imbibitional phase of germination caused significant reversal in oxidative damages to the newly assembled membrane system imposed by heat and chilling stress [evident from the data of TBARS, C = O, MPTL, ROS accumulation, membrane permeability status, membrane injury index and oxidative stress index] in seedlings of experimental rice cultivar. Imbibitional H2O2 pretreatment also caused up-regulation of antioxidative defense (activities of superoxide dismutase, catalase, ascorbate peroxidase, glutathione reductase and total thiol content) in the heat and chilling stress-raised rice seedlings. When the parameters of early growth performances were assessed (in terms of relative growth index, biomass accumulation, relative germination performance, mean daily germination, T50 value), it clearly exhibited significant improvement of early growth performances of the experimental rice cultivar. The result proposes that an 'inductive pulse' of H2O2 is required to switch on some stress acclimatory metabolism through which plant restores redox homeostasis and prevents or repairs oxidative damages to newly assembled membrane

  12. Evaluation of physiological and biochemical responses of two rice (Oryza sativa L.) cultivars to ambient air pollution using open top chambers at a rural site in India.

    PubMed

    Rai, Richa; Agrawal, Madhoolika

    2008-12-15

    Air pollutant concentrations are rising in India, causing potential threats to crop production. As air pollutants are known to interfere with physiological processes, this study was conducted to assess the relative responses of physiological and biochemical characteristics of two cultivars of rice (Oryza sativa L. cv. Saurabh 950 and NDR 97) leading to variable yield responses. Twelve hour monitoring of ambient concentrations of SO2, NO2 and O3 in filtered chambers (FCs), non-filtered chambers (NFCs) and open plots (OPs) showed that O3 was the main pollutant at the experimental site. Ozone concentrations often exceeded 40 ppb during anthesis but not during the vegetative growth period. Photosynthetic rate (Ps), stomatal conductance (g(s)) and Fv/Fm ratio, superoxide dismutase (SOD) and peroxidase (POD) activities and photosynthetic pigments, ascorbic acid, total phenolics and protein contents were assessed at different developmental stages and yield of grains were quantified. Lipid peroxidation, SOD and POD activities, ascorbic acid and total phenolics were higher, whereas Ps, g(s), Fv/Fm ratio and contents of protein and photosynthetic pigment were lower in plants of NFCs as compared to FCs. Yield decreased significantly in both cultivars grown in NFCs. NDR 97 showed less reductions in physiological characteristics, photosynthetic pigments and protein, but a greater increase in the antioxidative defense system as compared to Saurabh 950. Yield reduction was higher in NDR 97 than in Saurabh 950. This suggested that NDR 97 utilized more photosynthate in maintaining the metabolic machinery against O3 stress leading to lower translocation of photosynthate to reproductive parts. The study concluded that under natural field conditions, physiological and biochemical responses of plants varied with pollutant concentrations leading to different translocation strategies in plants, modifying their yield responses. NDR 97, a fast growing and high yielding cultivar was more

  13. Effect of hydrothermal processing on antioxidant contents and capacities in pigmented rice (Oryza sativa L.)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Purple and red bran rice cultivars (Oryza sativa L.) are rich sources of antioxidants including lipophilic antioxidants (vitamin E homologues and '-oryzanol), soluble phenolics (including anthocyanidins and proanthocyanidins), and cell-wall-bound phenolics. This study investigated impacts of hydroth...

  14. Cultivars effect on the physical characteristics of rice (rough and milled) (Oryza Sativa L.) of temperate region of Kashmir (India).

    PubMed

    Bhat, Farhan M; Riar, Charanjit S

    2016-12-01

    The aim of present research was to evaluate physical and engineering properties of traditional paddy and rice cultivars native to temperate region of India. Length, width, thickness, equivalent diameter, surface area, aspect ratio, volume, bulk density, true density, porosity, thousand kernels weight, angle of repose and coefficient of friction were evaluated, which are required in designing of various post harvest operations and storage structures. The low bulk density of cultivars, Mushki budgi, Mushki tujan and Kaw kareed may be due to the presence of long awns possessed by these cultivars which were bulky and occupied more space. The wide variations were found in rice kernels with respect to colour, which determined the functional properties and energy requirement during polishing of these cultivars. Results indicated significant differences in the physical properties among various paddy and brown rice cultivars when compared with earlier reported results. Thousand kernel weight, width, arithmetic mean diameter and equivalent diameter showed significant positive correlations with spherecity, surface area, volume, true density, and angle of repose; but negatively correlated with bulk density. These desirable characteristics exploit agriculturists/institutions to preserve these races and encourage farmers to cultivate these cherished rice cultivars.

  15. Different physiobiochemical and transcriptomic reactions of rice (Oryza sativa L.) cultivars differing in terms of salt sensitivity under salinity stress.

    PubMed

    Kordrostami, Mojtaba; Rabiei, Babak; Kumleh, Hassan Hassani

    2017-01-17

    Salinity stress is the most important and common environmental stresses throughout the world, including Iran. The aim of this study was to investigate the expression of several important genes involved in the salinity tolerance of the rice cultivars differing in salt sensitivity. In this research, the expression of four mitochondrial genes, H2O2, malondialdehyde (MDA), proline, sodium, potassium and superoxide dismutase (SOD), was measured in Iranian rice cultivars and two well-known international varieties as checks in response to 100 mM salt stress. The results show that the activity of SOD in the tolerant cultivars is much higher than in the susceptible ones under saline conditions (100 mM NaCl). The study of the gene expression in the tolerant and sensitive cultivars also showed that the expression of the genes increased in the early hours of the stress, with the exception of the OsGR1. Moreover, the amount of the expression in the tolerant cultivars was far more than the susceptible ones. The result of this study showed that the function of a set of antioxidant enzymes can lead to detoxification of the reactive oxygen species, so in order to better understand ROS scavengers, a comprehensive study on the antioxidant system should be conducted.

  16. Effect of salinity stress on growth and carbohydrate metabolism in three rice (Oryza sativa L.) cultivars differing in salinity tolerance.

    PubMed

    Pattanagul, Wattana; Thitisaksakul, Maysaya

    2008-10-01

    Rice seedlings cv. Khao Dawk Mali 105 (salt-sensitive), Luang Anan (moderately salt-tolerant) and Pokkali (salt-tolerant) were exposed to 0, 50, 100 and 150 mM NaCI for 9 d. Salinity stress caused reduction in leaf relative water contents in all cultivars. Shoot length of cv. Pokkali was least affected by salinity stress whereas increased root length in response to salinity stress was apparent in cvs. Khao Dawk Mali 105 and Luang Anan. Increased salinity level also caused reduction in fresh and dry weights in cvs. Khao Dawk Mali 105 and Luang Anan, but had no effect in cv. Pokkali except at 150 mM. Accumulation of total soluble sugars and sucrose in mature leaves were observed in cv. Khao Dawk Mali 105 exposed to high level of salinity whereas their concentrations in cvs. Luang Anan and Pokkali remained the same as control plants. Accumulation of sucrose in cv. Khao Dawk Mali 105 was suggested to be resulted from the alteration of photosynthate partitioning since the activities of sucrose phosphate synthase were not affected by salinity in this cultivar. On the contrary, salinity stress induced an accumulation of starch in cv. Pokkali. It is suggested that partitioning sugars into starch may involve in salinity tolerance by avoiding metabolic alterations.

  17. Identification of a new locus conferring antixenosis to the brown planthopper in rice cultivar Swarnalata (Oryza sativa L.).

    PubMed

    Qiu, Y F; Cheng, L; Liu, F; Li, R B

    2013-08-29

    The brown planthopper [Nilaparvata lugens (Stål); BPH] has caused severe damage to rice production. The identification of resistance genes and the development of BPH-resistant varieties are economical and effective ways to manage this pest. Using an F2 population from a cross between the Indica cultivars 93-11 and Swarnalata, we mapped the Qbph-8 locus to a 7.3-cM region on chromosome 8 in two tests, flanked by the markers RM339 and RM515. In this population, Qbph-8 explained 7.7 and 6.6% of the phenotypic variance of BPH preference in both tests. In the BPH host choice test, the average number of settled BPHs on the Qbph-8 plants was less than that on the 93-11 plants over the 24- to 120-h observation period. Furthermore, less BPH insects were observed on the BPH6+Qbph-8 plant compared with the BPH6 plant or Qbph-8 plant, indicating a stronger antixenotic effect shown in the gene pyramiding plants. Hence, this locus can be pyramided with other BPH resistance genes and applied to breed-resistant varieties, which possibly can improve the resistance level and durable resistance to the BPH.

  18. Genetic basis of multiple resistance to the brown planthopper (Nilaparvata lugens Stål) and the green rice leafhopper (Nephotettix cincticeps Uhler) in the rice cultivar ‘ASD7’ (Oryza sativa L. ssp. indica)

    PubMed Central

    Van Mai, Tan; Fujita, Daisuke; Matsumura, Masaya; Yoshimura, Atsushi; Yasui, Hideshi

    2015-01-01

    The rice cultivar ASD7 (Oryza sativa L. ssp. indica) is resistant to the brown planthopper (BPH; Nilaparvata lugens Stål) and the green leafhopper (Nephotettix virescens Distant). Here, we analyzed multiple genetic resistance to BPH and the green rice leafhopper (GRH; Nephotettix cincticeps Uhler). Using two independent F2 populations derived from a cross between ASD7 and Taichung 65 (Oryza sativa ssp. japonica), we detected two QTLs (qBPH6 and qBPH12) for resistance to BPH and one QTL (qGRH5) for resistance to GRH. Linkage analysis in BC2F3 populations revealed that qBPH12 controlled resistance to BPH and co-segregated with SSR markers RM28466 and RM7376 in plants homozygous for the ASD7 allele at qBPH6. Plants homozygous for the ASD7 alleles at both QTLs showed a much faster antibiosis response to BPH than plants homozygous at only one of these QTLs. It revealed that epistatic interaction between qBPH6 and qBPH12 is the basis of resistance to BPH in ASD7. In addition, qGRH5 controlled resistance to GRH and co-segregated with SSR markers RM6082 and RM3381. qGRH5 is identical to GRH1. Thus, we clarified the genetic basis of multiple resistance of ASD7 to BPH and GRH. PMID:26719745

  19. Genetic basis of multiple resistance to the brown planthopper (Nilaparvata lugens Stål) and the green rice leafhopper (Nephotettix cincticeps Uhler) in the rice cultivar 'ASD7' (Oryza sativa L. ssp. indica).

    PubMed

    Van Mai, Tan; Fujita, Daisuke; Matsumura, Masaya; Yoshimura, Atsushi; Yasui, Hideshi

    2015-12-01

    The rice cultivar ASD7 (Oryza sativa L. ssp. indica) is resistant to the brown planthopper (BPH; Nilaparvata lugens Stål) and the green leafhopper (Nephotettix virescens Distant). Here, we analyzed multiple genetic resistance to BPH and the green rice leafhopper (GRH; Nephotettix cincticeps Uhler). Using two independent F2 populations derived from a cross between ASD7 and Taichung 65 (Oryza sativa ssp. japonica), we detected two QTLs (qBPH6 and qBPH12) for resistance to BPH and one QTL (qGRH5) for resistance to GRH. Linkage analysis in BC2F3 populations revealed that qBPH12 controlled resistance to BPH and co-segregated with SSR markers RM28466 and RM7376 in plants homozygous for the ASD7 allele at qBPH6. Plants homozygous for the ASD7 alleles at both QTLs showed a much faster antibiosis response to BPH than plants homozygous at only one of these QTLs. It revealed that epistatic interaction between qBPH6 and qBPH12 is the basis of resistance to BPH in ASD7. In addition, qGRH5 controlled resistance to GRH and co-segregated with SSR markers RM6082 and RM3381. qGRH5 is identical to GRH1. Thus, we clarified the genetic basis of multiple resistance of ASD7 to BPH and GRH.

  20. Transgressive variation for yield components and dynamic traits in Jefferson (Oryza sativa) x O. rufipogon introgression lines

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Alleles from wild progenitors of crops can be a source of transgressive variation in modern cultivars. Introgressions from the Oryza rufipogon donor (IRGC104591) in an O. sativa tropical japonica cultivar (Jefferson) were shown to confer a yield advantage in multi-location field trials. Yield loci...

  1. Triterpenoid glycosides from Medicago sativa as antifungal agents against Pyricularia oryzae.

    PubMed

    Abbruscato, Pamela; Tosi, Solveig; Crispino, Laura; Biazzi, Elisa; Menin, Barbara; Picco, Anna M; Pecetti, Luciano; Avato, Pinarosa; Tava, Aldo

    2014-11-19

    The antifungal properties of saponin mixtures from alfalfa (Medicago sativa L.) tops and roots, the corresponding mixtures of prosapogenins from tops, and purified saponins and sapogenins against the causal agent of rice blast Pyricularia oryzae isolates are presented. In vitro experiments highlighted a range of activities, depending upon the assayed metabolite. The antifungal effects of the most promising prosapogenin mixture from alfalfa tops were confirmed by means of in planta tests using three different Italian cultivars of rice (Oryza sativa L. ssp. japonica), known to possess high, medium, and low blast resistance. The evidenced antifungal properties of the tested metabolites allowed some considerations on their structure-activity relationship. Results indicate that prosapogenins are active compounds to prevent the fungal attack of P. oryzae on different rice cultivars. Therefore, if properly formulated, these substances could represent a promising and environmentally friendly treatment to control rice blast.

  2. 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.

  3. 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.

  4. Improving Pharmaceutical Protein Production in Oryza sativa

    PubMed Central

    Kuo, Yu-Chieh; Tan, Chia-Chun; Ku, Jung-Ting; Hsu, Wei-Cho; Su, Sung-Chieh; Lu, Chung-An; Huang, Li-Fen

    2013-01-01

    Application of plant expression systems in the production of recombinant proteins has several advantages, such as low maintenance cost, absence of human pathogens, and possession of complex post-translational glycosylation capabilities. Plants have been successfully used to produce recombinant cytokines, vaccines, antibodies, and other proteins, and rice (Oryza sativa) is a potential plant used as recombinant protein expression system. After successful transformation, transgenic rice cells can be either regenerated into whole plants or grown as cell cultures that can be upscaled into bioreactors. This review summarizes recent advances in the production of different recombinant protein produced in rice and describes their production methods as well as methods to improve protein yield and quality. Glycosylation and its impact in plant development and protein production are discussed, and several methods of improving yield and quality that have not been incorporated in rice expression systems are also proposed. Finally, different bioreactor options are explored and their advantages are analyzed. PMID:23615467

  5. Analysis of nucleotide diversity among alleles of the major bacterial blight resistance gene Xa27 in cultivars of rice (Oryza sativa) and its wild relatives.

    PubMed

    Bimolata, Waikhom; Kumar, Anirudh; Sundaram, Raman Meenakshi; Laha, Gouri Shankar; Qureshi, Insaf Ahmed; Reddy, Gajjala Ashok; Ghazi, Irfan Ahmad

    2013-08-01

    Xa27 is one of the important R-genes, effective against bacterial blight disease of rice caused by Xanthomonas oryzae pv. oryzae (Xoo). Using natural population of Oryza, we analyzed the sequence variation in the functionally important domains of Xa27 across the Oryza species. DNA sequences of Xa27 alleles from 27 rice accessions revealed higher nucleotide diversity among the reported R-genes of rice. Sequence polymorphism analysis revealed synonymous and non-synonymous mutations in addition to a number of InDels in non-coding regions of the gene. High sequence variation was observed in the promoter region including the 5'UTR with 'π' value 0.00916 and 'θ w ' = 0.01785. Comparative analysis of the identified Xa27 alleles with that of IRBB27 and IR24 indicated the operation of both positive selection (Ka/Ks > 1) and neutral selection (Ka/Ks ≈ 0). The genetic distances of alleles of the gene from Oryza nivara were nearer to IRBB27 as compared to IR24. We also found the presence of conserved and null UPT (upregulated by transcriptional activator) box in the isolated alleles. Considerable amino acid polymorphism was localized in the trans-membrane domain for which the functional significance is yet to be elucidated. However, the absence of functional UPT box in all the alleles except IRBB27 suggests the maintenance of single resistant allele throughout the natural population.

  6. Soil Texture and Cultivar Effects on Rice (Oryza sativa, L.) Grain Yield, Yield Components and Water Productivity in Three Water Regimes

    PubMed Central

    Dou, Fugen; Soriano, Junel; Tabien, Rodante E.; Chen, Kun

    2016-01-01

    The objective of this study was to determine the effects of water regime/soil condition (continuous flooding, saturated, and aerobic), cultivar (‘Cocodrie’ and ‘Rondo’), and soil texture (clay and sandy loam) on rice grain yield, yield components and water productivity using a greenhouse trial. Rice grain yield was significantly affected by soil texture and the interaction between water regime and cultivar. Significantly higher yield was obtained in continuous flooding than in aerobic and saturated soil conditions but the latter treatments were comparable to each other. For Rondo, its grain yield has decreased with soil water regimes in the order of continuous flooding, saturated and aerobic treatments. The rice grain yield in clay soil was 46% higher than in sandy loam soil averaged across cultivar and water regime. Compared to aerobic condition, saturated and continuous flooding treatments had greater panicle numbers. In addition, panicle number in clay soil was 25% higher than in sandy loam soil. The spikelet number of Cocodrie was 29% greater than that of Rondo, indicating that rice cultivar had greater effect on spikelet number than soil type and water management. Water productivity was significantly affected by the interaction of water regime and cultivar. Compared to sandy loam soil, clay soil was 25% higher in water productivity. Our results indicated that cultivar selection and soil texture are important factors in deciding what water management option to practice. PMID:26978525

  7. RESPONSE OF OXIDATIVE STRESS DEFENSE SYSTEMS IN RICE (ORYZA SATIVA) LEAVES WITH SUPPLEMENTAL UV-B RADIATION

    EPA Science Inventory

    The impact of elevated ultraviolet-B radiation (UV-B, 280-320 nm) on membrane systems and lipid peroxidation, and possible involvement of active oxygen radicals was investigated in leaves of two UV-B susceptible rice cultivars (Oryza sativa L. cvs IR74 and Dular). Rice seedlings ...

  8. Transgressive variation for yield components measured throughout the growth cycle of Jefferson rice (Oryza sativa) x O. rufipogon introgression lines

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Previous studies demonstrated alleles introduced into elite rice (Oryza sativa) cultivars from the wild ancestral species, O. rufipogon, enhanced yield and yield components as a result of transgressive variation. A study was conducted to unveil phenological and agronomic mechanisms that underlie in...

  9. A novel two T-DNA binary vector allows efficient generation of marker-free transgenic plants in three elite cultivars of rice (Oryza sativa L.).

    PubMed

    Breitler, Jean-Christophe; Meynard, Donaldo; Van Boxtel, Jos; Royer, Monique; Bonnot, François; Cambillau, Laurence; Guiderdoni, Emmanuel

    2004-06-01

    A pilot binary vector was constructed to assess the potential of the 2 T-DNA system for generating selectable marker-free progeny plants in three elite rice cultivars (ZhongZuo321, Ariete and Khao Dawk Mali 105) known to exhibit contrasting amenabilities to transformation. The first T-DNA of the vector, delimited by Agrobacterium tumefaciens borders, contains the hygromycin phosphotransferase (hpt) selectable gene and the green fluorescent protein (gfp) reporter gene while the second T-DNA, delimited by Agrobacterium rhizogenes borders, bears the phosphinothricin acetyl transferase (bar) gene, featuring the gene of interest. 82-90% of the hygromycin-resistant primary transformants exhibited tolerance to ammonium glufosinate mediated by the bar gene suggesting very high co-transformation frequency in the three cultivars. All of the regenerated plants were analyzed by Southern blot which confirmed co-integration of the T-DNAs at frequencies consistent with those of co-expression and allowed determination of copy number for each gene as well as detection of two different vector backbone fragments extending between the two T-DNAs. Hygromycin susceptible, ammonium glufosinate tolerant phenotypes represented 14.4, 17.4 and 14.3% of the plants in T1 progenies of ZZ321, Ariete and KDML105 primary transformants, respectively. We developed a statistical model for deducing from the observed copy number of each T-DNA in T0 plants and phenotypic segregations in T1 progenies the most likely constitution and linkage of the T-DNA integration locus. Statistical analysis identified in 40 out of 42 lines a most likely linkage configuration theoretically allowing genetic separation of the two T-DNA types and out segregation of the T-DNA bearing the bar gene. Overall, though improvements of the technology would be beneficial, the 2 T-DNA system appeared to be a useful approach to generate selectable marker-free rice plants with a consistent frequency among cultivars.

  10. Recessive resistance genes and the Oryza sativa-Xanthomonas oryzae pv. oryzae pathosystem.

    PubMed

    Iyer-Pascuzzi, Anjali S; McCouch, Susan R

    2007-07-01

    Though recessive resistance is well-studied in viral systems, little is understood regarding the phenomenon in plant-bacterial interactions. The Oryza sativa-Xanthomonas oryzae pv. orzyae pathosystem provides an excellent opportunity to examine recessive resistance in plant-bacterial interactions, in which nine of 30 documented resistance (R) genes are recessively inherited. Infestations of X. oryzae pv. oryzae, the causal agent of bacterial blight, result in significant crop loss and damage throughout South and Southeast Asia. Two recently cloned novel recessive R genes, xa5 and xa13, have yielded insights to this system. Like their viral counterparts, these bacterial recessive R gene products do not conform to the five commonly described classes of R proteins. New findings suggest that such genes may more aptly be viewed as mutations in dominant susceptibility alleles and may also function in a gene-for-gene manner. In this review, we discuss recent accomplishments in the understanding of recessively inherited R genes in the rice-bacterial blight pathosystem and suggest a new model for the function of recessive resistance in plant-bacterial interactions.

  11. Map-based Cloning and Characterization of a Brown Planthopper Resistance Gene BPH26 from Oryza sativa L. ssp. indica Cultivar ADR52

    PubMed Central

    Tamura, Yasumori; Hattori, Makoto; Yoshioka, Hirofumi; Yoshioka, Miki; Takahashi, Akira; Wu, Jianzhong; Sentoku, Naoki; Yasui, Hideshi

    2014-01-01

    The brown planthopper (BPH) is the most serious insect pest of rice in Asia. The indica rice cultivar ADR52 carries two BPH resistance genes, BPH26 (BROWN PLANTHOPPER RESISTANCE 26) and BPH25. Map-based cloning of BPH26 revealed that BPH26 encodes a coiled-coil-nucleotide-binding-site–leucine-rich repeat (CC–NBS–LRR) protein. BPH26 mediated sucking inhibition in the phloem sieve element. BPH26 was identical to BPH2 on the basis of DNA sequence analysis and feeding ability of the BPH2-virulent biotype of BPH. BPH2 was widely incorporated in elite rice cultivars and was well-cultivated in many Asian countries as a favorable gene resource in rice breeding against BPH. However, BPH2 was rendered ineffective by a virulent biotype of BPH in rice fields in Asia. In this study, we suggest that BPH2 can be reused by combining with other BPH resistance genes, such as BPH25, to ensure durable resistance to BPH. PMID:25076167

  12. Characterization of Grain Quality and Starch Fine Structure of Two Japonica Rice (Oryza Sativa) Cultivars with Good Sensory Properties at Different Temperatures during the Filling Stage.

    PubMed

    Zhang, Changquan; Zhou, Lihui; Zhu, Zhengbin; Lu, Huwen; Zhou, Xingzhong; Qian, Yiting; Li, Qianfeng; Lu, Yan; Gu, Minghong; Liu, Qiaoquan

    2016-05-25

    Temperature during the growing season is a critical factor affecting grain quality. High temperatures at grain filling affect kernel development, resulting in reduced yield, increased chalkiness, reduced amylose content, and poor milling quality. Here, we investigated the grain quality and starch structure of two japonica rice cultivars with good sensory properties grown at different temperatures during the filling stage under natural field conditions. Compared to those grown under normal conditions, rice grains grown under hot conditions showed significantly reduced eating and cooking qualities, including a higher percentage of grains with chalkiness, lower protein and amylose contents, and higher pasting properties. Under hot conditions, rice starch contained reduced long-chain amylose (MW 10(7.1) to 10(7.4)) and significantly fewer short-chain amylopectin (DP 5-12) but more intermediate- (DP 13-34) and long- (DP 45-60) chain amylopectin than under normal conditions, as well as higher crystallinity and gelatinization properties.

  13. Changes in root hydraulic conductivity facilitate the overall hydraulic response of rice (Oryza sativa L.) cultivars to salt and osmotic stress.

    PubMed

    Meng, Delong; Fricke, Wieland

    2017-04-01

    The aim of the present work was to assess the significance of changes in root AQP gene expression and hydraulic conductivity (Lp) in the regulation of water balance in two hydroponically-grown rice cultivars (Azucena, Bala) which differ in root morphology, stomatal regulation and aquaporin (AQP) isoform expression. Plants were exposed to NaCl (25 mM, 50 mM) and osmotic stress (5%, 10% PEG6000). Root Lp was determined for exuding root systems (osmotic forces driving water uptake; 'exudation Lp') and transpiring plants (hydrostatic forces dominating; 'transpiration-Lp'). Gene expression was analysed by qPCR. Stress treatments caused a consistent and significant decrease in plant growth, transpirational water loss, stomatal conductance, shoot-to-root surface area ratio and root Lp. Comparison of exudation-with transpiration-Lp supported a significant contribution of AQP-facilitated water flow to root water uptake. Changes in root Lp in response to treatments were correlated much stronger with root morphological characteristics, such as the number of main and lateral roots, surface area ratio of root to shoot and plant transpiration rate than with AQP gene expression. Changes in root Lp, involving AQP function, form an integral part of the plant hydraulic response to stress and facilitate changes in the root-to-shoot surface area ratio, transpiration and stomatal conductance.

  14. Characterization of recombinant β-amylases from Oryza sativa.

    PubMed

    Koide, Tomojiro; Ohnishi, Yasuo; Horinouchi, Sueharu

    2011-01-01

    Four putative β-amylase genes found in the Oryza sativa cDNA sequence database (KOME) were expressed in Escherichia coli. Recombinant proteins from two of these genes showed β-amylase activity. Similarly to β-amylases from other plants, the optimum pH of the recombinant rice β-amylases was about 5.5-6.0, but they exhibited inferior heat stability to soybean β-amylase.

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  16. Transcriptome Analysis of Oryza sativa Calli Under Microgravity

    NASA Astrophysics Data System (ADS)

    Jin, Jing; Chen, Haiying; Cai, Weiming

    2015-11-01

    The transcriptome of Oryza sativacalli was analyzed on board the Chinese spaceship "Shenzhou 8" to study the effects of microgravity on plant signal transduction and secondary metabolism (as one of the experiments with SIMBOX on Shenzhou 8). Calli of Oryza sativa were pre-cultured for 4 days on ground and then loaded into the stationary platform or the rotating platform of a biological incubator, called SIMBOX, to grow in space under microgravity conditions or 1g-conditions, respectively. The calli were fixed by RNAlater after grew 324 h under microgravity. After 17 days, Shenzhou 8 returned to Earth carrying SIMBOX. Oryza sativa calli were recovered, and the RNA was extracted for transcriptome analysis. After comparing 1 gspaceflight controls-inflight controls with 1 g-ground controls, 157 probe sets with different expression levels (fold change ≥2, p<0.05) were identified. When comparing spaceflight controls to 1 g-ground controls and to 1 g-inflight controls, 678 probe sets with different expression levels (fold change ≥2, p<0.05) were identified. The fact that the same 678 probe sets were identified in these two comparisons suggests that transcription was affected under microgravity conditions. MapMan analysis was used to classify 627 microgravity responsive (MR) transcripts. The MR transcripts were mainly involved in cell wall structure, the TCA cycle, primary metabolism, transcription, protein modification and degradation, hormone metabolism, calcium regulation, receptor like kinase activity and transport.

  17. Root-associated bacterial diversities of Oryza rufipogon and Oryza sativa and their influencing environmental factors.

    PubMed

    Tian, Lei; Zhou, Xue; Ma, Lina; Xu, Shangqi; Nasir, Fahad; Tian, Chunjie

    2016-12-18

    Oryza rufipogon is the ancestor of human-cultivated Oryza sativa. However, little is known about the difference between the root-associated microorganisms of O. rufipogon and O. sativa. In this study, the root-associated bacteria of O. rufipogon, Leersia hexandra, and O. sativa from different latitudes in China were studied by DGGE analysis. Their bacterial community structures were compared by principal component analysis. The relationship between root-associated bacteria and soil properties was explored by canonical correspondence analysis. The relationships of glomalin-related soil protein (GRSP) content, soluble sugar content, proline content of the plant, and bacterial diversity indices of their root-associated microorganisms were also investigated. We found both broad-spectrum and host-specific bacteria, and the similarity, diversity and abundance indices of O. rufipogon and L. hexandra were higher than O. sativa root-associated bacteria. However, even living in the same habitat, O. rufipogon and L. hexandra selected different root-associated bacteria. Microbial composition was primarily correlated with available N, P, and K and the annual precipitation. We also found a positive correlation between the soluble sugar content of the plant and GRSP content of the root soil. The above results indicated that the community structure of root-associated bacteria differs between wild rice and cultivated rice. Human activity and the natural selection of the host plants shaped the differences, consistent with our hypothesis.

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

    PubMed Central

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

    2017-01-01

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

  19. Alternatively spliced transcripts of Pi-ta blast resistance gene in Oryza sativa

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The Pi-ta gene in rice (Oryza sativa L.) confers resistance to races of Magnaporthe oryzae containing its cognate avirulence gene AVR-Pita. Pi-ta is a single-copy gene belonging to the nucleotide-binding site leucine-rich repeat (NBS-LRR) class of plant resistance (R) genes. In the present study, w...

  20. Interspecific rice hybrid of Oryza sativa x Oryza nivara reveals a significant increase in seed protein content.

    PubMed

    Mahmoud, Ahmed A; Sukumar, S; Krishnan, Hari B

    2008-01-23

    Wild species offer a potential reservoir of genetic variation for crop improvement. Besides the valuable genes for disease resistance that the wild species have provided for rice improvement, recent studies have shown that these wild species could also provide favorable alleles for the improvement of yield and yield-related traits. The present study reports yet another potential of wild relatives of rice, which involves the improvement of seed protein content. A significant increase in seed protein content was observed in an interspecific hybrid between Oryza sativa ssp. indica and the wild species Oryza nivara. The hybrid showed a protein content of 12.4%, which was 28 and 18.2% higher than those of the parents O. nivara and IR 64, respectively. The increase in protein content was dependent on the genetic background of the rice variety used in the hybridization. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis of seed storage proteins demonstrated that a significant increase in prolamins and glutelins was mainly responsible for the elevated protein content of the hybrid. Amino acid analysis of seed proteins revealed that the hybrid had net gains of 19.5% in lysine and 19.4% in threonine over the O. nivara parent on a seed dry weight basis. Molecular analysis indicated that the increase in protein content of the hybrid was not a result of chromosomal rearrangements or transposable element activation, at least in the chromosomal regions containing seed storage protein genes. A preliminary genetic analysis of the F 2 segregating population showed that the inheritance of the increased protein content was polygenic in nature. The development of this interspecific hybrid offers a great potential for selecting new rice cultivars that combine the high yield and superior cooking quality of IR 64 with improved seed protein content.

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

    PubMed

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

    2014-02-01

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

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

    PubMed Central

    Lee, Gyu-Ho; Kang, In-Kyu

    2016-01-01

    The critical evolutionary step during domestication of major cereals was elimination of seed shattering because the easy-to-shatter trait in wild relatives results in a severe reduction in yield. In this study, we analyzed the QTLs associated with shattering employing a high-density genetic map in doubled haploid (DH) population of rice (Oryza sativa L.). A genetic linkage map was generated with 217 microsatellite markers spanning 2082.4 cM and covering 12 rice chromosomes with an average interval of 9.6 cM between markers based on 120 DHLs derived from a cross between Cheongcheong indica type cultivar and Nagdong japonica type cultivar. In the QTL analysis, five QTLs pertaining to the breaking tensile strength (BTS) were detected in 2013 and 2015. Two regions of the QTLs related to BTS on chromosome 1 and chromosome 6 were detected. Several important genes are distributed in 1 Mbp region of the QTL on chromosome 6 and they are related to the formation of abscission layer. We decide to name this QTL qSh6 and the candidate genes in the qSh6 region can be employed usefully in further research for cloning. PMID:27419124

  3. Effects of Colonization of the Roots of Domestic Rice (Oryza sativa L. cv. Amaroo) by Burkholderia pseudomallei.

    PubMed

    Prasertsincharoen, Noppadol; Constantinoiu, Constantin; Gardiner, Christopher; Warner, Jeffrey; Elliman, Jennifer

    2015-07-01

    Burkholderia pseudomallei is a saprophytic bacterium that causes melioidosis and is often isolated from rice fields in Southeast Asia, where the infection incidence is high among rice field workers. The aim of this study was to investigate the relationship between this bacterium and rice through growth experiments where the effect of colonization of domestic rice (Oryza sativa L. cv Amaroo) roots by B. pseudomallei could be observed. When B. pseudomallei was exposed to surface-sterilized seeds, the growth of both the root and the aerosphere was retarded compared to that in controls. The organism was found to localize in the root hairs and endodermis of the plant. A biofilm formed around the root and root structures that were colonized. Growth experiments with a wild rice species (Oryza meridionalis) produced similar retardation of growth, while another domestic cultivar (O. sativa L. cv Koshihikari) did not show retarded growth. Here we report B. pseudomallei infection and inhibition of O. sativa L. cv Amaroo, which might provide insights into plant interactions with this important human pathogen.

  4. Assessing the impact of ambient ozone on growth and yield of a rice (Oryza sativa L.) and a wheat (Triticum aestivum L.) cultivar grown in the Yangtze Delta, China, using three rates of application of ethylenediurea (EDU).

    PubMed

    Wang, Xiaoke; Zheng, Qiwei; Yao, Fangfang; Chen, Zhan; Feng, Zhaozhong; Manning, W J

    2007-07-01

    Foliar applications of ethylenediurea (abbreviated as EDU) were made at 0, 150, 300 or 450 ppm to field-grown rice and wheat in the Yangtze Delta in China. Rice and wheat responded differently to ambient ozone and EDU applications. For wheat, some growth characteristics, such as yield, seed number per plant, seed set rate and harvest index, increased significantly at 300 ppm EDU treatment, while for rice no parameters measured were statistically different regarding EDU application. The reason may be that the wheat cultivar used may be more sensitive to ozone than the rice cultivar. EDU was effective in demonstrating ozone effects on the wheat cultivar, but not on the rice cultivar. Cultivar sensitivity might be an important consideration when assessing the effects of ambient ozone on plants.

  5. Analyses of Old “Prokaryotic” Proteins Indicate Functional Diversification in Arabidopsis and Oryza sativa

    PubMed Central

    Singh, Anupama; Jethva, Minesh; Singla-Pareek, Sneh L.; Pareek, Ashwani; Kushwaha, Hemant R.

    2016-01-01

    During evolution, various processes such as duplication, divergence, recombination, and many other events leads to the evolution of new genes with novel functions. These evolutionary events, thus significantly impact the evolution of cellular, physiological, morphological, and other phenotypic trait of organisms. While evolving, eukaryotes have acquired large number of genes from the earlier prokaryotes. This work is focused upon identification of old “prokaryotic” proteins in Arabidopsis and Oryza sativa genome, further highlighting their possible role(s) in the two genomes. Our results suggest that with respect to their genome size, the fraction of old “prokaryotic” proteins is higher in Arabidopsis than in Oryza sativa. The large fractions of such proteins encoding genes were found to be localized in various endo-symbiotic organelles. The domain architecture of the old “prokaryotic” proteins revealed similar distribution in both Arabidopsis and Oryza sativa genomes showing their conserved evolution. In Oryza sativa, the old “prokaryotic” proteins were more involved in developmental processes, might be due to constant man-made selection pressure for better agronomic traits/productivity. While in Arabidopsis, these proteins were involved in metabolic functions. Overall, the analysis indicates the distinct pattern of evolution of old “prokaryotic” proteins in Arabidopsis and Oryza sativa. PMID:27014324

  6. Analysis of sialyltransferase-like proteins from Oryza sativa.

    PubMed

    Takashima, Shou; Abe, Tomoko; Yoshida, Shigeo; Kawahigashi, Hiroyuki; Saito, Tamio; Tsuji, Shuichi; Tsujimoto, Masafumi

    2006-02-01

    Sialic acids are widely distributed among living creatures, from bacteria to mammals, but it has been commonly accepted that they do not exist in plants. However, with the progress of genome analyses, putative gene homologs of animal sialyltransferases have been detected in the genome of some plants. In this study, we cloned three genes from Oryza sativa (Japanese rice) that encode sialyltransferase-like proteins, designated OsSTLP1, 2, and 3, and analyzed the enzymatic activity of the proteins. OsSTLP1, 2, and 3 consist of 393, 396, and 384 amino acids, respectively, and each contains sequences similar to the sialyl motifs that are highly conserved among animal sialyltransferases. The recombinant soluble forms of OsSTLPs produced by COS-7 cells were analyzed for sialyltransferase-like activity. OsSTLP1 exhibited such activity toward the oligosaccharide Galbeta1,4GlcNAc and such glycoproteins as asialofetuin, alpha1-acid glycoprotein, and asialo-alpha1-acid glycoprotein; OsSTLP3 exhibited similar activity toward asialofetuin; and OsSTLP2 exhibited no sialyltransferase-like activity. The sialic acid transferred by OsSTLP1 or 3 was linked to galactose of Galbeta1,4GlcNAc through alpha2,6-linkage. This is the first report of plant proteins having sialyltransferase-like activity.

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

    PubMed

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

    2016-02-01

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

  8. Investigation of tocotrienol biosynthesis in rice (Oryza sativa L.).

    PubMed

    Matsuzuka, Kentaro; Kimura, Eiichi; Nakagawa, Kiyotaka; Murata, Kazumasa; Kimura, Toshiyuki; Miyazawa, Teruo

    2013-09-01

    Rice tocotrienol (T3) has gained attention due to its physiological activities (e.g., antiangiogenesis). However, the biosynthetic pathway for T3 production in rice grain has not been well studied. We hypothesized that T3 biosynthesis enzymes and/or precursors play an important role in T3 production in whole grain. This proposal was evaluated in rice (Oryza sativa L.) by PCR and HPLC techniques. Grain tocopherol as well as flag leaf vitamin E levels were also investigated for comparison. For rice samples 14 days after flowering, grain was abundant in T3, but not in flag leaf. Expression of a gene encoding homogentisate geranylgeranyltransferase (HGGT, which has long been believed to be important for T3 production) differed significantly between grain and flag leaf. We then investigated rice samples during the grain maturation period, and found that grain T3 and HGGT levels increased in the early stage and then reached a plateau. T3 precursors such as homogentisate and geranylgeranyl pyrophosphate decreased during maturation. No increase in grain T3 from the middle to late stages of maturation and a decrease in T3 precursors during maturation suggest that HGGT would be an essential, but not limiting factor for T3 biosynthesis, and T3 precursors could regulate the T3 level in grain. The results of this study would be useful for nutraceutical purposes (e.g., development of T3-overproducing rice for the prevention of angiogenic disorders).

  9. The process of methylmercury accumulation in rice (Oryza sativa L.).

    PubMed

    Meng, Bo; Feng, Xinbin; Qiu, Guangle; Liang, Peng; Li, Ping; Chen, Chunxiao; Shang, Lihai

    2011-04-01

    Recent studies have shown that rice consumption can be an important pathway of methylmercury (MeHg) exposure to humans in Hg mining areas and also in certain inland areas of Southwestern China. The seed of rice has the highest ability to accumulate MeHg compared to other tissues. The main objective of this study was to investigate the process of (MeHg) accumulation in rice seed (Oryza sativa L.) by monitoring MeHg levels in specific tissues of rice plants experiencing various levels of Hg multisource pollution during a full rice growing season. Four groups of experimental plantations were utilized, distributed among a rural artisanal Hg production site and a regional background control site. Our results suggest that the newly deposited Hg is more readily transformed to MeHg and accumulated in rice plants than Hg forms with an extended residence time in soil, and soil is the potential source of MeHg in the tissues of rice plants. MeHg in soil was first absorbed by roots and then translocated to the above-ground parts (leaf and stalk). During the full rice growing season only a very small amount of MeHg was retained in the root section. In the premature plant, the majority of MeHg is located in the leaf and stalk; however, most of this MeHg was transferred to seed during the ripening period.

  10. Proteomic analysis of rice (Oryza sativa) seeds during germination.

    PubMed

    Yang, Pingfang; Li, Xiaojuan; Wang, Xiaoqin; Chen, Hui; Chen, Fan; Shen, Shihua

    2007-09-01

    Although seed germination is a major subject in plant physiological research, there is still a long way to go to elucidate the mechanism of seed germination. Recently, functional genomic strategies have been applied to study the germination of plant seeds. Here, we conducted a proteomic analysis of seed germination in rice (Oryza sativa indica cv. 9311) - a model monocot. Comparison of 2-DE maps showed that there were 148 proteins displayed differently in the germination process of rice seeds. Among the changed proteins, 63 were down-regulated, 69 were up-regulated (including 20 induced proteins). The down-regulated proteins were mainly storage proteins, such as globulin and glutelin, and proteins associated with seed maturation, such as "early embryogenesis protein" and "late embryogenesis abundant protein", and proteins related to desiccation, such as "abscisic acid-induced protein" and "cold-regulated protein". The degradation of storage proteins mainly happened at the late stage of germination phase II (48 h imbibition), while that of seed maturation and desiccation associated proteins occurred at the early stage of phase II (24 h imbibition). In addition to alpha-amylase, the up-regulated proteins were mainly those involved in glycolysis such as UDP-glucose dehydrogenase, fructokinase, phosphoglucomutase, and pyruvate decarboxylase. The results reflected the possible biochemical and physiological processes of germination of rice seeds.

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

    PubMed

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

    2017-01-01

    Iron deficiency is an important abiotic stress that limits productivity of crops all over the world. We selected a hybrid rice (Oryza sativa L.), LYPJ, which is super high-yield and widely cultured in China, to investigate changes in the components and structure of thylakoid membranes and photosynthetic performance in response to iron deficiency. Our results demonstrated that photosystem I (PSI) is the primary target for iron deficiency, while the changes in photosystem II (PSII) are important for rebuilding a balance in disrupted energy utilization and dissipation caused by differential degradation of photosynthetic components. The result of immunoblot analysis suggested that the core subunit PsaA declined drastically, while PsbA remained relatively stable. Furthermore, several organizational changes of the photosynthetic apparatus were found by BN-PAGE, including a marked decrease in the PSI core complexes, the Cytb 6 /f complex, and the trimeric form of the LHCII antenna, consistent with the observed unstacking grana. The fluorescence induction analysis indicated a descending PSII activity with energy dissipation enhanced markedly. In addition, we proposed that the crippled CO2 assimilation could be compensated by the enhanced of phosphoenolpyruvate carboxylase (PEPC), which is suggested by the decreased ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) and photosynthetic efficiency.

  12. CO2 Enhancement of Growth and Photosynthesis in Rice (Oryza sativa) 1

    PubMed Central

    Ziska, Lewis H.; Teramura, Alan H.

    1992-01-01

    Two cultivars of rice (Oryza sativa L.) IR-36 and Fujiyama-5 were grown at ambient (360 microbars) and elevated CO2 (660 microbars) from germination through reproduction in unshaded greenhouses at the Duke University Phytotron. Growth at elevated CO2 resulted in significant decreases in nighttime respiration and increases in photosynthesis, total biomass, and yield for both cultivars. However, in plants exposed to simultaneous increases in CO2 and ultraviolet-B (UV-B) radiation, CO2 enhancement effects on respiration, photosynthesis, and biomass were eliminated in IR-36 and significantly reduced in Fujiyama-5. UV-B radiation simulated a 25% depletion in stratospheric ozone at Durham, North Carolina. Analysis of the response of CO2 uptake to internal CO2 concentration at light saturation suggested that, for IR-36, the predominant limitation to photosynthesis with increased UV-B radiation was the capacity for regeneration of ribulose bisphosphate (RuBP), whereas for Fujiyama-5 the primary photosynthetic decrease appeared to be related to a decline in apparent carboxylation efficiency. Changes in the RuBP regeneration limitation in IR-36 were consistent with damage to the photochemical efficiency of photosystem II as estimated from the ratio of variable to maximum chlorophyll fluorescence. Little change in RuBP regeneration and photochemistry was evident in cultivar Fujiyama-5, however. The degree of sensitivity of photochemical reactions with increased UV-B radiation appeared to be related to leaf production of UV-B-absorbing compounds. Fujiyama-5 had a higher concentration of these compounds than IR-36 in all environments, and the production of these compounds in Fujiyama-5 was stimulated by UV-B fluence. Results from this study suggest that in rice alterations in growth or photosynthesis as a result of enhanced CO2 may be eliminated or reduced if UV-B radiation continues to increase. PMID:16668910

  13. Spikelet-specific variation in ethylene production and constitutive expression of ethylene receptors and signal transducers during grain filling of compact- and lax-panicle rice (Oryza sativa) cultivars.

    PubMed

    Sekhar, Sudhanshu; Panda, Binay B; Mohapatra, Trupti; Das, Kaushik; Shaw, Birendra P; Kariali, Ekamber; Mohapatra, Pravat K

    2015-05-01

    Grain yields in modern super rice cultivars do not always meet the expectations because many spikelets are located on secondary branches in closely packed homogeneous distribution in these plants, and they do not fill properly. The factors limiting grain filling of such spikelets, especially in the lower panicle branches, are elusive. Two long-duration rice cultivars differing in panicle density, Mahalaxmi (compact) and Upahar (lax), were cultivated in an open field plot. Grain filling, ethylene production and constitutive expression of ethylene receptors and ethylene signal transducers in apical and basal spikelets of the panicle were compared during the early post-anthesis stage, which is the most critical period for grain development. In another experiment, a similar assessment was made for the medium-duration cultivars compact-panicle OR-1918 and lax-panicle Lalat. Grain weight of the apical spikelets was always higher than that of the basal spikelets. This gradient of grain weight was wide in the compact-panicle cultivars and narrow in the lax-panicle cultivars. Compared to apical spikelets, the basal spikelets produced more ethylene at anthesis and retained the capacity for post-anthesis expression of ethylene receptors and ethylene signal transducers longer. High ethylene production enhanced the expression of the RSR1 gene, but reduced expression of the GBSS1 gene. Ethylene inhibited the partitioning of assimilates of developing grains resulting in low starch biosynthesis and high accumulation of soluble carbohydrates. It is concluded that an increase in grain/spikelet density in rice panicles reduces apical dominance to the detriment of grain filling by production of ethylene and/or enhanced perception of the ethylene signal. Ethylene could be a second messenger for apical dominance in grain filling. The manipulation of the ethylene signal would possibly improve rice grain yield.

  14. QTL Detection and Elite Alleles Mining for Stigma Traits in Oryza sativa by Association Mapping

    PubMed Central

    Dang, Xiaojing; Liu, Erbao; Liang, Yinfeng; Liu, Qiangming; Breria, Caleb M.; Hong, Delin

    2016-01-01

    Stigma traits are very important for hybrid seed production in Oryza sativa, which is a self-pollinated crop; however, the genetic mechanism controlling the traits is poorly understood. In this study, we investigated the phenotypic data of 227 accessions across 2 years and assessed their genotypic variation with 249 simple sequence repeat (SSR) markers. By combining phenotypic and genotypic data, a genome-wide association (GWA) map was generated. Large phenotypic variations in stigma length (STL), stigma brush-shaped part length (SBPL) and stigma non-brush-shaped part length (SNBPL) were found. Significant positive correlations were identified among stigma traits. In total, 2072 alleles were detected among 227 accessions, with an average of 8.3 alleles per SSR locus. GWA mapping detected 6 quantitative trait loci (QTLs) for the STL, 2 QTLs for the SBPL and 7 QTLs for the SNBPL. Eleven, 5, and 12 elite alleles were found for the STL, SBPL, and SNBPL, respectively. Optimal cross designs were predicted for improving the target traits. The detected genetic variation in stigma traits and QTLs provides helpful information for cloning candidate STL genes and breeding rice cultivars with longer STLs in the future. PMID:27555858

  15. Sequence analysis of ORF IV RTBV isolated from tungro infected Oryza sativa L. cv Ciherang

    NASA Astrophysics Data System (ADS)

    Hastilestari, Bernadetta Rina; Astuti, Dwi; Estiati, Amy; Nugroho, Satya

    2015-09-01

    The Effort to increase rice production is often constrained by pest and disease such as Tungro. The Tungro disease is caused by the joint infection with two dissimilar viruses; a bacil-form-DNA virus, the Rice tungro bacilliform virus(RTBV) and the spherical RNA virus, Rice tungro spherical virus (RTSV) and transmitted by Green leafhopper (Nephotettix virescens). The symptom of disease is caused by the presence of RTBV. The genome of RTBV consists of four Open reading frames (ORFs) which encode functional proteins. Of the four, ORF IV is unique because it exists only in RTBV. The most efficient method of generating disease resistance plants is to look for natural sources of resistance genes in wild or germplasm and then transfer the gene and the accompanying resistance in cultivated crop varieties. The aim of this study is, therefore, to isolate and analyze of 1170 bp gene of ORF 4 of Tungro virus isolated from an Indonesian rice cultivar, Ciherang (Oryza sativa L. cv Indica). DNA sequencing analysis using BLAST showed 94% similarity with the reference sequence gen bank Acc.M65026.1. The comparisons and mutation analysis of DNA sequences were discussed in this research.

  16. Rice (Oryza sativa L.) roots have iodate reduction activity in response to iodine

    PubMed Central

    Kato, Shota; Wachi, Takanori; Yoshihira, Kei; Nakagawa, Takuya; Ishikawa, Akifumi; Takagi, Daichi; Tezuka, Aya; Yoshida, Hideharu; Yoshida, Satoshi; Sekimoto, Hitoshi; Takahashi, Michiko

    2013-01-01

    Although iodine is not an essential nutrient for higher plants, their roots take up and transport the element. However, the exact mechanisms involved in iodine uptake and metabolism in higher plants have yet to be elucidated. In this study, we compared two cultivars differing in iodine tolerance (“Nipponbare” and “Gohyakumangoku”) to increasing levels of I− and IO−3 in the root solutions of water-cultured rice (Oryza sativa L.). We found that IO−3 added to the root solutions was converted to I− in the presence of roots. Iodate reduction occurred over the course of several hours. Furthermore, the iodate reduction activity of “Nipponbare” (iodine-sensitive) and “Gohyakumangoku” (iodine-tolerant) roots increased after adding IO−3 or I−. The roots of barley and soybean also showed iodate reduction activity and the activity responded to iodine treatment either with IO−3 and I−. This study suggests that plant roots biologically reduce iodate to iodide and indicates that the iodate reduction activity of roots responds to external iodine conditions. PMID:23847633

  17. Genetic diversity and association mapping of seed vigor in rice (Oryza sativa L.).

    PubMed

    Dang, Xiaojing; Thi, Thu Giang Tran; Dong, Guanshan; Wang, Hui; Edzesi, Wisdom Mawuli; Hong, Delin

    2014-06-01

    Seed vigor is closely related to direct seeding in rice (Oryza sativa L.). Previous quantitative trait locus (QTL) studies for seed vigor were mainly derived from bi-parental segregating populations and no report from natural populations. In this study, association mapping for seed vigor was performed on a selected sample of 540 rice cultivars (419 from China and 121 from Vietnam). Population structure was estimated on the basis of 262 simple sequence repeat (SSR) markers. Seed vigor was evaluated by root length (RL), shoot length (SL) and shoot dry weight in 2011 and 2012. Abundant phenotypic and genetic diversities were found in the studied population. The population was divided into seven subpopulations, and the levels of linkage disequilibrium (LD) ranged from 10 to 80 cM. We identified 27 marker-trait associations involving 18 SSR markers for three traits. According to phenotypic effects for alleles of the detected QTLs, elite alleles were mined. These elite alleles could be used to design parental combinations and the expected results would be obtained by pyramiding or substituting the elite alleles per QTL (apart from possible epistatic effects). Our results demonstrate that association mapping can complement and enhance previous QTL information for marker-assisted selection and breeding by design.

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

    PubMed

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

    2015-11-01

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

  19. Differential expression of the microRNAs in superior and inferior spikelets in rice (Oryza sativa).

    PubMed

    Peng, Ting; Lv, Qiang; Zhang, Jing; Li, Junzhou; Du, Yanxiu; Zhao, Quanzhi

    2011-10-01

    MicroRNAs (miRNAs) play a critical role in post-transcriptional gene regulation and have been shown to control many genes involved in various biological and metabolic processes. This work investigated miRNAs in rice (Oryza sativa), an important food crop. High-throughput sequencing technology was used to reveal expression differences in miRNAs between superior and inferior spikelets in rice (japonica cultivar Xinfeng 2) at 18 d after fertilization. Totals of 351 and 312 known miRNAs were obtained from the superior and inferior spikelets, respectively. Analysis of the expression profiles of these miRNAs showed that 189 miRNAs were differentially expressed between superior spikelets and inferior spikelets. In addition, 43 novel miRNAs were identified mostly by the accumulation of miRNA*s expressed differentially between the superior and inferior spikelets. Further analysis with bioinformatics software and comparison with existing databases showed that these differentially expressed miRNAs may individually participate in regulating hormone metabolism, carbohydrate metabolic pathways, and cell division during rice grain development. The results indicate that the slow grain-filling and low grain weight of rice inferior spikelets are attributed partly to differences in expression and function between superior and inferior spikelet miRNAs.

  20. Variation in grain arsenic assessed in a diverse panel of rice (Oryza sativa) grown in multiple sites.

    PubMed

    Norton, Gareth J; Pinson, Shannon R M; Alexander, Jill; McKay, Susan; Hansen, Helle; Duan, Gui-Lan; Rafiqul Islam, M; Islam, Shofiqul; Stroud, Jacqueline L; Zhao, Fang-Jie; McGrath, Steve P; Zhu, Yong-Guan; Lahner, Brett; Yakubova, Elena; Guerinot, Mary Lou; Tarpley, Lee; Eizenga, Georgia C; Salt, David E; Meharg, Andrew A; Price, Adam H

    2012-02-01

    • Inorganic arsenic (As(i) ) in rice (Oryza sativa) grains is a possible threat to human health, with risk being strongly linked to total dietary rice consumption and consumed rice As(i) content. This study aimed to identify the range and stability of genetic variation in grain arsenic (As) in rice. • Six field trials were conducted (one each in Bangladesh and China, two in Arkansas, USA over 2 yr, and two in Texas, USA comparing flooded and nonflood treatments) on a large number of common rice cultivars (c. 300) representing genetic diversity among international rice cultivars. • Within each field there was a 3-34 fold range in grain As concentration which varied between rice subpopulations. Importantly, As(i) correlated strongly with total As among a subset of 40 cultivars harvested in Bangladesh and China. • Genetic variation at all field sites was a large determining factor for grain As concentration, indicating that cultivars low in grain As could be developed through breeding. The temperate japonicas exhibited lower grain As compared with other subpopulations. Effects for year, location and flooding management were also statistically significant, suggesting that breeding strategies must take into account environmental factors.

  1. 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

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  3. Genome-wide association mapping reveals rich genetic architecture of complex traits in Oryza sativa

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Domesticated Asian rice, Oryza sativa, is a cultivated, inbreeding species that feeds over half of the world’s population. Understanding the genetic basis of diverse physiological, developmental, and morphological traits provides the basis for improving yield, quality and sustainability. Here, we pr...

  4. 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.

  5. Silicon decreases chloride transport in rice (Oryza sativa L.) in saline conditions.

    PubMed

    Shi, Yu; Wang, Yichao; Flowers, Timothy J; Gong, Haijun

    2013-06-15

    Silicon can alleviate salt damage to plants, although the mechanism(s) still remains to be elucidated. In this paper, we report the effect of silicon on chloride transport in rice (Oryza sativa L.) seedlings in saline conditions. In the absence of salinity, silicon enhanced the growth of shoots, but not roots in three cultivars (cv. GR4, IR36, and CSR10). Salinity reduced the growth of both shoots and roots in all three genotypes. In saline conditions, addition of silicon to the culture solution again improved the growth of shoots, but not of roots. Under these saline conditions, the concentrations of chloride in the shoot were markedly decreased by adding silicon and the ratio of K(+)/Cl(-) was significantly increased, while the concentration of chloride in the roots was unchanged. The decrease in chloride concentration in the shoot was correlated with the decrease in transpirational bypass flow in rice, as shown by the transport of the apoplastic tracer trisodium-8-hydroxy-1,3,6-pyrenetrisulphonic acid (PTS). Addition of silicon increased the net photosynthetic rate, stomata conductance, and transpiration of salt-stressed plants in cv. IR36, indicating that the reduction of chloride (and sodium) uptake by silicon was not through a reduction in transpiration rate. Silicon addition also increased the instantaneous water use efficiency of salt-stressed plants, while it did not change the relative growth rate of shoots. The results suggest that silicon addition decreased transpirational bypass flow in the roots, and therefore decreased the transport of chloride to the shoot.

  6. Selenium addition alters mercury uptake, bioavailability in the rhizosphere and root anatomy of rice (Oryza sativa)

    PubMed Central

    Wang, Xun; Tam, Nora Fung-Yee; Fu, Shi; Ametkhan, Aray; Ouyang, Yun; Ye, Zhihong

    2014-01-01

    Background and Aims Mercury (Hg) is an extremely toxic pollutant, especially in the form of methylmercury (MeHg), whereas selenium (Se) is an essential trace element in the human diet. This study aimed to ascertain whether addition of Se can produce rice with enriched Se and lowered Hg content when growing in Hg-contaminated paddy fields and, if so, to determine the possible mechanisms behind these effects. Methods Two cultivars of rice (Oryza sativa, japonica and indica) were grown in either hydroponic solutions or soil rhizobags with different Se and Hg treatments. Concentrations of total Hg, MeHg and Se were determined in the roots, shoots and brown rice, together with Hg uptake kinetics and Hg bioavailability in the soil. Root anatonmy was also studied. Key Results The high Se treatment (5 μg g–1) significantly increased brown rice yield by 48 % and total Se content by 2·8-fold, and decreased total Hg and MeHg by 47 and 55 %, respectively, compared with the control treatments. The high Se treatment also markedly reduced ‘water-soluble’ Hg and MeHg concentrations in the rhizosphere soil, decreased the uptake capacity of Hg by roots and enhanced the development of apoplastic barriers in the root endodermis. Conclusions Addition of Se to Hg-contaminated soil can help produce brown rice that is simultaneously enriched in Se and contains less total Hg and MeHg. The lowered accumulation of total Hg and MeHg appears to be the result of reduced bioavailability of Hg and production of MeHg in the rhizosphere, suppression of uptake of Hg into the root cells and an enhancement of the development of apoplastic barriers in the endodermis of the roots. PMID:24948669

  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. Differential Transcript Levels of Genes Associated with Glycolysis and Alcohol Fermentation in Rice Plants (Oryza sativa L.) under Submergence Stress.

    PubMed Central

    Umeda, M.; Uchimiya, H.

    1994-01-01

    Expression of genes encoding enzymes involved in specialized metabolic pathways is assumed to be regulated coordinately to maintain homeostasis in plant cells. We analyzed transcript levels of rice (Oryza sativa L.) genes associated with glycolysis and alcohol fermentation under submergence stress. When each transcript was quantified at several times, two types (I and II) of mRNA accumulation were observed in response to submergence stress. Transcripts of type I genes reached a maximum after 24 h of submergence and were reduced by transfer to aerobic conditions or by partial exposure of shoot tips to air. In a submergence-tolerant rice cultivar, transcript amounts of several type I genes, such as glucose phosphate isomerase, phosphofructokinase, glyceraldehyde phosphate dehydrogenase, and enolase, increased significantly compared to an intolerant cultivar after 24 h of submergence. This suggests that the mRNA accumulation of type I genes increases in response to anaerobic stress. mRNA accumulation of type II genes, such as aldolase and pyruvate kinase, reached a maximum after 10 h of submergence. Following transfer to aerobic conditions, their transcript levels were not so rapidly decreased as were type I genes. These results suggest that the mRNA levels of genes engaged in glycolysis and alcohol fermentation may be regulated differentially under submergence stress. PMID:12232382

  9. Differential Transcript Levels of Genes Associated with Glycolysis and Alcohol Fermentation in Rice Plants (Oryza sativa L.) under Submergence Stress.

    PubMed

    Umeda, M.; Uchimiya, H.

    1994-11-01

    Expression of genes encoding enzymes involved in specialized metabolic pathways is assumed to be regulated coordinately to maintain homeostasis in plant cells. We analyzed transcript levels of rice (Oryza sativa L.) genes associated with glycolysis and alcohol fermentation under submergence stress. When each transcript was quantified at several times, two types (I and II) of mRNA accumulation were observed in response to submergence stress. Transcripts of type I genes reached a maximum after 24 h of submergence and were reduced by transfer to aerobic conditions or by partial exposure of shoot tips to air. In a submergence-tolerant rice cultivar, transcript amounts of several type I genes, such as glucose phosphate isomerase, phosphofructokinase, glyceraldehyde phosphate dehydrogenase, and enolase, increased significantly compared to an intolerant cultivar after 24 h of submergence. This suggests that the mRNA accumulation of type I genes increases in response to anaerobic stress. mRNA accumulation of type II genes, such as aldolase and pyruvate kinase, reached a maximum after 10 h of submergence. Following transfer to aerobic conditions, their transcript levels were not so rapidly decreased as were type I genes. These results suggest that the mRNA levels of genes engaged in glycolysis and alcohol fermentation may be regulated differentially under submergence stress.

  10. Seed priming with polyethylene glycol regulating the physiological and molecular mechanism in rice (Oryza sativa L.) under nano-ZnO stress

    PubMed Central

    Salah, Sheteiwy Mohamed; Yajing, Guan; Dongdong, Cao; Jie, Li; Aamir, Nawaz; Qijuan, Hu; Weimin, Hu; Mingyu, Ning; Jin, Hu

    2015-01-01

    The present study was designed to highlight the impact of seed priming with polyethylene glycol on physiological and molecular mechanism of two cultivars of Oryza sativa L. under different levels of zinc oxide nanorods (0, 250, 500 and 750 mg L−1). Plant growth parameters were significantly increased in seed priming with 30% PEG under nano-ZnO stress in both cultivars. Whereas, this increase was more prominent in cultivar Qian You No. 1 as compared to cultivar Zhu Liang You 06. Significant increase in photosynthetic pigment with PEG priming under stress. Antioxidant enzymes activities of superoxide dismutase (SOD), peroxidase (POD) and catalase (CAT) as well as malondialdehyde (MDA) contents were significantly reduced with PEG priming under nano-ZnO stress. Gene expression analysis also suggested that expression of APXa, APXb, CATa, CATb, CATc, SOD1, SOD2 and SOD3 genes were down regulated with PEG priming as compared to non-primed seeds under stress. The ultrastructural analysis showed that leaf mesophyll and root cells were significantly damaged under nano-ZnO stress in both cultivars but the damage was prominent in Zhu Liang You 06. However, seed priming with PEG significantly alleviate the toxic effects of nano-ZnO stress and improved the cell structures of leaf and roots in both cultivars. PMID:26419216

  11. Seed priming with polyethylene glycol regulating the physiological and molecular mechanism in rice (Oryza sativa L.) under nano-ZnO stress.

    PubMed

    Salah, Sheteiwy Mohamed; Yajing, Guan; Dongdong, Cao; Jie, Li; Aamir, Nawaz; Qijuan, Hu; Weimin, Hu; Mingyu, Ning; Jin, Hu

    2015-09-30

    The present study was designed to highlight the impact of seed priming with polyethylene glycol on physiological and molecular mechanism of two cultivars of Oryza sativa L. under different levels of zinc oxide nanorods (0, 250, 500 and 750 mg L(-1)). Plant growth parameters were significantly increased in seed priming with 30% PEG under nano-ZnO stress in both cultivars. Whereas, this increase was more prominent in cultivar Qian You No. 1 as compared to cultivar Zhu Liang You 06. Significant increase in photosynthetic pigment with PEG priming under stress. Antioxidant enzymes activities of superoxide dismutase (SOD), peroxidase (POD) and catalase (CAT) as well as malondialdehyde (MDA) contents were significantly reduced with PEG priming under nano-ZnO stress. Gene expression analysis also suggested that expression of APXa, APXb, CATa, CATb, CATc, SOD1, SOD2 and SOD3 genes were down regulated with PEG priming as compared to non-primed seeds under stress. The ultrastructural analysis showed that leaf mesophyll and root cells were significantly damaged under nano-ZnO stress in both cultivars but the damage was prominent in Zhu Liang You 06. However, seed priming with PEG significantly alleviate the toxic effects of nano-ZnO stress and improved the cell structures of leaf and roots in both cultivars.

  12. Convergent Loss of Awn in Two Cultivated Rice Species Oryza sativa and Oryza glaberrima Is Caused by Mutations in Different Loci.

    PubMed

    Furuta, Tomoyuki; Komeda, Norio; Asano, Kenji; Uehara, Kanako; Gamuyao, Rico; Angeles-Shim, Rosalyn B; Nagai, Keisuke; Doi, Kazuyuki; Wang, Diane R; Yasui, Hideshi; Yoshimura, Atsushi; Wu, Jianzhong; McCouch, Susan R; Ashikari, Motoyuki

    2015-09-02

    A long awn is one of the distinct morphological features of wild rice species. This organ is thought to aid in seed dispersal and prevent predation by animals. Most cultivated varieties of Oryza sativa and Oryza glaberrima, however, have lost the ability to form long awns. The causal genetic factors responsible for the loss of awn in these two rice species remain largely unknown. Here, we evaluated three sets of chromosome segment substitution lines (CSSLs) in a common O. sativa genetic background (cv. Koshihikari) that harbor genomic fragments from Oryza nivara, Oryza rufipogon, and Oryza glaberrima donors. Phenotypic analyses of these libraries revealed the existence of three genes, Regulator of Awn Elongation 1 (RAE1), RAE2, and RAE3, involved in the loss of long awns in cultivated rice. Donor segments at two of these genes, RAE1 and RAE2, induced long awn formation in the CSSLs whereas an O. sativa segment at RAE3 induced long awn formation in O. glaberrima. These results suggest that the two cultivated rice species, O. sativa and O. glaberrima, have taken independent paths to become awnless.

  13. Combination Patterns of Major R Genes Determine the Level of Resistance to the M. oryzae in Rice (Oryza sativa L.).

    PubMed

    Wu, Yunyu; Xiao, Ning; Yu, Ling; Pan, Cunhong; Li, Yuhong; Zhang, Xiaoxiang; Liu, Guangqing; Dai, Zhengyuan; Pan, Xuebiao; Li, Aihong

    2015-01-01

    Rice blast caused by Magnaporthe oryzae is the most devastating disease of rice and poses a serious threat to world food security. In this study, the distribution and effectiveness of 18 R genes in 277 accessions were investigated based on pathogenicity assays and molecular markers. The results showed that most of the accessions exhibited some degree of resistance (resistance frequency, RF >50%). Accordingly, most of the accessions were observed to harbor two or more R genes, and the number of R genes harbored in accessions was significantly positively correlated with RF. Some R genes were demonstrated to be specifically distributed in the genomes of rice sub-species, such as Pigm, Pi9, Pi5 and Pi1, which were only detected in indica-type accessions, and Pik and Piz, which were just harbored in japonica-type accessions. By analyzing the relationship between R genes and RF using a multiple stepwise regression model, the R genes Pid3, Pi5, Pi9, Pi54, Pigm and Pit were found to show the main effects against M. oryzae in indica-type accessions, while Pita, Pb1, Pik, Pizt and Pia were indicated to exhibit the main effects against M. oryzae in japonica-type accessions. Principal component analysis (PCA) and cluster analysis revealed that combination patterns of major R genes were the main factors determining the resistance of rice varieties to M. oryzae, such as 'Pi9+Pi54', 'Pid3+Pigm', 'Pi5+Pid3+Pigm', 'Pi5+Pi54+Pid3+Pigm', 'Pi5+Pid3' and 'Pi5+Pit+Pid3' in indica-type accessions and 'Pik+Pib', 'Pik+Pita', 'Pik+Pb1', 'Pizt+Pia' and 'Pizt+Pita' in japonica-type accessions, which were able to confer effective resistance against M. oryzae. The above results provide good theoretical support for the rational utilization of combinations of major R genes in developing rice cultivars with broad-spectrum resistance.

  14. Outcrossing potential between U.S. red rice (Oryza sativa) and Chinese indica rice (Oryza sativa) lines

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Red rice in southern U.S. rice fields remains a widespread, economically challenging problem despite nearly a decade of rice production systems that include true-breeding rice cultivars and indica-derived hybrid rice with resistance to imazethapyr. Both of these herbicide-resistant rice systems hav...

  15. Aquaporin plays an important role in mediating chloroplastic CO2 concentration under high-N supply in rice (Oryza sativa) plants.

    PubMed

    Ding, Lei; Gao, Limin; Liu, Wei; Wang, Min; Gu, Mian; Ren, Binbin; Xu, Guohua; Shen, Qirong; Guo, Shiwei

    2015-09-18

    Our previous studies demonstrated that chloroplastic CO2 concentration (Cc) is not sufficient under high-nitrogen (N) supply in rice plants. In this research, we studied how aquaporins- (AQPs) mediated Cc under different N-supply levels. A hydroponic experiment was conducted in a greenhouse with three different N levels (low N, 0.71 mM; intermediate N, 2.86 mM; and high N, 7.14 mM) in a rice cultivar (Oryza sativa cv. Shanyou 63) and with an ospip1;1 mutant (Oryza sativa cv. Nipponbare). The photosynthetic nitrogen-use efficiency (PNUE) decreased with increasing leaf-N content. Under high-N supply, the estimated Cc was significantly lower than the theoretical Cc and the specific Rubisco activity (carboxylation efficiency/Rubisco content, CE/Rubisco) decreased, because of a decrease of relative CO2 diffusion conductance (total CO2 diffusion conductance/leaf-N content, gt /N) in mesophyll cells. Real Time Quantitative PCR (Q-RT-PCR) showed that most OsPIP1s and OsPIP2s expression were downregulated under the high-N supply. Furthermore, Cc and gm decreased in the ospip1;1 mutant line compared with that of the wild-type plant. It was concluded that under high-N supply, the decreased PNUE was associated with non-sufficient Cc, mediated by AQP in mesophyll conductance.

  16. N-glycan transition of the early developmental stage in Oryza sativa.

    PubMed

    Horiuchi, Risa; Hirotsu, Naoki; Miyanishi, Nobumitsu

    2016-08-26

    N-Glycosylation is one of the post-translational modifications. In animals, N-glycans linked to proteins function in cell-cell recognition, sorting, transport, and other biological phenomena. However, in plants, N-glycan-mediated biological functions remain obscure. In a previous study, we showed that the main type of N-glycan transition is from the paucimannosidic to complex type before and after germination in Oryza sativa, suggesting that transitions of N-glycan, including those of glycoproteins and glycosyltransferases, are closely associated with plant growth. To further elucidate the relationship between N-glycan structure and plant growth, we analyzed the structures of N-glycans expressed in O. sativa seedlings grown under light conditions and performed comparative analyses of the structures in the shoot and root. The analyses show that fundamental N-glycan structures are common to the shoot and root, whereas paucimannosidic-type N-glycans dramatically decreased in the root grown under light conditions. Further, to investigate the effects of light on N-glycan structures in O. sativa seedlings, we analyzed N-glycan structures in O. sativa seedlings grown in the dark. Understandably, N-glycan expression in the root was almost unaffected by light. However, despite a marked difference in phenotype, N-glycan expression in the shoot was also unaffected by light. This result suggests that the shoot and root of O. sativa have different glycoproteins and distinct N-glycan synthetic systems. Thus, we propose that the N-glycan synthetic system of the O. sativa shoot is almost unaffected by light conditions and that many photosynthesis-related proteins are not modified by N-glycans.

  17. Comparative Physical Mapping Between Oryza sativa (AA Genome Type) and O. punctata (BB Genome Type)

    PubMed Central

    Kim, HyeRan; Miguel, Phillip San; Nelson, William; Collura, Kristi; Wissotski, Marina; Walling, Jason G.; Kim, Jun Pyo; Jackson, Scott A.; Soderlund, Carol; Wing, Rod A.

    2007-01-01

    A comparative physical map of the AA genome (Oryza sativa) and the BB genome (O. punctata) was constructed by aligning a physical map of O. punctata, deduced from 63,942 BAC end sequences (BESs) and 34,224 fingerprints, onto the O. sativa genome sequence. The level of conservation of each chromosome between the two species was determined by calculating a ratio of BES alignments. The alignment result suggests more divergence of intergenic and repeat regions in comparison to gene-rich regions. Further, this characteristic enabled localization of heterochromatic and euchromatic regions for each chromosome of both species. The alignment identified 16 locations containing expansions, contractions, inversions, and transpositions. By aligning 40% of the punctata BES on the map, 87% of the punctata FPC map covered 98% of the O. sativa genome sequence. The genome size of O. punctata was estimated to be 8% larger than that of O. sativa with individual chromosome differences of 1.5–16.5%. The sum of expansions and contractions observed in regions >500 kb were similar, suggesting that most of the contractions/expansions contributing to the genome size difference between the two species are small, thus preserving the macro-collinearity between these species, which diverged ∼2 million years ago. PMID:17339227

  18. Identification of a Candidate Gene for Panicle Length in Rice (Oryza sativa L.) Via Association and Linkage Analysis

    PubMed Central

    Liu, Erbao; Liu, Yang; Wu, Guocan; Zeng, Siyuan; Tran Thi, Thu G.; Liang, Lijun; Liang, Yinfeng; Dong, Zhiyao; She, Dong; Wang, Hui; Zaid, Imdad U.; Hong, Delin

    2016-01-01

    Panicle length (PL) is an important trait for improving panicle architecture and grain yield in rice (Oryza sativa L.). Three populations were used to identify QTLs and candidate genes associated with PL. Four QTLs for PL were detected on chromosomes 4, 6, and 9 through linkage mapping in the recombinant inbred line population derived from a cross between the cultivars Xiushui79 (short panicle) and C-bao (long panicle). Ten SSR markers associated with PL were detected on chromosomes 2, 3, 5, 6, 8, 9, and 10 in the natural population consisting of 540 accessions collected from East and Southeast Asia. A major locus on chromosome 9 with the largest effect was identified via both linkage and association mapping. LONG PANICLE 1 (LP1) locus was delimited to a 90-kb region of the long arm of chromosome 9 through fine mapping using a single segment segregating F2 population. Two single nucleotide polymorphisms (SNPs) leading to amino acid changes were detected in the third and fifth exons of LP1. LP1 encodes a Remorin_C-containing protein of unknown function with homologs in a variety of species. Sequencing analysis of LP1 in two parents and 103 rice accessions indicated that SNP1 is associated with panicle length. The LP1 allele of Xiushui79 leads to reduced panicle length, whereas the allele of C-bao relieves the suppression of panicle length. LP1 and the elite alleles can be used to improve panicle length in rice. PMID:27200064

  19. Hybrid breakdown caused by epistasis-based recessive incompatibility in a cross of rice (Oryza sativa L.).

    PubMed

    Matsubara, Kazuki; Yamamoto, Eiji; Mizobuchi, Ritsuko; Yonemaru, Jun-ichi; Yamamoto, Toshio; Kato, Hiroshi; Yano, Masahiro

    2015-01-01

    Viability and fertility in organisms depend on epistatic interactions between loci maintained in lineages. Here, we describe reduced fitness of segregants (hybrid breakdown, HB) that emerged in an F2 population derived from a cross between 2 rice (Oryza sativa L.) cultivars, "Tachisugata" (TS) and "Hokuriku 193" (H193), despite both parents and F1s showing normal fitness. Quantitative trait locus (QTL) analyses detected 13 QTLs for 4 morphological traits associated with the HB and 6 associated with principal component scores calculated from values of the morphological traits in the F2 population. Two-way analysis of variance of the putative QTLs identified 4 QTL pairs showing significant epistasis; among them, a pair on chromosomes 1 and 12 made the greatest contribution to HB. The finding was supported by genetic experiments using F3 progeny. HB emerged only when a plant was homozygous for the TS allele at the QTL on chromosome 1 and homozygous for the H193 allele at the QTL on chromosome 12, indicating that each allele behaves as recessive to the other. Our results support the idea that epistasis is an essential part of hybrid fitness.

  20. Determination of some minerals and β-carotene contents in aromatic indica rice (Oryza sativa L.) germplasm.

    PubMed

    Renuka, N; Mathure, Sarika V; Zanan, Rahul L; Thengane, Ratnakar J; Nadaf, Altafhusain B

    2016-01-15

    39 aromatic indica rice (Oryza sativa L.) cultivars were characterized for Iron, Zinc, Calcium, Magnesium, Copper and β-carotene contents. The β-carotene contents were ranging from 1.23 to 9.9μg/g in brown and 0.08 to 1.99μg/g in milled rice. Among the mineral contents, Magnesium was found ranging from 855μg/g (Gham) to maximum of 1636μg/g (Badshahbhog) followed by Iron in 32μg/g (Jirga) to 218μg/g (Kalsal), Copper content from 2μg/g (Girga) to 1004μg/g (Gham), Zinc content from 25 (Gham) to 165μg/g (Ambemohar-157) and Calcium ranged from 14μg/g (Ambemohar pandhara) to 67μg/g (Kate chinoor). The study showed that the germplasm assessed is a good source of micronutrients and can be further exploited in breeding programme.

  1. Characterization and gene cloning of the rice (Oryza sativa L.) dwarf and narrow-leaf mutant dnl3.

    PubMed

    Shi, L; Wei, X J; Adedze, Y M N; Sheng, Z H; Tang, S Q; Hu, P S; Wang, J L

    2016-09-16

    The dwarf and narrow-leaf rice (Oryza sativa L.) mutant dnl3 was isolated from the Japonica cultivar Zhonghua 11 (wild-type). dnl3 exhibited pleiotropic developmental defects. The narrow-leaf phenotype resulted from a marked reduction in the number of vascular bundles, while the dwarf stature was caused by the formation of foreshortened internodes and a reduced number of parenchyma cells. The suggestion that cell division is impaired in the mutant was consistent with the transcriptional behavior of various genes associated with cell division. The mutant was less responsive to exogenously supplied gibberellic acid than the wild-type, and profiling the transcription of genes involved in gibberellin synthesis and response revealed that a lesion in the mutant affected gibberellin signal transduction. The dnl3 phenotype was inherited as a single-dominant gene, mapping within a 19.1-kb region of chromosome 12, which was found to harbor three open reading frames. Resequencing the open reading frames revealed that the mutant carried an allele at one of the three genes that differed from the wild-type sequence by 2-bp deletions; this gene encoded a cellulose synthase-like D4 (CSLD4) protein. Therefore, OsCSLD4 is a candidate gene for DNL3. DNL3 was expressed in all of the rice organs tested at the heading stage, particularly in the leaves, roots, and culms. These results suggest that DNL3 plays important roles in rice leaf morphogenesis and vegetative development.

  2. Novel Phr1 mutations and the evolution of phenol reaction variation in US weedy rice (Oryza sativa).

    PubMed

    Gross, Briana L; Skare, Karl J; Olsen, Kenneth M

    2009-12-01

    *Red rice, a major agricultural weed, is phenotypically diverse and possesses traits that are similar to both wild and cultivated rice. The genetic resources available for rice make it possible to examine the molecular basis and evolution of traits characterizing this weed. Here, we assess the phenol reaction - a classical trait for distinguishing among cultivated rice varieties - in red rice at the phenotypic and molecular levels. *We phenotyped more than 100 US weed samples for the phenol reaction and sequenced the underlying Phr1 locus in a subset of samples. Data were analyzed in combination with previously published Phr1 data for cultivated rice. *Most weed accessions (96.3%) are positive for the phenol reaction, and samples with a negative response carry loss-of-function alleles that are rare or heretofore undocumented. One such allele may have evolved through mutational convergence of a 1-bp frameshift insertion. Haplotype sharing between red rice and US cultivars suggests occasional crop-weed hybridization. *Our discovery of previously undocumented nonfunctional phr1 alleles suggests that there are likely to be other loss-of-function mutations segregating in Oryza sativa around the world. Red rice may provide a useful study system for understanding the adaptive significance of Phr1 variation in agricultural settings.

  3. Pectin enhances rice (Oryza sativa) root phosphorus remobilization.

    PubMed

    Zhu, Xiao Fang; Wang, Zhi Wei; Wan, Jiang Xue; Sun, Ying; Wu, Yun Rong; Li, Gui Xin; Shen, Ren Fang; Zheng, Shao Jian

    2015-02-01

    Plants growing in phosphorus (P)-deficient conditions can either increase their exploration of the environment (hence increasing P uptake) or can solubilize and reutilize P from established tissue sources. However, it is currently unclear if P stored in root cell wall can be reutilized. The present study shows that culture of the rice cultivars 'Nipponbare' (Nip) and 'Kasalath' (Kas) in P-deficient conditions results in progressive reductions in root soluble inorganic phosphate (Pi). However, Nip consistently maintains a higher level of soluble Pi and lower relative cell wall P content than does Kas, indicating that more cell wall P is released in Nip than in Kas. P-deficient Nip has a greater pectin and hemicellulose 1 (HC1) content than does P-deficient Kas, consistent with the significant positive relationship between pectin and root-soluble Pi levels amongst multiple rice cultivars. These observations suggest that increased soluble Pi might result from increased pectin content during P starvation. In vitro experiments showed that pectin releases Pi from insoluble FePO4. Furthermore, an Arabidopsis thaliana mutant with reduced pectin levels (qua1-2), has less root soluble Pi and is more sensitive to P deficiency than the wild type (WT) Col-0, whereas NaCl-treated WT plants exhibit both an increased root pectin content and an elevated soluble Pi content during P-starvation. These observations indicate that pectin can facilitate the remobilization of P deposited in the cell wall. This is a previously unknown mechanism for the reutilization of P in P-starved plants.

  4. AVR1-CO39 is a predominant locus governing the broad avirulence of Magnaporthe oryzae 2539 on cultivated rice (Oryza sativa L.).

    PubMed

    Zheng, Yan; Zheng, Wenhui; Lin, Fucheng; Zhang, Ying; Yi, Yunping; Wang, Baohua; Lu, Guodong; Wang, Zonghua; Wu, Weiren

    2011-01-01

    Magnaporthe oryzae 2539 was previously found to be avirulent to most rice cultivars and, therefore, was assumed to carry many avirulence (AVR) genes. However, only one AVR gene, AVR1-CO39, which corresponds to a resistance (R) gene Pi-CO39(t) in rice cv. CO39, has been found from 2539 thus far. In order to identify more AVR genes, we isolated 228 progeny strains from a cross between 2539 and Guy11, an M. oryzae strain with strong virulence on rice, and inoculated these strains onto 23 rice accessions (22 individual cultivars and a mixture of 14 cultivars) that are all resistant to 2539 but susceptible to Guy11. Unexpectedly, the experimental results indicated that the avirulence of 2539 on these rice cultivars appeared to be controlled only by the AVR1-CO39 locus. Consistent with this result, we further found that all except one of the rice cultivars were resistant to two transformed Guy11 strains carrying a 1.05-kb fragment containing the AVR1-CO39 gene from 2539. These results suggest that AVR1-CO39 is a predominant locus controlling the broad avirulence of 2539 on cultivated rice. Based on the results of this study and other previous studies, we infer that AVR1-CO39 is a species-wise rather than a cultivar-wise host-specific AVR locus of M. oryzae for rice.

  5. Interaction of elevated CO sub 2 and UV-B radiation on growth and photosynthesis in rice. [Oryza sativa L

    SciTech Connect

    Ziska, L.H.; Termura, A.H. )

    1991-05-01

    Rice (Oryza sativa L. ev IR-36 and Fujiyama) was grown at the Duke University Phytotron to determine if CO{sub 2} induced increases in biomass, yield and photosynthesis were modified by increases in ultraviolet (UV-B) radiation resulting from stratospheric ozone depletion. Two levels of CO{sub 2}(360 and 650 {mu}l l{sup {minus}1}) and two levels of UV-B radiation (8.8 and 15.8 kJm{sup {minus}2}UV-B{sub BE}) were used as the experimental treatments. The levels of UV-B used in the experiment approximated that currently received at Durham, NC (35{degree}N) and that anticipated at the equator (0{degree}N) with a 10% ozone depletion under clear sky conditions during the seasonal maxima. Total plant and panicle dry weight increased significantly with elevated CO{sub 2} in both cultivars when compared to the control. However, if UV-B and CO{sub 2} increased concurrently, no difference in biomass or panicle weight was observed in cv IR-36 relative to the control. In cv Fujiyama, biomass and yield were still significantly higher under an elevated CO{sub 2} treatment alone. Photosynthesis increased and dark respiration decreased for single leaves in both cultivars at high CO{sub 2} but the effect of CO{sub 2} was reduced relative to the ambient condition if supplemental UV-B radiation was included. Data from this experiment indicate that increased UV-B radiation may modify CO{sub 2}-induced increases in biomass, yield or photosynthetic components, and that current data based solely on elevated CO{sub 2} effects may be inadequate to predict future changes in plant development based on anticipated, future increases in CO{sub 2} and stratospheric ozone depletion.

  6. Expression Variations of miRNAs and mRNAs in Rice (Oryza sativa)

    PubMed Central

    Wen, Ming; Xie, Munan; He, Lian; Wang, Yushuai; Shi, Suhua; Tang, Tian

    2016-01-01

    Differences in expression levels are an important source of phenotypic variation within and between populations. MicroRNAs (miRNAs) are key players in post-transcriptional gene regulation that are important for plant development and stress responses. We surveyed expression variation of miRNAs and mRNAs of six accessions from two rice subspecies Oryza sativa L. ssp. indica and Oryza sativa L. ssp. japonica using deep sequencing. While more than half (53.7%) of the mature miRNAs exhibit differential expression between grains and seedlings of rice, only 11.0% show expression differences between subspecies, with an additional 2.2% differentiated for the development-by-subspecies interaction. Expression variation is greater for lowly conserved miRNAs than highly conserved miRNAs, whereas the latter show stronger negative correlation with their targets in expression changes between subspecies. Using a permutation test, we identified 51 miRNA–mRNA pairs that correlate negatively or positively in expression level among cultivated rice. Genes involved in various metabolic processes and stress responses are enriched in the differentially expressed genes between rice indica and japonica subspecies. Our results indicate that stabilizing selection is the major force governing miRNA expression in cultivated rice, albeit positive selection may be responsible for much of the between-subspecies expression divergence. PMID:27797952

  7. Characterization of oats (Avena sativa L.) cultivars using machine vision.

    PubMed

    Sumathi, S; Balamurugan, P

    2013-10-15

    Machine vision or image analysis is an important tool in the study of morphology of any materials. This technique has been used successfully to differentiate the eleven oats cultivars based on morphological characters. The geometry of seeds was measured through image analyzer and the variation was observed and recorded. From the recorded data, the cluster analysis was carried out and it revealed that the cultivars could be grouped into two main clusters based on similarity in the measured parameters. Cultivar Sabzar, UPO 212, OL 9 and OL 88 formed one main cluster. The another main cluster includes cv. Kent, OS 6, UPO 94, HFO 114, OS 7, HJ 8 and JHO 822 with many sub clusters. Among the cultivars HJ 8 and JHO 822 has more similarity in all measured parameters than other cultivars. Thus morphological characterization through seed image analysis was found useful to discriminate the cultivars.

  8. Genetic Architecture of Cold Tolerance in Rice (Oryza sativa) Determined through High Resolution Genome-Wide Analysis

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Cold temperature is an important abiotic stress which negatively affects morphological development and seed production in rice (Oryza sativa L.). At the seedling stage, cold stress causes poor germination, seedling injury and poor stand establishment; and at the reproductive stage cold decreases se...

  9. Lack of Zn inhibition of Cd accumulation by rice (Oryza sativa L.) supports non-Zn transporter uptake of Cd

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Rice (Oryza sativa L.) grown on Cd contaminated soils has been linked to health problems in subsistence rice farmers in Japan and China. For other crops, normal geogenic Zn inhibits the increased uptake of Cd on contaminated soils. A study was conducted using a multi-chelator buffered nutrient sol...

  10. Gene Space Dynamics during the Evolution of Aegilops tauschii, Brachypodium distachyon, Oryza sativa, and Sorghum bicolor Genomes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Nine different regions totaling 9.7 Mb of the 4.02 Gb Aegilops tauschii genome were sequenced using the Sanger sequencing technology and compared with orthologous Brachypodium distachyon, Oryza sativa (rice) and Sorghum bicolor (sorghum) genomic sequences. The ancestral gene content in these regio...

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

    PubMed

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

    2014-10-01

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

  12. High temperature effects on Pi54 conferred resistance to Magnaporthe oryzae in two genetic backgrounds of Oryza sativa.

    PubMed

    Onaga, Geoffrey; Wydra, Kerstin; Koopmann, Birger; Chebotarov, Dmytro; Séré, Yakouba; Von Tiedemann, Andreas

    2017-02-21

    The global temperatures are predicted to rise due to climate change. However, knowledge on the mechanisms underlying the effect of high temperature (HT) on plant pathogen interaction is limited. We investigated the effect of elevated temperature on host phenotypic, biochemical and gene expression patterns in the rice-Magnaporthe oryzae (Mo) pathosystem using two genetic backgrounds, Co39 (Oryzae sativa-indica) and LTH (O. sativa-japonica) with (CO and LT) and without (Co39 and LTH) R gene (Pi54). After exposure to 28°C and 35°C the two genetic backgrounds showed contrasting responses to Mo. At 28°C, CO, Co39 and LTH displayed a more severe disease phenotype than LT. Surprisingly, CO became resistant to Mo after exposure to 35°C. CO and LT were used for further analysis to determine the defence related biochemical and transcriptome changes associated with HT induced resistance. Pre-exposure to 35°C triggered intense callose deposits and cell wall fluorescence of the attacked epidermal cells, as well as, increased hydrogen peroxide (H2O2) and salicylic acid (SA) levels. Transcriptional changes due to combined stress (35°C+Mo) were largely overridden by pathogen infection in both backgrounds, suggesting that the plants tended to shift their response to the pathogen. However, significant differences in global gene expression patterns occurred between CO and LT in response to both single (35°C and Mo) and double stress (35°C+Mo). Collectively, our results suggest that rice lines carrying Pi54 respond to Mo by rapid induction of callose and H2O2, and that these resistance mechanisms are amplified at HT. The relative difference in disease severity between CO and LT at 28°C suggests that the genetic background of japonica rice facilitates the function of Pi54 more than the background of indica rice. The phenotypic plasticity and gene expression differences between CO and LT reveal the presence of intricate background specific molecular signatures that may

  13. 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.

  14. Photochemical properties in flag leaves of a super-high-yielding hybrid rice and a traditional hybrid rice (Oryza sativa L.) probed by chlorophyll a fluorescence transient.

    PubMed

    Zhang, Meiping; Shan, YongJie; Kochian, Leon; Strasser, Reto J; Chen, GuoXiang

    2015-12-01

    Chlorophyll a fluorescence of flag leaves in a super-high-yielding hybrid rice (Oryza sativa L.) LYPJ, and a traditional hybrid rice SY63 cultivar with lower grain yield, which were grown in the field, were investigated from emergence through senescence of flag leaves. As the flag leaf matured, there was an increasing trend in photosynthetic parameters such as quantum efficiency of primary photochemistry ([Formula: see text] Po) and efficiency of electron transport from PS II to PS I (Ψ Eo). The overall photosynthetic performance index (PIABS) was significantly higher in the high-yielding LYPJ compared to SY63 during the entire reproductive stage of the plant, the same to MDA content. However, [Formula: see text] Po(=F V/F M), an indicator of the primary photochemistry of the flag leaf, did not display significant changes with leaf age and was not significantly different between the two cultivars, suggesting that PIABS is a more sensitive parameter than [Formula: see text] Po (=F V/F M) during leaf age for distinguishing between cultivars differing in yield.

  15. Greenhouse validation of yield component transgressive variation effects of wild Oryza species introgressions in an elite US rice cultivar

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A number of global studies have been conducted which have shown that the wild ancestral species, Oryza rufipogon, possesses beneficial alleles that can be used to improve cultivated rice, O. sativa, for biotic and abiotic stress tolerance as well as yield. Introgression lines (IL) were developed thr...

  16. Development and validation of cross-transferable and polymorphic DNA markers for detecting alien genome introgression in Oryza sativa from Oryza brachyantha.

    PubMed

    Ray, Soham; Bose, Lotan K; Ray, Joshitha; Ngangkham, Umakanta; Katara, Jawahar L; Samantaray, Sanghamitra; Behera, Lambodar; Anumalla, Mahender; Singh, Onkar N; Chen, Meingsheng; Wing, Rod A; Mohapatra, Trilochan

    2016-08-01

    African wild rice Oryza brachyantha (FF), a distant relative of cultivated rice Oryza sativa (AA), carries genes for pests and disease resistance. Molecular marker assisted alien gene introgression from this wild species to its domesticated counterpart is largely impeded due to the scarce availability of cross-transferable and polymorphic molecular markers that can clearly distinguish these two species. Availability of the whole genome sequence (WGS) of both the species provides a unique opportunity to develop markers, which are cross-transferable. We observed poor cross-transferability (~0.75 %) of O. sativa specific sequence tagged microsatellite (STMS) markers to O. brachyantha. By utilizing the genome sequence information, we developed a set of 45 low cost PCR based co-dominant polymorphic markers (STS and CAPS). These markers were found cross-transferrable (84.78 %) between the two species and could distinguish them from each other and thus allowed tracing alien genome introgression. Finally, we validated a Monosomic Alien Addition Line (MAAL) carrying chromosome 1 of O. brachyantha in O. sativa background using these markers, as a proof of concept. Hence, in this study, we have identified a set molecular marker (comprising of STMS, STS and CAPS) that are capable of detecting alien genome introgression from O. brachyantha to O. sativa.

  17. Effect of three insecticides and two herbicides on rice (Oryza sativa) seedling germination and growth.

    PubMed

    Moore, M T; Kröger, R

    2010-11-01

    Rice (Oryza sativa L.) is one of the most important food crops worldwide. However, it is also a valuable tool in assessing toxicity of organic and inorganic compounds. For more than 20 years, it has been an approved species for standardized phytotoxicity experiments. The objective of this study is to determine germination and radicle (root) and coleoptile (shoot) growth of rice seeds exposed to three insecticides and two herbicides, commonly used in the agricultural production landscape. Although no germination effects of pesticide exposure were observed, significant growth effects were noted between pesticide treatments. Coleoptile growth was significantly (p ≤ 0.05) lowered in metolachlor/atrazine mixture, diazinon, and lambda-cyhalothrin exposures when compared with controls. Radicles of fipronil-exposed seeds were significantly larger (p ≤ 0.05) when compared with controls. This research contributes to the phytotoxicity assessment database, in addition to laying the foundation for the use of rice as a phytoremediation tool for agricultural pesticide runoff.

  18. Effect of iron plaque on antimony uptake by rice (Oryza sativa L.).

    PubMed

    Cui, Xiao-Dan; Wang, Yu-Jun; Hockmann, Kerstin; Zhou, Dong-Mei

    2015-09-01

    Although iron (Fe) plaque has been shown to significantly affect the uptake of toxic antimony (Sb) by rice, knowledge about the influence of iron plaque on antimony (Sb) (amount, mechanisms, etc) is, however, limited. Here, the effect of Fe plaque on Sb(III) and Sb(V) (nominal oxidation states) uptake by rice (Oryza sativa L.) was investigated using hydroponic experiments and synchrotron-based techniques. The results showed that iron plaque immobilized Sb on the surface of rice roots. Although the binding capacity of iron plaque for Sb(III) was markedly greater than that for Sb(V), significantly more Sb(III) was taken up by roots and transported to shoots. In the presence of Fe plaque, Sb uptake into rice roots was significantly reduced, especially for Sb(III). However, this did not translate into decreasing Sb concentrations in rice shoots and even increased shoot Sb concentrations during high Fe-Sb(III) treatment.

  19. Expression of non-symbiotic hemoglobin 1 and 2 genes in rice (Oryza sativa) embryonic organs

    PubMed Central

    Lira-Ruan, Verónica; Ruiz-Kubli, Mariel

    2011-01-01

    Rice (Oryza sativa) contains five copies of the non-symbiotic hemoglobin (hb) gene, namely hb1 to hb5. Previous analysis by RT-PCR revealed that rice hb1 expresses in roots and leaves and hb2 expresses in leaves. However, it is not known whether or not hb1 and hb2 express in rice embryonic organs. Here, we report the expression of hb1 and hb2 genes in rice embryonic organs using RT-PCR and specific oligos for Hb1 and Hb2. Our results indicate that hb1 and hb2 genes express in embryonic organs in rice growing under normal conditions. Specifically, hb1 expresses in rice embryos and seminal roots, and hb2 expresses in embryos, coleoptiles and seminal roots. These observations suggest that Hb1 and Hb2 coexist and function in rice embryonic organs. PMID:21966570

  20. Phosphate Uptake and Allocation – A Closer Look at Arabidopsis thaliana L. and Oryza sativa L.

    PubMed Central

    Młodzińska, Ewa; Zboińska, Magdalena

    2016-01-01

    This year marks the 20th anniversary of the discovery and characterization of the two Arabidopsis PHT1 genes encoding the phosphate transporter in Arabidopsis thaliana. So far, multiple inorganic phosphate (Pi) transporters have been described, and the molecular basis of Pi acquisition by plants has been well-characterized. These genes are involved in Pi acquisition, allocation, and/or signal transduction. This review summarizes how Pi is taken up by the roots and further distributed within two plants: A. thaliana and Oryza sativa L. by plasma membrane phosphate transporters PHT1 and PHO1 as well as by intracellular transporters: PHO1, PHT2, PHT3, PHT4, PHT5 (VPT1), SPX-MFS and phosphate translocators family. We also describe the role of the PHT1 transporters in mycorrhizal roots of rice as an adaptive strategy to cope with limited phosphate availability in soil. PMID:27574525

  1. Flavonoids from the grains of C1/R-S transgenic rice, the transgenic Oryza sativa spp. japonica, and their radical scavenging activities.

    PubMed

    Cho, Jin-Gyeong; Song, Na-Young; Nam, Tae-Gyu; Shrestha, Sabina; Park, Hee-Jung; Lyu, Ha-Na; Kim, Dae-Ok; Lee, Gihwan; Woo, Young-Min; Jeong, Tae-Sook; Baek, Nam-In

    2013-10-30

    The transgenic rice cultivar of Oryza sativa spp. japonica cv. Hwa-Young, C1/R-S transgenic rice (C1/R-S rice), is a flavonoid-rich cultivar of rice. The grains of C1/R-S rice were extracted with aqueous MeOH, and the concentrated extract was partitioned with EtOAc, n-BuOH, and H2O, successively. Repeated silica gel, octadecyl silica gel (ODS), and Sephadex LH-20 column chromatographies for the EtOAc and n-BuOH fractions afforded four new flavonoids (compounds 2, 3, 7, and 8) along with four known flavonoids: (+)-3'-O-methyltaxifolin (1), brassicin (4), isorhamnetin-4'-O-β-D-glucosyranoside (5), and 3'-O-methyltaxifolin-5-O-β-D-glucopyranoside (6). The new flavonoids were identified as 3'-O-methyltaxifolin-7-O-β-D-glucopyranoside (2), 3'-O-methyltaxifolin-4'-O-β-D-glucopyranoside (3), isorhamnetin-7-O-β-D-cellobioside (brassicin-4″-O-β-D-glucopyranoside) (7), and brassicin-4'-O-β-D-glucosyranoside (8) from the result of spectroscopic data including nuclear magnetic resonance spectrometry (NMR), mass spectrometry (MS), and infrared spectroscopy (IR). Also, quantitative analysis of major flavonoids (compounds 2, 3, and 8) in C1/R-S rice, O. sativa spp. japonica cv. Hwa-Young (HY), and a hybrid of two cultivar (C1/R-S rice/HY) extracts was performed using HPLC experiment. The isolated flavonoids were evaluated for their radical-scavenging effect on DPPH and ABTS radicals.

  2. Diversity of the Ty-1 copia retrotransposon Tos17 in rice (Oryza sativa L.) and the AA genome of the Oryza genus.

    PubMed

    Petit, Julie; Bourgeois, Emmanuelle; Stenger, Wilfried; Bès, Martine; Droc, Gaétan; Meynard, Donaldo; Courtois, Brigitte; Ghesquière, Alain; Sabot, François; Panaud, Olivier; Guiderdoni, Emmanuel

    2009-12-01

    Retrotransposons are mobile genetic elements, ubiquitous in Eukaryotic genomes, which have proven to be major genetic tools in determining phylogeny and structuring genetic diversity, notably in plants. We investigate here the diversity of the Ty1-copia retrotransposon Tos17 in the cultivated rice of Asian origin (Oryza sativa L.) and related AA genome species of the Oryza genus, to contribute understanding of the complex evolutionary history in this group of species through that of the element in the lineages. In that aim, we used a combination of Southern hybridization with a reverse transcriptase (RT) probe and an adapter-PCR mediated amplification, which allowed the sequencing of the genomic regions flanking Tos17 insertions. This analysis was carried out in a collection of 47 A-genome Oryza species accessions and 202 accessions of a core collection of Oryza sativa L. representative of the diversity of the species. Our Southern hybridization results show that Tos17 is present in all the accessions of the A-genome Oryza species, except for the South American species O. glumaepatula and the African species O. glaberrima and O. breviligulata. In O. sativa, the number of putative copies of Tos17 per accession ranged from 1 to 11 and multivariate analysis based on presence/absence of putative copies yielded a varietal clustering which is consistent with the isozyme classification of rice. Adapter PCR amplification and sequencing of flanking regions of Tos17 insertions in A-genome species other than O. sativa, followed by anchoring on the Nipponbare genome sequence, revealed 13 insertion sites of Tos17 in the surveyed O. rufipogon and O. longistaminata accessions, including one shared by both species. In O. sativa, the same approach revealed 25 insertions in the 6 varietal groups. Four insertion sites located on chromosomes 1, 2, 10, and 11 were found orthologous in O. rufipogon and O. sativa. The chromosome 1 insertion was also shared between O. rufipogon and O

  3. The organelle genomes of Hassawi rice (Oryza sativa L.) and its hybrid in saudi arabia: genome variation, rearrangement, and origins.

    PubMed

    Zhang, Tongwu; Hu, Songnian; Zhang, Guangyu; Pan, Linlin; Zhang, Xiaowei; Al-Mssallem, Ibrahim S; Yu, Jun

    2012-01-01

    Hassawi rice (Oryza sativa L.) is a landrace adapted to the climate of Saudi Arabia, characterized by its strong resistance to soil salinity and drought. Using high quality sequencing reads extracted from raw data of a whole genome sequencing project, we assembled both chloroplast (cp) and mitochondrial (mt) genomes of the wild-type Hassawi rice (Hassawi-1) and its dwarf hybrid (Hassawi-2). We discovered 16 InDels (insertions and deletions) but no SNP (single nucleotide polymorphism) is present between the two Hassawi cp genomes. We identified 48 InDels and 26 SNPs in the two Hassawi mt genomes and a new type of sequence variation, termed reverse complementary variation (RCV) in the rice cp genomes. There are two and four RCVs identified in Hassawi-1 when compared to 93-11 (indica) and Nipponbare (japonica), respectively. Microsatellite sequence analysis showed there are more SSRs in the genic regions of both cp and mt genomes in the Hassawi rice than in the other rice varieties. There are also large repeats in the Hassawi mt genomes, with the longest length of 96,168 bp and 96,165 bp in Hassawi-1 and Hassawi-2, respectively. We believe that frequent DNA rearrangement in the Hassawi mt and cp genomes indicate ongoing dynamic processes to reach genetic stability under strong environmental pressures. Based on sequence variation analysis and the breeding history, we suggest that both Hassawi-1 and Hassawi-2 originated from the Indonesian variety Peta since genetic diversity between the two Hassawi cultivars is very low albeit an unknown historic origin of the wild-type Hassawi rice.

  4. Genotype × Environment Interactions of Yield Traits in Backcross Introgression Lines Derived from Oryza sativa cv. Swarna/Oryza nivara

    PubMed Central

    Balakrishnan, Divya; Subrahmanyam, Desiraju; Badri, Jyothi; Raju, Addanki Krishnam; Rao, Yadavalli Venkateswara; Beerelli, Kavitha; Mesapogu, Sukumar; Surapaneni, Malathi; Ponnuswamy, Revathi; Padmavathi, G.; Babu, V. Ravindra; Neelamraju, Sarla

    2016-01-01

    Advanced backcross introgression lines (BILs) developed from crosses of Oryza sativa var. Swarna/O. nivara accessions were grown and evaluated for yield and related traits. Trials were conducted for consecutive three seasons in field conditions in a randomized complete block design with three replications. Data on yield traits under irrigated conditions were analyzed using the Additive Main Effect and Multiplicative Interaction (AMMI), Genotype and Genotype × Environment Interaction (GGE) and modified rank-sum statistic (YSi) for yield stability. BILs viz., G3 (14S) and G6 (166S) showed yield stability across the seasons along with high mean yield performance. G3 is early in flowering with high yield and has good grain quality and medium height, hence could be recommended for most of the irrigated locations. G6 is a late duration genotype, with strong culm strength, high grain number and panicle weight. G6 has higher yield and stability than Swarna but has Swarna grain type. Among the varieties tested DRRDhan 40 and recurrent parent Swarna showed stability for yield traits across the seasons. The component traits thousand grain weight, panicle weight, panicle length, grain number and plant height explained highest genotypic percentage over environment and interaction factors and can be prioritized to dissect stable QTLs/ genes. These lines were genotyped using microsatellite markers covering the entire rice genome and also using a set of markers linked to previously reported yield QTLs. It was observed that wild derived lines with more than 70% of recurrent parent genome were stable and showed enhanced yield levels compared to genotypes with higher donor genome introgressions. PMID:27807437

  5. Salinity tolerance, Na+ exclusion and allele mining of HKT1;5 in Oryza sativa and O. glaberrima: many sources, many genes, one mechanism?

    PubMed Central

    2013-01-01

    Background Cultivated rice species (Oryza sativa L. and O. glaberrima Steud.) are generally considered among the crop species most sensitive to salt stress. A handful of lines are known to be tolerant, and a small number of these have been used extensively as donors in breeding programs. However, these donors use many of the same genes and physiological mechanisms to confer tolerance. Little information is available on the diversity of mechanisms used by these species to cope with salt stress, and there is a strong need to identify varieties displaying additional physiological and/or genetic mechanisms to confer higher tolerance. Results Here we present data on 103 accessions from O. sativa and 12 accessions from O. glaberrima, many of which are identified as salt tolerant for the first time, showing moderate to high tolerance of high salinity. The correlation of salinity-induced senescence (as judged by the Standard Evaluation System for Rice, or SES, score) with whole-plant and leaf blade Na+ concentrations was high across nearly all accessions, and was almost identical in both O. sativa and O. glaberrima. The association of leaf Na+ concentrations with cultivar-groups was very weak, but association with the OsHKT1;5 allele was generally strong. Seven major and three minor alleles of OsHKT1;5 were identified, and their comparisons with the leaf Na+ concentration showed that the Aromatic allele conferred the highest exclusion and the Japonica allele the least. A number of exceptions to this association with the Oryza HKT1;5 allele were identified; these probably indicate the existence of additional highly effective exclusion mechanisms. In addition, two landraces were identified, one from Thailand and the other from Senegal, that show high tissue tolerance. Conclusions Significant variation in salinity tolerance exists within both cultivated Oryza species, and this is the first report of significant tolerance in O. glaberrima. The majority of accessions display a

  6. Selectivity of thiobencarb between two lettuce (Lactuca sativa, L. ) cultivars

    SciTech Connect

    Reiners, S.

    1987-01-01

    Thiobencarb (S-(4-chlorobenzyl)N,N-diethylthiocarbamate) was examined for weed control on muck grown lettuce. Weed control results were erratic though differential lettuce tolerance was observed in the field. This led to the testing of five lettuce cultivars for tolerance to the herbicide. Of the five lettuce cultivars evaluated, two were selected with the widest tolerance differences: Great Lakes 366 (GLA) (tolerant) and Dark Green Boston (BOS) (susceptible). Studies examining the mechanism of thiobencarb tolerance were conducted with these two cultivars. Within four days after the addition of thiobencarb to the nutrient solution, BOS had significant reductions in the foliar dry weight. In addition, growth abnormalities including fused leaves were observed, indicating inhibition early in leaf development. Greater amounts of /sup 14/C-thiobencarb were absorbed from nutrient solution by BOS, likely due to a significantly greater root system at the time of treatment. The greater uptake and accumulation of /sup 14/C-label in the leaves, as well as significantly greater amounts of unmetabolized /sup 14/C-thiobencarb in the foliage of BOS may account for the selectivity observed. A thiobencarb sulfoxide was not identified in these studies. This indicates that the metabolism of thiobencarb in lettuce differs from other members of the thiocarbamate family of herbicides.

  7. Optimal Estimation of Phenological Crop Model Parameters for Rice (Oryza sativa)

    NASA Astrophysics Data System (ADS)

    Sharifi, H.; Hijmans, R. J.; Espe, M.; Hill, J. E.; Linquist, B.

    2015-12-01

    Crop phenology models are important components of crop growth models. In the case of phenology models, generally only a few parameters are calibrated and default cardinal temperatures are used which can lead to a temperature-dependent systematic phenology prediction error. Our objective was to evaluate different optimization approaches in the Oryza2000 and CERES-Rice phenology sub-models to assess the importance of optimizing cardinal temperatures on model performance and systematic error. We used two optimization approaches: the typical single-stage (planting to heading) and three-stage model optimization (for planting to panicle initiation (PI), PI to heading (HD), and HD to physiological maturity (MT)) to simultaneously optimize all model parameters. Data for this study was collected over three years and six locations on seven California rice cultivars. A temperature-dependent systematic error was found for all cultivars and stages, however it was generally small (systematic error < 2.2). Both optimization approaches in both models resulted in only small changes in cardinal temperature relative to the default values and thus optimization of cardinal temperatures did not affect systematic error or model performance. Compared to single stage optimization, three-stage optimization had little effect on determining time to PI or HD but significantly improved the precision in determining the time from HD to MT: the RMSE reduced from an average of 6 to 3.3 in Oryza2000 and from 6.6 to 3.8 in CERES-Rice. With regards to systematic error, we found a trade-off between RMSE and systematic error when optimization objective set to minimize RMSE or systematic error. Therefore, it is important to find the limits within which the trade-offs between RMSE and systematic error are acceptable, especially in climate change studies where this can prevent erroneous conclusions.

  8. Detection of DNA polymerase λ activity during seed germination and enhancement after salinity stress and dehydration in the plumules of indica rice (Oryza sativa L.

    PubMed

    Sihi, Sayantani; Bakshi, Sankar; Sengupta, Dibyendu Narayan

    2015-02-01

    DNA polymerase λ (DNA pol λ) is the only reported X-family DNA polymerases in plants and has been shown to play a significant role in dry quiescent seeds, growth, development and nuclear DNA repair. cDNA for DNA pol λ has been reported in Arabidopsis and japonica rice cultivar and has been characterized from E. coli expressed protein, but very little is known about its activity at protein level in plants. The enzymatic activity of DNA pol λ was studied in dry, imbibed and during different germination stages of indica rice IR-8 (salt sensitive) by in-gel activity assay to determine its physiological role in important stages of growth and development. The upstream sequence was also analyzed using plantCARE database and was found to contain several cis-acting elements, including light responsive elements, dehydration responsive elements, Myb binding sites, etc. Hence, 4-day-old germinating seedlings of IR29, a salt-sensitive, but high yielding indica rice cultivar and Nonabokra, a salt-tolerant, but low yielding cultivar were treated with water (control) or 250 mM NaCl or 20% polyethyleneglycol-6000 for 4 and 8 h. The protein was analyzed by in vitro DNA pol λ activity assay, in-gel activity assay and Western blot analysis. DNA pol λ was not detected in dry seeds, but enhanced after imbibition and detectable from low level to high level during subsequent germination steps. Both salinity and dehydration stress led to the enhancement of the activity and protein level of DNA pol λ, as compared to control tissues. This is the first evidence of the salinity or dehydration stress induced enhancement of DNA pol λ activity in the plumules of rice (Oryza sativa L.) cultivars.

  9. Effects of short-term high temperature on grain quality and starch granules of rice (Oryza sativa L.) at post-anthesis stage.

    PubMed

    Chen, Jianlin; Tang, Liang; Shi, Peihua; Yang, Baohua; Sun, Ting; Cao, Weixing; Zhu, Yan

    2017-03-01

    High temperature causes negative effects on grain yield and quality of rice (Oryza sativa L.). In this study, the effects of short-term high temperature (SHT) on grain quality and starch granules were investigated in two rice cultivars Nanjing 41 (NJ41, heat-sensitive) and Wuxiangjing 14 (WJ14, heat-tolerant) at post-anthesis stage (anthesis and early grain-filling stage). The results of rice quality analysis showed that chalky rate and chalkiness increased while brown rice rate, milled rice rate, and head rice rate decreased in two rice cultivars with the increase of high temperature and prolonged duration. Moreover, SHT stress reduced the accumulation of amylose as well as starch accumulation. The starch accumulation and eating quality were more sensitive to SHT than the appearance and milling quality. The starch structure data observed by scanning electron microscope further showed that the starch granules are arranged loosely and more single starch granules appeared after SHT treatment. The extent of change in rice quality and starch traits of WJ14 under SHT was lower than that of NJ41. The effects of SHT at anthesis stage were greater than that at grain-filling stage. Taken together, the results could help further understand the physiological and biochemical processes governing rice quality under high-temperature conditions.

  10. A Standardized Inoculation Protocol to Test Wheat Cultivars for Reaction to Head Blast caused by Magnaporthe oryzae (Triticum pathotype)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Wheat blast, caused by the Triticum pathotype of M. oryzae (MoT), poses a significant threat to wheat production worldwide. Because this pathotype does not occur in the U.S., it is important to prepare for its possible introduction. As part of this preparation, over 500 U.S. wheat cultivars were tes...

  11. Practical Utilization of OryzaExpress and Plant Omics Data Center Databases to Explore Gene Expression Networks in Oryza Sativa and Other Plant Species.

    PubMed

    Kudo, Toru; Terashima, Shin; Takaki, Yuno; Nakamura, Yukino; Kobayashi, Masaaki; Yano, Kentaro

    2017-01-01

    Analysis of a gene expression network (GEN), which is constructed based on similarity of gene expression profiles, is a widely used approach to gain clues for new biological insights. The recent abundant availability of transcriptome data in public databases is enabling GEN analysis under various experimental conditions, and even comparative GEN analysis across species. To provide a platform to gain biological insights from public transcriptome data, valuable databases have been created and maintained. This chapter introduces the web database OryzaExpress, providing omics information on Oryza sativa (rice). The integrated database Plant Omics Data Center, supporting a wide variety of plant species, is also described to compare omics information among multiple plant species.

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

    PubMed

    Ohara, Kazuaki; Sasaki, Kanako; Yazaki, Kazufumi

    2010-06-01

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

  13. Gene expression and nucleotide composition are associated with genic methylation level in Oryza sativa

    PubMed Central

    2014-01-01

    Background The methylation of cytosines at CpG dinucleotides, which plays an important role in gene expression regulation, is one of the most studied epigenetic modifications. Thus far, the detection of DNA methylation has been determined mostly by experimental methods, which are not only prone to bench effects and artifacts but are also time-consuming, expensive, and cannot be easily scaled up to many samples. It is therefore useful to develop computational prediction methods for DNA methylation. Our previous studies highlighted the existence of correlations between the GC content of the third codon position (GC3), methylation, and gene expression. We thus designed a model to predict methylation in Oryza sativa based on genomic sequence features and gene expression data. Results We first derive equations to describe the relationship between gene methylation levels, GC3, expression, length, and other gene compositional features. We next assess gene compositional features involving sixmers and their association with methylation levels and other gene level properties. By applying our sixmer-based approach on rice gene expression data we show that it can accurately predict methylation (Pearson’s correlation coefficient r = 0.79) for the majority (79%) of the genes. Matlab code with our model is included. Conclusions Gene expression variation can be used as predictors of gene methylation levels. PMID:24447369

  14. Genetic evidence for natural product-mediated plant-plant allelopathy in rice (Oryza sativa).

    PubMed

    Xu, Meimei; Galhano, Rita; Wiemann, Philipp; Bueno, Emilio; Tiernan, Mollie; Wu, William; Chung, Ill-Min; Gershenzon, Jonathan; Tudzynski, Bettina; Sesma, Ane; Peters, Reuben J

    2012-02-01

    • There is controversy as to whether specific natural products play a role in directly mediating antagonistic plant-plant interactions - that is, allelopathy. If proved to exist, such phenomena would hold considerable promise for agronomic improvement of staple food crops such as rice (Oryza sativa). • However, while substantiated by the presence of phytotoxic compounds at potentially relevant concentrations, demonstrating a direct role for specific natural products in allelopathy has been difficult because of the chemical complexity of root and plant litter exudates. This complexity can be bypassed via selective genetic manipulation to ablate production of putative allelopathic compounds, but such an approach previously has not been applied. • The rice diterpenoid momilactones provide an example of natural products for which correlative biochemical evidence has been obtained for a role in allelopathy. Here, we apply reverse genetics, using knock-outs of the relevant diterpene synthases (copalyl diphosphate synthase 4 (OsCPS4) and kaurene synthase-like 4 (OsKSL4)), to demonstrate that rice momilactones are involved in allelopathy, including suppressing growth of the widespread rice paddy weed, barnyard grass (Echinochloa crus-galli). • Thus, our results not only provide novel genetic evidence for natural product-mediated allelopathy, but also furnish a molecular target for breeding and metabolic engineering of this important crop plant.

  15. Retrogenes in rice (Oryza sativa L. ssp. japonica) exhibit correlated expression with their source genes.

    PubMed

    Sakai, Hiroaki; Mizuno, Hiroshi; Kawahara, Yoshihiro; Wakimoto, Hironobu; Ikawa, Hiroshi; Kawahigashi, Hiroyuki; Kanamori, Hiroyuki; Matsumoto, Takashi; Itoh, Takeshi; Gaut, Brandon S

    2011-01-01

    Gene duplication occurs by either DNA- or RNA-based processes; the latter duplicates single genes via retroposition of messenger RNA. The expression of a retroposed gene copy (retrocopy) is expected to be uncorrelated with its source gene because upstream promoter regions are usually not part of the retroposition process. In contrast, DNA-based duplication often encompasses both the coding and the intergenic (promoter) regions; hence, expression is often correlated, at least initially, between DNA-based duplicates. In this study, we identified 150 retrocopies in rice (Oryza sativa L. ssp japonica), most of which represent ancient retroposition events. We measured their expression from high-throughput RNA sequencing (RNAseq) data generated from seven tissues. At least 66% of the retrocopies were expressed but at lower levels than their source genes. However, the tissue specificity of retrogenes was similar to their source genes, and expression between retrocopies and source genes was correlated across tissues. The level of correlation was similar between RNA- and DNA-based duplicates, and they decreased over time at statistically indistinguishable rates. We extended these observations to previously identified retrocopies in Arabidopsis thaliana, suggesting they may be general features of the process of retention of plant retrogenes.

  16. Retrogenes in Rice (Oryza sativa L. ssp. japonica) Exhibit Correlated Expression with Their Source Genes

    PubMed Central

    Sakai, Hiroaki; Mizuno, Hiroshi; Kawahara, Yoshihiro; Wakimoto, Hironobu; Ikawa, Hiroshi; Kawahigashi, Hiroyuki; Kanamori, Hiroyuki; Matsumoto, Takashi; Itoh, Takeshi; Gaut, Brandon S.

    2011-01-01

    Gene duplication occurs by either DNA- or RNA-based processes; the latter duplicates single genes via retroposition of messenger RNA. The expression of a retroposed gene copy (retrocopy) is expected to be uncorrelated with its source gene because upstream promoter regions are usually not part of the retroposition process. In contrast, DNA-based duplication often encompasses both the coding and the intergenic (promoter) regions; hence, expression is often correlated, at least initially, between DNA-based duplicates. In this study, we identified 150 retrocopies in rice (Oryza sativa L. ssp japonica), most of which represent ancient retroposition events. We measured their expression from high-throughput RNA sequencing (RNAseq) data generated from seven tissues. At least 66% of the retrocopies were expressed but at lower levels than their source genes. However, the tissue specificity of retrogenes was similar to their source genes, and expression between retrocopies and source genes was correlated across tissues. The level of correlation was similar between RNA- and DNA-based duplicates, and they decreased over time at statistically indistinguishable rates. We extended these observations to previously identified retrocopies in Arabidopsis thaliana, suggesting they may be general features of the process of retention of plant retrogenes. PMID:22042334

  17. Impact of Thiamethoxam Seed Treatment on Growth and Yield of Rice, Oryza sativa.

    PubMed

    Lanka, S K; Senthil-Nathan, S; Blouin, D J; Stout, M J

    2017-03-07

    Neonicotinoid seed treatments are widely used in agriculture. In rice, Oryza sativa L., in the southern United States, neonicotinoid seed treatments are used to manage early-season populations of the rice water weevil, Lissorhoptrus oryzophilus Kuschel. In addition to their effects on pests, neonicotinoid seed treatments may benefit crop plants directly by increasing plant growth or altering plant responses to stresses. As part of an effort to assess the overall benefits of thiamethoxam seed treatment in rice, rice emergence, growth, and yield were evaluated. In a growth chamber, rice emergence from the soil was 1-2 d more rapid from treated than untreated seeds. These laboratory results were supported by field experiments that revealed higher stand counts from thiamethoxam-treated plots than from untreated plots. Yields from thiamethoxam treatments were no higher than those from untreated plots under conditions in which weevil larvae were absent, a result inconsistent with the hypothesis that thiamethoxam imparts direct yield benefits. In a series of field experiments conducted to compare the relationship between weevil larval densities and rice yields in plots treated with several rates of thiamethoxam or chlorantraniliprole (another widely used seed treatment insecticide), the relationship between weevil density and yield did not differ markedly among both seed treatments. Overall yields from both seed treatments did not differ significantly, despite more effective control in chlorantraniliprole-treated plots. These results provide strong support for effect of thiamethoxam on early-season growth of rice, but only weak support for its direct effect on rice yields.

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

    PubMed

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

    2016-02-01

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

  19. OsABCB14 functions in auxin transport and iron homeostasis in rice (Oryza sativa L.).

    PubMed

    Xu, Yanxia; Zhang, Saina; Guo, Haipeng; Wang, Suikang; Xu, Ligen; Li, Chuanyou; Qian, Qian; Chen, Fan; Geisler, Markus; Qi, Yanhua; Jiang, De An

    2014-07-01

    Members of the ATP Binding Cassette B/Multidrug-Resistance/P-glyco-protein (ABCB/MDR/PGP) subfamily were shown to function primarily in Oryza sativa (rice) auxin transport; however, none of the rice ABCB transporters have been functionally characterized. Here, we describe that a knock-down of OsABCB14 confers decreased auxin concentrations and polar auxin transport rates, conferring insensitivity to 2,4-dichlorophenoxyacetic acid (2,4-D) and indole-3-acetic acid (IAA). OsABCB14 displays enhanced specific auxin influx activity in yeast and protoplasts prepared from rice knock-down alleles. OsABCB14 is localized at the plasma membrane, pointing to an important directionality under physiological conditions. osabcb14 mutants were surprisingly found to be insensitive to iron deficiency treatment (-Fe). Their Fe concentration is higher and upregulation of Fe deficiency-responsive genes is lower in osabcb14 mutants than in wild-type rice (Nipponbare, NIP). Taken together, our results strongly support the role of OsABCB14 as an auxin influx transporter involved in Fe homeostasis. The functional characterization of OsABCB14 provides insights in monocot auxin transport and its relationship to Fe nutrition.

  20. A collection of glycosyltransferases from rice (Oryza sativa) exposed to atrazine.

    PubMed

    Lu, Yi Chen; Yang, Sheng Ning; Zhang, Jing Jing; Zhang, Jia Jun; Tan, Li Rong; Yang, Hong

    2013-12-01

    The rice (Oryza sativa) GTs belong to a super family possibly with hundreds of members. However, which GTs are involved in plant response to toxic chemicals is unknown. Here, we demonstrated 59 novel GT genes screened from our recent genome-wide sequencing datasets of rice crops exposed to atrazine (a herbicide persistent in ecosystems). Analysis of GT genes showed that most of the GTs contain functional domains typically found in proteins transferring glycosyl moieties to their target compounds. A phylogenetic analysis revealed that many GT genes from different families have diverse cis-elements necessary for response to biotic and environmental stresses. Experimental validation for the GTs was undertaken through a microarray, and 36 GT genes were significantly detected with an expression pattern similar to that from deep-sequencing datasets. Furthermore, 12 GT genes were randomly selected and confirmed by quantitative real-time RT-PCR. Finally, the special activity of total GTs was determined in rice roots and shoots, with an increased activity under the atrazine exposure. This response was closely associated with atrazine absorption in the rice tissues. These results indicate that exposure to atrazine can trigger specific GT genes and enzyme activities in rice.

  1. Physiological and molecular level effects of silver nanoparticles exposure in rice (Oryza sativa L.) seedlings.

    PubMed

    Nair, Prakash M Gopalakrishnan; Chung, Ill Min

    2014-10-01

    The physiological and molecular level changes of silver nanoparticles (AgNPs) exposure were investigated in rice (Oryza sativa L.) seedlings. The seedlings were exposed to different concentrations of (0, 0.2, 0.5 and 1 mg L(-1)) AgNPs for one week. Significant reduction in root elongation, shoot and root fresh weights, total chlorophyll and carotenoids contents were observed. Exposure to 0.5 and 1 mg L(-1) of AgNPs caused significant increase in hydrogen peroxide formation and lipid peroxidation in shoots and roots, increased foliar proline accumulation and decreased sugar contents. AgNPs exposure resulted in a dose dependant increase in reactive oxygen species generation and also caused cytotoxicity as evidenced by increased dihydroethidium, 3'-(p-hydroxyphenyl) fluorescein and propidium iodide fluorescence. Tetramethylrhodamine methyl ester assay showed decreased mitochondrial membrane potential with increasing concentrations of AgNPs exposure in roots. Real Time PCR analysis showed differential transcription of genes related to oxidative stress tolerance viz. FSD1, MSD1, CSD1, CSD2, CATa, CATb, CATc, APXa and APXb in shoots and roots of rice seedlings. The overall results suggest that exposure to AgNPs caused significant physiological and molecular level changes, oxidative stress and also resulted in the induction oxidative stress tolerance mechanisms in rice seedlings.

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

    NASA Astrophysics Data System (ADS)

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

    2017-01-01

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

  3. Effects of cadmium on bioaccumulation and biochemical stress response in rice (Oryza sativa L.).

    PubMed

    Xie, Pan-pan; Deng, Juan-wei; Zhang, Hui-min; Ma, You-hua; Cao, De-ju; Ma, Ru-xiao; Liu, Ren-jing; Liu, Cheng; Liang, Yue-gan

    2015-12-01

    This study investigated the effects of various Cd concentrations on the bioaccumulation, antioxidative defense, and stress responses of rice (Oryza sativa L.). The distribution characteristics of Cd in rice were in the following order: roots>stems>grains. The bioconcentration factor values of Cd increased at concentrations lower than 3.00 mg Cd/kg and approximately decreased to a constant value at concentrations higher than 3.00 mg Cd/kg. Rice showed a higher Cd accumulation potential at low Cd concentrations than at high Cd concentrations. The Freundlich isotherm model described well the adsorption isotherms of Cd in rice roots. The biosorption mechanism of rice roots was determined to be cooperative adsorption. The malondialdehyde (MDA) content increased at a concentration range of 0.00-5.00 mg/L, indicating the enhancement of lipid peroxidation. By contrast, the MDA content slightly decreased at concentrations higher than 5.00 mg/L. Peroxidase (POD) activity exhibited active response to oxidative stress at concentrations lower than 5.00 mg/L but was inhibited at concentrations higher than 5.00 mg/L. The response to Cd stress of the N-H, O-H and C-O functional groups in rice shoots was observed via Fourier transform infrared spectroscopy.

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

    PubMed

    Pires, Inês S; Negrão, Sónia; Oliveira, M Margarida; Purugganan, Michael D

    2015-09-01

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

  5. Red and blue lights induced oxidative stress tolerance promote cadmium rhizocomplexation in Oryza sativa.

    PubMed

    Sebastian, Abin; Prasad, M N V

    2014-08-01

    Cadmium (Cd) accumulation and related stress responses have been investigated in red, blue and white lights exposed Oryza sativa L. cv MTU 7029. Cd translocation was reduced significantly by red and blue lights. Increase in amount of organic acids, thiols, and nutrients in the roots that cause Cd rhizocomplexation was the reason for reduction in Cd translocation. These effects were due to higher efficiency to perform photosynthesis and transpiration under red or blue lights compare with white light during Cd stress. Increased photosynthetic assimilate turnover was witnessed as a function of sugar content. Amount of redox regulators such as glutathione and ascorbate were also increased under red and blue light exposure. Together with up regulation of antioxidant enzyme activities, these metabolites ensured redox balance in presence of reactive oxygen species produced due to Cd toxicity. Protection of photosynthesis from Cd inducible oxidative stress ensured supplies of sugar intermediates essential for the synthesis of metal chelators in roots. Therefore, it was inferred that red and blue lights promote Cd rhizocomplexation and ameliorated Cd stress in rice seedlings.

  6. Genes for iron-sulphur cluster assembly are targets of abiotic stress in rice, Oryza sativa.

    PubMed

    Liang, Xuejiao; Qin, Lu; Liu, Peiwei; Wang, Meihuan; Ye, Hong

    2014-03-01

    Iron-sulphur (Fe-S) cluster assembly occurs in chloroplasts, mitochondria and cytosol, involving dozens of genes in higher plants. In this study, we have identified 41 putative Fe-S cluster assembly genes in rice (Oryza sativa) genome, and the expression of all genes was verified. To investigate the role of Fe-S cluster assembly as a metabolic pathway, we applied abiotic stresses to rice seedlings and analysed Fe-S cluster assembly gene expression by qRT-PCR. Our data showed that genes for Fe-S cluster assembly in chloroplasts of leaves are particularly sensitive to heavy metal treatments, and that Fe-S cluster assembly genes in roots were up-regulated in response to iron toxicity, oxidative stress and some heavy metal assault. The effect of each stress treatment on the Fe-S cluster assembly machinery demonstrated an unexpected tissue or organelle specificity, suggesting that the physiological relevance of the Fe-S cluster assembly is more complex than thought. Furthermore, our results may reveal potential candidate genes for molecular breeding of rice.

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

    PubMed

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

    2016-07-01

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

  8. Microsporomyces hainanensis sp. nov., Isolated from Hybrid Rice (Oryza sativa L.) Seeds.

    PubMed

    Bai, Feirong; Liu, Yang; Li, Ni; Yao, Su; Li, Nannan; Wang, Weiping; Cheng, Chi

    2016-10-01

    A total of five strains were isolated from two different hybrid rice seeds samples (Oryza sativa L. Shenliangyou 5814 and Yliangyou 900) in Sanya city, Hainan province, China. Sequence analysis and physiological characteristics indicated that these strains were identical and represented a novel species. Molecular phylogenetic analysis of the D1/D2 domain of the large subunit rRNA gene and the internal transcribed spacer regions revealed that this new species is located in the Microsporomyces clade, with four closely related species, namely, M. magnisporus, M. orientalis, M. bloemfonteinensis, and M. pini. The novel species differed from these four described species in ability to assimilate sorbose, cellobiose, lactose, D-arabinose, and maltose. Based on these results, the following novel yeast species is proposed: Microsporomyces hainanensis sp. nov. with the type strain of Z8(T) (CICC 33066(T) = CBS 14092(T)) belongs to phylum Basidiomycota, subphylum Pucciniomycotina, class Cystobasidiomycetes, family Microsporomycetaceae. The new species were registered in MycoBank under MB 815471.

  9. Diel activity of sucrose phosphate synthase in rice. [Oryza sativa L

    SciTech Connect

    Hussain, M.W.; Bowes, G.; Rowland-Bamford, A.J.; Allen, L.H. )

    1991-05-01

    Rice (Oryza sativa L.) was grown in growth chambers at 28/23C day/night temperatures with 16-h photoperiod at 600 umol m{sup {minus}2} s{sup {minus}1}. Diel sucrose phosphate synthase (SPS) activity, at 21 days after planting, was measured at saturating substrate concentrations. Data suggests that SPS activity increased during illumination to a maximum of 0.8 nmol mg{sup {minus}1} protein min{sup {minus}1} after 5h. Throughout the remainder of the light period there was a slow decline in activity. Upon darkening, activity further declined to 0.4 nmol mg{sup {minus}1} protein min{sup {minus}1}, a basal level that was maintained throughout the night. It appears that rice SPS undergoes light/dark transitions, suggesting there may be two kinetic forms of SPS. Changes in SPS activity will be discussed in relation to kinetic studies, and also CO{sub 2} enrichment of rice during growth.

  10. Heterologous Expression of AtWRKY57 Confers Drought Tolerance in Oryza sativa.

    PubMed

    Jiang, Yanjuan; Qiu, Yuping; Hu, Yanru; Yu, Diqiu

    2016-01-01

    Drought stress is a severe environmental factor that greatly restricts plant distribution and crop production. Recently, we have found that overexpressing AtWRKY57 enhanced drought tolerance in Arabidopsis thaliana. In this study, we further reported that the Arabidopsis WRKY57 transcription factor was able to confer drought tolerance to transgenic rice (Oryza sativa) plants. The enhanced drought tolerance of transgenic rice was resulted from the lower water loss rates, cell death, malondialdehyde contents and relative electrolyte leakage while a higher proline content and reactive oxygen species-scavenging enzyme activities was observed during stress conditions. Moreover, further investigation revealed that the expression levels of several stress-responsive genes were up-regulated in drought-tolerant transgenic rice plants, compared with those in wild-type plants. In addition to the drought tolerance, the AtWRKY57 over-expressing plants also had enhanced salt and PEG stress tolerances. Taken together, our study indicates that over-expressing AtWRKY57 in rice improved not only drought tolerance but also salt and PEG tolerance, demonstrating its potential role in crop improvement.

  11. Heterologous Expression of AtWRKY57 Confers Drought Tolerance in Oryza sativa

    PubMed Central

    Jiang, Yanjuan; Qiu, Yuping; Hu, Yanru; Yu, Diqiu

    2016-01-01

    Drought stress is a severe environmental factor that greatly restricts plant distribution and crop production. Recently, we have found that overexpressing AtWRKY57 enhanced drought tolerance in Arabidopsis thaliana. In this study, we further reported that the Arabidopsis WRKY57 transcription factor was able to confer drought tolerance to transgenic rice (Oryza sativa) plants. The enhanced drought tolerance of transgenic rice was resulted from the lower water loss rates, cell death, malondialdehyde contents and relative electrolyte leakage while a higher proline content and reactive oxygen species-scavenging enzyme activities was observed during stress conditions. Moreover, further investigation revealed that the expression levels of several stress-responsive genes were up-regulated in drought-tolerant transgenic rice plants, compared with those in wild-type plants. In addition to the drought tolerance, the AtWRKY57 over-expressing plants also had enhanced salt and PEG stress tolerances. Taken together, our study indicates that over-expressing AtWRKY57 in rice improved not only drought tolerance but also salt and PEG tolerance, demonstrating its potential role in crop improvement. PMID:26904091

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

    PubMed Central

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

    2017-01-01

    Vacuole fusion is a necessary process for the establishment of a large central vacuole, which is the central location of various hydrolytic enzymes and other factors involved in death at the beginning of plant programmed cell death (PCD). In our report, the fusion of vacuoles has been presented in two ways: i) small vacuoles coalesce to form larger vacuoles through membrane fusion, and ii) larger vacuoles combine with small vacuoles when small vacuoles embed into larger vacuoles. Regardless of how fusion occurs, a large central vacuole is formed in rice (Oryza sativa) aleurone cells. Along with the development of vacuolation, the rupture of the large central vacuole leads to the loss of the intact plasma membrane and the degradation of the nucleus, resulting in cell death. Stabilizing or disrupting the structure of actin filaments (AFs) inhibits or promotes the fusion of vacuoles, which delays or induces PCD. In addition, the inhibitors of the vacuolar processing enzyme (VPE) and cathepsin B (CathB) block the occurrence of the large central vacuole and delay the progression of PCD in rice aleurone layers. Overall, our findings provide further evidence for the rupture of the large central vacuole triggering the PCD in aleruone layers. PMID:28117452

  13. Experimental and theoretical approaches for Cd(II) biosorption from aqueous solution using Oryza sativa biomass.

    PubMed

    Fawzy, Manal; Nasr, Mahmoud; Helmi, Shacker; Nagy, Heba

    2016-11-01

    Biomass of Oryza sativa (OS) was tested for the removal of Cd(II) ions from synthetic and real wastewater samples. Batch experiments were conducted to investigate the effects of operating parameters on Cd(II) biosorption. Fourier transform infrared spectroscopy, scanning electron microscopy, and energy-dispersive x-ray spectroscopy were used to examine the surface characteristics of the Cd(II)-loaded biomass. The maximum removal efficiency of Cd(II) was 89.4% at optimum pH 6.0, biosorbent dose 10.0 g L(-1), initial Cd(II) 50 mg L(-1), and biosorbent particle size 0.5 mm. The applicability of Langmuir and Freundlich isotherms to the sorbent system implied the existence of both monolayer and heterogeneous surface conditions. Kinetic studies revealed that the adsorption process of Cd(II) followed the pseudo-second-order model (r2: 0.99). On the theoretical side, an adaptive neuro-fuzzy inference system (ANFIS) was applied to select the operating parameter that mostly influences the Cd(II) biosorption process. Results from ANFIS indicated that pH was the most influential parameter affecting Cd(II) removal efficiency, indicating that the biomass of OS was strongly pH sensitive. Finally, the biomass was confirmed to adsorb Cd(II) from real wastewater samples with removal efficiency close to 100%. However, feasibility studies of such systems on a large-scale application remain to be investigated.

  14. Antimicrobial compounds from endophytic Streptomyces sp. BCC72023 isolated from rice (Oryza sativa L.).

    PubMed

    Supong, Khomsan; Thawai, Chitti; Choowong, Wilunda; Kittiwongwattana, Chokchai; Thanaboripat, Dusanee; Laosinwattana, Chamroon; Koohakan, Prommart; Parinthawong, Nonglak; Pittayakhajonwut, Pattama

    2016-05-01

    An endophytic actinomycete strain BCC72023 was isolated from rice (Oryza sativa L.) and identified as the genus Streptomyces, based on phenotypic, chemotaxonomic and 16S rRNA gene sequence analyses. The strain showed 99.80% similarity compared with Streptomyces samsunensis M1463(T). Chemical investigation led to the isolation of three macrolides, efomycins M (1), G (2) and oxohygrolidin (3), along with two polyethers, abierixin (4) and 29-O-methylabierixin (5). To our knowledge, this is the first report of efomycin M being isolated from a natural source. The compounds were identified using spectroscopic techniques and comparison with previously published data. All compounds exhibited antimalarial activity against the Plasmodium falciparum, K-1 strain, a multidrug-resistant strain, with IC50 values in a range of 1.40-5.23 μg/ml. In addition, these compounds were evaluated for biological activity against Mycobacterium tuberculosis, Bacillus cereus, Colletotrichum gloeosporioides and Colletotrichum capsici, as well as cytotoxicity against both cancerous (MCF-7, KB, NCI-H187) and non-cancerous (Vero) cells.

  15. Crystal structure of α-amylase from Oryza sativa: molecular insights into enzyme activity and thermostability.

    PubMed

    Ochiai, Akihito; Sugai, Hiroshi; Harada, Kazuki; Tanaka, Seiya; Ishiyama, Yohei; Ito, Kosuke; Tanaka, Takaaki; Uchiumi, Toshio; Taniguchi, Masayuki; Mitsui, Toshiaki

    2014-01-01

    AmyI-1 is an α-amylase from Oryza sativa (rice) and plays a crucial role in degrading starch in various tissues and at various growth stages. This enzyme is a glycoprotein with an N-glycosylated carbohydrate chain, a unique characteristic among plant α-amylases. In this study, we report the first crystal structure of AmyI-1 at 2.2-Å resolution. The structure consists of a typical (β/α)8-barrel, which is well-conserved among most α-amylases in the glycoside hydrolase family-13. Structural superimposition indicated small variations in the catalytic domain and carbohydrate-binding sites between AmyI-1 and barley α-amylases. By contrast, regions around the N-linked glycosylation sites displayed lower conservation of amino acid residues, including Asn-263, Asn-265, Thr-307, Asn-342, Pro-373, and Ala-374 in AmyI-1, which are not conserved in barley α-amylases, suggesting that these residues may contribute to the construction of the structure of glycosylated AmyI-1. These results increase the depths of our understanding of the biological functions of AmyI-1.

  16. Assessing the arsenic-contaminated rice (Oryza sativa) associated children skin lesions.

    PubMed

    Liao, Chung-Min; Lin, Tzu-Ling; Hsieh, Nan-Hung; Chen, Wei-Yu

    2010-04-15

    The purpose of this study was to assess the potential risk of children skin lesions from arsenic-contaminated rice (Oryza sativa) consumption in West Bengal (India). Published age- and gender-specific skin lesions data in West Bengal were reanalyzed and incorporated into a Weibull dose-response model to predict children skin lesion prevalence. Monomethylarsonous acid (MMA(III)) levels in urine was used as a biomarker that could be predicted from a human physiologically based pharmacokinetic (PBPK) model. This study integrated arsenic contents in irrigation water, bioaccumulation factors of paddy soil, cooking methods, and arsenic bioavailability of cooked rice in gastrointestinal tract into a probabilistic risk model. Results indicated that children aged between 13 and 18 years might pose a relative higher potential risk of skin lesions to arsenic-contaminated cooked rice (odds ratios (ORs)=1.18 (95% CI 1.12-2.15)) than those of 1-6 years children (ORs=0.98 (0.85-1.40)). This study revealed the need to consider the relationships between cooking method and arsenic in cooked rice when assessing the risk associated with children skin lesions from rice consumption. This study suggested that arsenic-associated skin lesions risk from arsenic-contaminated rice consumption would be reduced significantly by adopting traditional rice cooking method (wash until clean; rice:water=1:6; discard excess water) as followed in West Bengal (India) and using water containing lower arsenic (e.g., <10 microg L(-1)) for cooking.

  17. Brevundimonas diminuta mediated alleviation of arsenic toxicity and plant growth promotion in Oryza sativa L.

    PubMed

    Singh, Namrata; Marwa, Naina; Mishra, Shashank K; Mishra, Jyoti; Verma, Praveen C; Rathaur, Sushma; Singh, Nandita

    2016-03-01

    Arsenic (As), a toxic metalloid adversely affects plant growth in polluted areas. In the present study, we investigated the possibility of improving phytostablization of arsenic through application of new isolated strain Brevundimonas diminuta (NBRI012) in rice plant [Oryza sativa (L.) Var. Sarju 52] at two different concentrations [10ppm (low toxic) and 50ppm (high toxic)] of As. The plant growth promoting traits of bacterial strains revealed the inherent ability of siderophores, phosphate solubilisation, indole acetic acid (IAA), 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase production which may be associated with increased biomass, chlorophyll and MDA content of rice and thereby promoting plant growth. The study also revealed the As accumulation property of NBRI012 strain which could play an important role in As removal from contaminated soil. Furthermore, NBRI012 inoculation significantly restored the hampered root epidermal and cortical cell growth of rice plant and root hair elimination. Altogether our study highlights the multifarious role of B. diminuta in mediating stress tolerance and modulating translocation of As in edible part of rice plant.

  18. K+ efflux and retention in response to NaCl stress do not predict salt tolerance in contrasting genotypes of rice (Oryza sativa L.).

    PubMed

    Coskun, Devrim; Britto, Dev T; Jean, Yuel-Kai; Kabir, Imtiaz; Tolay, Inci; Torun, Ayfer A; Kronzucker, Herbert J

    2013-01-01

    Sudden elevations in external sodium chloride (NaCl) accelerate potassium (K(+)) efflux across the plasma membrane of plant root cells. It has been proposed that the extent of this acceleration can predict salt tolerance among contrasting cultivars. However, this proposal has not been considered in the context of plant nutritional history, nor has it been explored in rice (Oryza sativa L.), which stands among the world's most important and salt-sensitive crop species. Using efflux analysis with (42)K, coupled with growth and tissue K(+) analyses, we examined the short- and long-term effects of NaCl exposure to plant performance within a nutritional matrix that significantly altered tissue-K(+) set points in three rice cultivars that differ in salt tolerance: IR29 (sensitive), IR72 (moderate), and Pokkali (tolerant). We show that total short-term K(+) release from roots in response to NaCl stress is small (no more than 26% over 45 min) in rice. Despite strong varietal differences, the extent of efflux is shown to be a poor predictor of plant performance on long-term NaCl stress. In fact, no measure of K(+) status was found to correlate with plant performance among cultivars either in the presence or absence of NaCl stress. By contrast, shoot Na(+) accumulation showed the strongest correlation (a negative one) with biomass, under long-term salinity. Pharmacological evidence suggests that NaCl-induced K(+) efflux is a result of membrane disintegrity, possibly as result of osmotic shock, and not due to ion-channel mediation. Taken together, we conclude that, in rice, K(+) status (including efflux) is a poor predictor of salt tolerance and overall plant performance and, instead, shoot Na(+) accumulation is the key factor in performance decline on NaCl stress.

  19. Gene interactions and genetics of blast resistance and yield attributes in rice (Oryza sativa L.).

    PubMed

    Divya, B; Biswas, A; Robin, S; Rabindran, R; Joel, A John

    2014-08-01

    Blast disease caused by the pathogen Pyricularia oryzae is a serious threat to rice production. Six generations viz., P1, P2, F1, F2, B1 and B2 of a cross between blast susceptible high-yielding rice cultivar ADT 43 and resistant near isogenic line (NIL) CT13432-3R, carrying four blast resistance genes Pi1, Pi2, Pi33 and Pi54 in combination were used to study the nature and magnitude of gene action for disease resistance and yield attributes. The epistatic interaction model was found adequate to explain the gene action in most of the traits. The interaction was complementary for number of productive tillers, economic yield, lesion number, infected leaf area and potential disease incidence but duplicate epistasis was observed for the remaining traits. Among the genotypes tested under epiphytotic conditions, gene pyramided lines were highly resistant to blast compared to individuals with single genes indicating that the nonallelic genes have a complementary effect when present together. The information on genetics of various contributing traits of resistance will further aid plant breeders in choosing appropriate breeding strategy for blast resistance and yield enhancement in rice.

  20. High-resolution genetic mapping of Xa27(t), a new bacterial blight resistance gene in rice, Oryza sativa L.

    PubMed

    Gu, K; Tian, D; Yang, F; Wu, L; Sreekala, C; Wang, D; Wang, G-L; Yin, Z

    2004-03-01

    Bacterial blight of rice, caused by Xanthomonas oryzae pv. oryzae ( Xoo) (Ishyama) Dye, is one of the serious diseases prevalent throughout Asia. In a previous study, a resistance ( R) locus was transferred from the tetraploid wild rice Oryza minuta to the cultivated rice species, Oryza sativa L. Here, we report the fine genetic mapping of the R locus, tentatively designated as Xa27(t). We performed disease evaluation with an Xa27(t) near-isogenic line, IRBB27, testing 35 Xoo strains collected from 11 countries. The Xa27(t) locus conferred a high level of resistance to 27 strains and moderate resistance to three strains. Resistance of the Xa27(t) gene was developmentally regulated in IRBB27 and showed semi-dominant or a dosage effect in the cv. CO39 genetic background. As a prelude to cloning Xa27(t), a molecular mapping strategy was employed with a large mapping population consisting of 3,875 gametes. Three molecular markers, M336, M1081, and M1059, closely linked to Xa27(t), were identified to facilitate the mapping of Xa27(t) to the long arm of chromosome 6. The Xa27(t) locus was confirmed by chromosome landing of M1081 and M1095 markers on the rice genome. Markers derived from the genomic sequence of O. sativa cv. Nipponbare were used to further saturate the Xa27(t) genomic region. Xa27(t) was finally located within a genetic interval of 0.052 cM, flanked by markers M964 and M1197, and co-segregated with markers M631, M1230, and M449.

  1. Identification of β-phenylalanine as a non-protein amino acid in cultivated rice, Oryza sativa

    PubMed Central

    Yokoo, Takayuki; Takata, Ryo; Yan, Jian; Matsumoto, Fuka; Teraishi, Masayoshi; Okumoto, Yutaka; Jander, Georg; Mori, Naoki

    2015-01-01

    Non-protein amino acids, often analogs of the standard 20 protein amino acids, have been discovered in many plant species. Recent research with cultivated rice (Oryza sativa) identified (3R)-β-tyrosine, as well as a tyrosine amino mutase that synthesizes (3R)-β-tyrosine from the protein amino acid (2S)-α-tyrosine. Gas chromatography-mass spectrometry (GC-MS) assays and comparison to an authentic standard showed that β-phenylalanine is also a relatively abundant non-protein amino acid in rice leaves and that its biosynthesis occurs independently from that of β-tyrosine. PMID:27066169

  2. Brassinosteroids are involved in Fe homeostasis in rice (Oryza sativa L.)

    PubMed Central

    Wang, Baolan; Li, Gen; Zhang, Wen-Hao

    2015-01-01

    Brassinosteroids (BRs) are steroid hormones that modulate numerous physiological processes in plants. However, few studies have focused on the involvement of BRs in sensing and responding to the stress of mineral nutrient deficiency. In the present study, we evaluated the roles of BRs in the response of rice (Oryza sativa) to iron (Fe) deficiency during Fe uptake, transport, and translocation. Exogenous application of 24-epibrassinolide (EBR) to wild-type (WT) plants exaggerated leaf symptoms of Fe deficiency and suppressed growth. EBR increased and decreased Fe concentrations in roots and shoots, respectively, under both Fe-deficient and Fe-sufficient conditions. Transcripts involved in Fe homeostasis, including OsIRT1, OsYSL15, OsYSL2, OsNAS1, and OsNAS2, were enhanced by EBR under Fe-deficient conditions. EBR depressed expression of OsNAS1, OsNAS2, and OsYSL2 in shoots, and inhibited Fe transport and translocation via the phloem. Rice mutant d2-1, which is defective in BR biosynthesis, was more tolerant to Fe deficiency than the WT, and accumulated greater amounts of Fe in roots than the WT under Fe-sufficient conditions. A greater upregulation of OsIRT1, OsYSL15, OsYSL2, OsNAS1, and OsNAS2 in the d2-1 mutant compared to the WT was found under Fe-sufficient conditions, while expression of these genes in the d2-1 mutant was lower than in the WT under Fe-deficient conditions. The greater tolerance of the d2-1 mutant could be partly mitigated by exogenous application of EBR. These novel findings highlight the important role of BR in mediating the response of strategy II plants to Fe deficiency by regulating Fe uptake and translocation in rice. PMID:25770588

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

    PubMed

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

    2016-11-03

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

  4. Brassinosteroids are involved in Fe homeostasis in rice (Oryza sativa L.).

    PubMed

    Wang, Baolan; Li, Gen; Zhang, Wen-Hao

    2015-05-01

    Brassinosteroids (BRs) are steroid hormones that modulate numerous physiological processes in plants. However, few studies have focused on the involvement of BRs in sensing and responding to the stress of mineral nutrient deficiency. In the present study, we evaluated the roles of BRs in the response of rice (Oryza sativa) to iron (Fe) deficiency during Fe uptake, transport, and translocation. Exogenous application of 24-epibrassinolide (EBR) to wild-type (WT) plants exaggerated leaf symptoms of Fe deficiency and suppressed growth. EBR increased and decreased Fe concentrations in roots and shoots, respectively, under both Fe-deficient and Fe-sufficient conditions. Transcripts involved in Fe homeostasis, including OsIRT1, OsYSL15, OsYSL2, OsNAS1, and OsNAS2, were enhanced by EBR under Fe-deficient conditions. EBR depressed expression of OsNAS1, OsNAS2, and OsYSL2 in shoots, and inhibited Fe transport and translocation via the phloem. Rice mutant d2-1, which is defective in BR biosynthesis, was more tolerant to Fe deficiency than the WT, and accumulated greater amounts of Fe in roots than the WT under Fe-sufficient conditions. A greater upregulation of OsIRT1, OsYSL15, OsYSL2, OsNAS1, and OsNAS2 in the d2-1 mutant compared to the WT was found under Fe-sufficient conditions, while expression of these genes in the d2-1 mutant was lower than in the WT under Fe-deficient conditions. The greater tolerance of the d2-1 mutant could be partly mitigated by exogenous application of EBR. These novel findings highlight the important role of BR in mediating the response of strategy II plants to Fe deficiency by regulating Fe uptake and translocation in rice.

  5. A hemicellulose-bound form of silicon inhibits cadmium ion uptake in rice (Oryza sativa) cells.

    PubMed

    Ma, Jie; Cai, Hongmei; He, Congwu; Zhang, Wenjun; Wang, Lijun

    2015-05-01

    Silicon (Si) alleviates cadmium (Cd) toxicity in rice (Oryza sativa). However, the chemical mechanisms at the single-cell level are poorly understood. Here, a suspension of rice cells exposed to Cd and/or Si treatments was investigated using a combination of plant cell nutritional, molecular biological, and physical techniques including in situ noninvasive microtest technology (NMT), polymerase chain reaction (PCR), inductively coupled plasma mass spectroscopy (ICP-MS), and atomic force microscopy (AFM) in Kelvin probe mode (KPFM). We found that Si-accumulating cells had a significantly reduced net Cd(2+) influx, compared with that in Si-limited cells. PCR analyses of the expression levels of Cd and Si transporters in rice cells showed that, when the Si concentration in the medium was increased, expression of the Si transporter gene Low silicon rice 1 (Lsi1) was up-regulated, whereas expression of the gene encoding the transporter involved in the transport of Cd, Natural resistance-associated macrophage protein 5 (Nramp5), was down-regulated. ICP-MS results revealed that 64% of the total Si in the cell walls was bound to hemicellulose constituents following the fractionation of the cell walls, and consequently inhibited Cd uptake. Furthermore, AFM in KPFM demonstrated that the heterogeneity of the wall surface potential was higher in cells cultured in the presence of Si than in those cultured in its absence, and was homogenized after the addition of Cd. These results suggest that a hemicellulose-bound form of Si with net negative charges is responsible for inhibition of Cd uptake in rice cells by a mechanism of [Si-hemicellulose matrix]Cd complexation and subsequent co-deposition.

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

    PubMed

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

    2014-09-01

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

  7. Micromonospora endophytica sp. nov., an endophytic actinobacteria of Thai upland rice (Oryza sativa).

    PubMed

    Thanaboripat, Dusanee; Thawai, Chitti; Kittiwongwattana, Chokchai; Laosinwattana, Chamroon; Koohakan, Prommart; Parinthawong, Nonglak

    2015-11-01

    An actinobacterial strain, DCWR9-8-2(T), was isolated from a leaf of Thai upland rice (Oryza sativa) collected in Chumporn province, Thailand. Strain DCWR9-8-2(T) is Gram-stain-positive aerobic bacteria that produce single spores directly on the vegetative hypha. Cell wall peptidoglycan of this strain exhibits meso-diaminopimelic acid and glycine, the reducing sugars of whole-cell hydrolysate are arabinose, glucose, ribose, xylose and small amount of mannose. The phospholipid profiles in the membrane are comprised of phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannosides. The major menaquinones are MK-9(H4) and MK-10(H6). The diagnostic cellular fatty acids are iso-C16:0 and iso-C15:0. The G+C content of the genomic DNA is 72.5 mol%. The result of 16S rRNA sequence analysis of the strain revealed that this strain was closely related to Micromonospora auratinigra TT1-11(T) (99.25%). On the other hand, the result of gyrB gene sequence analysis revealed that this strain was closed to M. eburnea JCM 12345(T) (96.30%). In addition, a combination of DNA-DNA hybridization results and some phenotypic properties supported that this strain should be judged as a novel species of the genus Micromonospora, for which the name M. endophytica sp. nov. is proposed. The type strain is DCWR9-8-2(T) (=BCC 67267(T)=NBRC 110008(T)).

  8. Elicitation of Diterpene Biosynthesis in Rice (Oryza sativa L.) by Chitin 1

    PubMed Central

    Ren, Yue-Ying; West, Charles A.

    1992-01-01

    Cell-free extracts of UV-irradiated rice (Oryza sativa L.) leaves have a much greater capacity for the synthesis from geranylgeranyl pyrophosphate of diterpene hydrocarbons, including the putative precursors of rice phytoalexins, than extracts of unstressed leaves (KA Wickham, CA West [1992] Arch Biochem Biophys 293: 320-332). An elicitor bioassay was developed on the basis of these observations in which 6-day-old rice cell suspension cultures were incubated for 40 hours with the substance to be tested, and an enzyme extract of the treated cells was assayed for its diterpene hydrocarbon synthesis activity as a measure of the response to elicitor. Four types of cell wall polysaccharides and oligosaccharide fragments that have elicitor activity for other plants were tested. Of these, polymeric chitin was the most active; a suspension concentration of approximately 7 micrograms per milliliter gave 50% of the maximum response in the bioassay. Chitosan and a branched β-1,3-glucan fraction from Phytophthora megasperma f. sp. glycinea cell walls were only weakly active, and a mixture of oligogalacturonides was only slightly active. A crude mycelial cell wall preparation from the rice pathogen, Fusarium moniliforme, gave a response comparable to that of chitin, and this activity was sensitive to predigestion of the cell wall material with chitinase before the elicitor assay. N-Acetylglucosamine, chitobiose, chitotriose, and chitotetrose were inactive as elicitors, whereas a mixture of chitin fragments solubilized from insoluble chitin by partial acid hydrolysis was highly active. Constitutive chitinase activity was detected in the culture filtrate and enzyme extract of cells from a 6-day-old rice cell culture; the amount of chitinase activity increased markedly in both the culture filtrate and cell extracts after treatment of the culture with chitin. We propose on the basis of these results that soluble chitin fragments released from fungal cell walls through the action

  9. Fine Mapping of Two Additive Effect Genes for Awn Development in Rice (Oryza sativa L.)

    PubMed Central

    Li, Jinjie; Yao, Guoxin; Pan, Huiqiao; Hu, Guanglong; Chen, Chao; Zhang, Hongliang; Li, Zichao

    2016-01-01

    Awns, important domestication and agronomic traits in rice (Oryza sativa L.), are conferred by polygenes and the environment. Near isogenic line (NIL) pairs BM33 and BM38 were constructed from crosses between awnless japonica cv Nipponbare as recurrent parent, and lines SLG or Funingxiaohongmang (awned japonica accessions), respectively, as donors. In order to study the genetic and molecular mechanism of awning, two unknown, independent genes with additive effects were identified in a cross between the NILs. To map and clone the two genes, a BC4F4 population of 8,103 individuals and a BC4F6 population of 11,206 individuals were constructed. Awn3-1 was fine mapped to a 101.13 kb genomic region between Indel marker In316 and SNP marker S9-1 on chromosome 3. Nine predicted genes in the interval were annotated in the Rice Annotation Project Database (RAP-DB), and Os03g0418600 was identified as the most likely candidate for Awn3-1 through sequence comparisons and RT-PCR assays. Awn4-2 was fine mapped to a 62.4 kb genomic region flanked by simple sequence repeat (SSR) marker M1126 and Indel maker In73 on chromosome 4L. This region contained the previously reported gene An-1 that regulates awn development. Thus, An-1 may be the candidate gene of Awn4-2. These results will facilitate cloning of the awn genes and thereby provide an understanding of the molecular basis of awn development. PMID:27494628

  10. Evidence for selection on gene expression in cultivated rice (Oryza sativa).

    PubMed

    House, Megan A; Griswold, Cortland K; Lukens, Lewis N

    2014-06-01

    Artificial selection has been used throughout plant domestication and breeding to develop crops that are adapted to diverse environments. Here, we investigate whether gene regulatory changes have been widespread targets of lineage-specific selection in cultivated lines Minghui 63 and Zhenshan 97 of rice, Oryza sativa. A line experiencing positive selection for either an increase or a decrease in genes' transcript abundances is expected to have an overabundance of expression quantitative trait locus (eQTL) alleles that increase or decrease those genes' expression, respectively. Results indicate that several genes that share Gene Ontology terms or are members of the same coexpression module have eQTL alleles from one parent that consistently increase gene expression relative to the second parent. A second line of evidence for lineage-specific selection is an overabundance of cis-trans pairs of eQTL alleles that affect gene expression in the same direction (are reinforcing). Across all cis-trans pairs of eQTL, including pairs that both weakly and strongly affect gene expression, there is no evidence for selection. However, the frequency of genes with reinforcing eQTL increases with eQTL strength. Therefore, there is evidence that eQTL with strong effects were positively selected during rice cultivation. Among 41 cis-trans pairs with strong trans eQTL, 31 have reinforcing eQTL. Several of the candidate genes under positive selection accurately predict phenotypic differences between Minghui 63 and Zhenshan 97. Overall, our results suggest that positive selection for regulatory alleles may be a key factor in plant improvement.

  11. Molecular phylogenetics and comparative modeling of MnSOD, an enzyme involved during environmental stress conditions in Oryza sativa.

    PubMed

    Tripathi, Vijay; Tripathi, Pooja

    2014-12-01

    Superoxide dismutases are a class of enzymes that catalyze the dismutation of superoxide into oxygen and hydrogen peroxide. As such, they are an important antioxidant defense in nearly all cells exposed to oxygen. Superoxide dismutase (SOD) acts as first line of defense against oxidative and genetic stress. Manganese superoxide dismutase (MnSOD), found in mitochondria or peroxisomes, contains Mn (III) at the active site. The three dimensional structure of MnSOD of Oryza sativa is not yet available in protein data bank so we have predicted the structure model of O. sativa MnSOD using homology modeling. The predicted model can further be explored for identification of ligand binding sites which may be useful for understanding specific role in functional site residues during catalysis. This study also demonstrated that the phylogenetic analysis of O. sativa MnSOD protein with distinct dicot and monocot plant species. The MnSOD protein of O. sativa has shown similarity with both monocot and as well as dicot plant species.

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

    PubMed

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

    2016-02-01

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

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

    PubMed Central

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

    2016-01-01

    The root-knot nematode Meloidogyne graminicola is one of the most serious nematode pests worldwide and represents a major constraint on rice production. While variation in the susceptibility of Asian rice (Oryza sativa) exists, so far no strong and reliable resistance has been reported. Quantitative trait loci for partial resistance have been reported but no underlying genes have been tagged or cloned. Here, 332 accessions of the Rice Diversity Panel 1 were assessed for gall formation, revealing large variation across all subpopulations of rice and higher susceptibility in temperate japonica accessions. Accessions Khao Pahk Maw and LD 24 appeared to be resistant, which was confirmed in large pot experiments where no galls were observed. Detailed observations on these two accessions revealed no nematodes inside the roots 2 days after inoculation and very few females after 17 days (5 in Khao Pahk Maw and <1 in LD 24, in comparison with >100 in the susceptible controls). These two cultivars appear ideal donors for breeding root-knot nematode resistance. A genome-wide association study revealed 11 quantitative trait loci, two of which are close to epistatic loci detected in the Bala x Azucena population. The discussion highlights a small number of candidate genes worth exploring further, in particular many genes with lectin domains and genes on chromosome 11 with homology to the Hordeum Mla locus. PMID:26552884

  14. Variation in Preference for Rhizobium meliloti Within and Between Medicago sativa Cultivars Grown in Soil †

    PubMed Central

    Bromfield, E. S. P.

    1984-01-01

    Variation in nodulation preferences for Rhizobium strains within and between Medicago sativa cultivars was assessed in the greenhouse with plants grown in Leonard jars and two soils of diverse origin (Lanark and Ottawa), using inocula consisting of effective individual or paired strains of R. meliloti which could be recognized by high-concentration antibiotic resistance. The results indicated considerable variability in host preferences for R. meliloti among plants within cultivars but not between cultivars. The implications of this variation are discussed from the point of view of possible improvement of symbiotic nitrogen fixation. With one exception, the differences in nodulation success between inoculant R. meliloti strains were consistent in Leonard jars and both soils. All introduced strains formed significantly more nodules in Renfrew soil containing few native rhizobia than in Ottawa soil with a large resident R. meliloti population. Plants grown in Lanark soil without inoculation were ineffectively nodulated by native rhizobia and yielded significantly less growth than those receiving inoculation. In contrast, the yield of inoculated plants in Ottawa soil did not significantly differ from those without inoculation due to effective nodulation by native R. meliloti. The data indicated synergistic effects on yield by certain paired strain inocula relative to the same strains inoculated individually in Lanark but not in Ottawa soil or Leonard jars. PMID:16346682

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

    PubMed Central

    Xu, Xia; Wei, Yan-lin; Wang, Hui-mei; Zhang, Xiao-bo; Wu, Jian-li

    2015-01-01

    A rice chlorophyll-deficient mutant w67 was isolated from an ethyl methane sulfonate (EMS)–induced IR64 (Oryza sativa L. ssp. indica) mutant bank. The mutant exhibited a distinct yellow-green leaf phenotype in the whole plant growth duration with significantly reduced levels of chlorophyll and carotenoid, impaired chloroplast development and lowered capacity of photosynthesis compared with the wild-type IR64. Expression of a number of genes associated with chlorophyll metabolism, chloroplast biogenesis and photosynthesis was significantly altered in the mutant. Genetic analysis indicated that the yellow-green phenotype was controlled by a single recessive nuclear gene located on the short arm of chromosome 3. Using map-based strategy, the mutation was isolated and predicted to encode a chloroplast signal recognition particle 43 KD protein (cpSRP43) with 388 amino acid residuals. A single base substitution from A to T at position 160 resulted in a premature stop codon. OscpSRP43 was constitutively expressed in various organs with the highest level in the leaf. Functional complementation could rescue the mutant phenotype and subcellular localization showed that the cpSRP43:GFP fusion protein was targeted to the chloroplast. The data suggested that Oryza sativa cpSRP43 (OscpSRP43) was required for the normal development of chloroplasts and photosynthesis in rice. PMID:26600124

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

    PubMed

    Lv, Xiang-guang; Shi, Yong-feng; Xu, Xia; Wei, Yan-lin; Wang, Hui-mei; Zhang, Xiao-bo; Wu, Jian-li

    2015-01-01

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

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

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

    PubMed

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

    2017-01-01

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

  19. Transcriptomic analysis of rice (Oryza sativa) developing embryos using the RNA-Seq technique.

    PubMed

    Xu, Hong; Gao, Yi; Wang, Jianbo

    2012-01-01

    Rice (Oryza sativa) is an excellent model monocot with a known genome sequence for studying embryogenesis. Here we report the transcriptome profiling analysis of rice developing embryos using RNA-Seq as an attempt to gain insight into the molecular and cellular events associated with rice embryogenesis. RNA-Seq analysis generated 17,755,890 sequence reads aligned with 27,190 genes, which provided abundant data for the analysis of rice embryogenesis. A total of 23,971, 23,732, and 23,592 genes were identified from embryos at three developmental stages (3-5, 7, and 14 DAP), while an analysis between stages allowed the identification of a subset of stage-specific genes. The number of genes expressed stage-specifically was 1,131, 1,443, and 1,223, respectively. In addition, we investigated transcriptomic changes during rice embryogenesis based on our RNA-Seq data. A total of 1,011 differentially expressed genes (DEGs) (log(2)Ratio ≥ 1, FDR ≤ 0.001) were identified; thus, the transcriptome of the developing rice embryos changed considerably. A total of 672 genes with significant changes in expression were detected between 3-5 and 7 DAP; 504 DEGs were identified between 7 and 14 DAP. A large number of genes related to metabolism, transcriptional regulation, nucleic acid replication/processing, and signal transduction were expressed predominantly in the early and middle stages of embryogenesis. Protein biosynthesis-related genes accumulated predominantly in embryos at the middle stage. Genes for starch/sucrose metabolism and protein modification were highly expressed in the middle and late stages of embryogenesis. In addition, we found that many transcription factor families may play important roles at different developmental stages, not only in embryo initiation but also in other developmental processes. These results will expand our understanding of the complex molecular and cellular events in rice embryogenesis and provide a foundation for future studies on embryo

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

    PubMed Central

    Wang, Liping; Zhang, Cuiying; Wang, Yukun

    2017-01-01

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

  1. Starch characterization in seven raw, boiled and roasted chestnuts (Castanea sativa Mill.) cultivars from Portugal.

    PubMed

    Silva, A P; Oliveira, I; Silva, M E; Guedes, C M; Borges, O; Magalhães, B; Gonçalves, B

    2016-01-01

    Changes occurring in seven chestnut (Castanea sativa sp.) cultivars, caused by boiling and roasting, on starch content, cell and starch granules dimension were evaluated, and morphological changes were characterized by scanning electron microscopy. Three clear patterns of variation were detected after processing, namely: i) decrease of starch content with processing; ii) starch increase with the applied treatments; iii) increase of starch with boiling and decrease with roasting. Starch granules of raw chestnuts presented round, oval or elliptical form, external smooth surface and eccentric hilum, with rather ellipsoid-shaped growth rings. Processing resulted in modifications of the granules, with fusion of individual granules, and gelatinization taking place with the formation of elongated clusters. The present results indicate that boiling and roasting, besides changing the starch content of chestnut, causes important modifications in the starch granules, which can affect the sensory, rheological and chemical characteristics of chestnuts.

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

    PubMed

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

    2015-03-01

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

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

    PubMed Central

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

    2015-01-01

    A decline in rice (Oryza sativa L.) production caused by heat stress is one of the biggest concerns resulting from future climate change. Rice spikelets are most susceptible to heat stress at flowering. The early-morning flowering (EMF) trait mitigates heat-induced spikelet sterility at the flowering stage by escaping heat stress during the daytime. We attempted to develop near-isogenic lines (NILs) for EMF in the indica-type genetic background by exploiting the EMF locus from wild rice, O. officinalis (CC genome). A stable quantitative trait locus (QTL) for flower opening time (FOT) was detected on chromosome 3. A QTL was designated as qEMF3 and it shifted FOT by 1.5–2.0h earlier for cv. Nanjing 11 in temperate Japan and cv. IR64 in the Philippine tropics. NILs for EMF mitigated heat-induced spikelet sterility under elevated temperature conditions completing flower opening before reaching 35°C, a general threshold value leading to spikelet sterility. Quantification of FOT of cultivars popular in the tropics and subtropics did not reveal the EMF trait in any of the cultivars tested, suggesting that qEMF3 has the potential to advance FOT of currently popular cultivars to escape heat stress at flowering under future hotter climates. This is the first report to examine rice with the EMF trait through marker-assisted breeding using wild rice as a genetic resource. PMID:25534925

  4. Effects of ripening temperature on starch structure and gelatinization, pasting, and cooking properties in rice (Oryza sativa).

    PubMed

    Chun, Areum; Lee, Ho-Jin; Hamaker, Bruce R; Janaswamy, Srinivas

    2015-04-01

    The effect of ripening temperature on rice (Oryza sativa) grain quality was evaluated by assessing starch structure and gelatinization, pasting, and cooking properties. As the ripening temperature increased, the amylose content and number of short amylopectin chains decreased, whereas intermediate amylopectin chains increased, resulting in higher gelatinization temperatures and enthalpy in the starch. These results suggested that an increase in cooking temperature and time would be required for rice grown at higher temperatures. A high ripening temperature increased the peak, trough, and final viscosities and decreased the setback due to the reduction in amylose and the increase in long amylopectin chains. With regard to starch crystallinity and amylopectin molecular structure, the highest branches and compactness were observed at 28/20 °C. Rice that was grown at temperatures above 28/20 °C showed a deterioration of cooking quality and a tendency toward decreased palatability in sensory tests.

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

    PubMed

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

    2015-09-01

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

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

    DOE PAGES

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

    2017-03-29

    The role of seemingly non-enzymatic proteins in complexes interconverting UDP-arabinopyranose and UDP-arabinofuranose (UDP-arabinosemutases; UAMs) in the plant cytosol remains unknown. To shed light on their function, crystallographic and functional studies of the seemingly non-enzymatic UAM2 protein from Oryza sativa (OsUAM2) were undertaken. Here, X-ray diffraction data are reported, as well as analysis of the oligomeric state in the crystal and in solution. OsUAM2 crystallizes readily but forms highly radiation-sensitive crystals with limited diffraction power, requiring careful low-dose vector data acquisition. Using size-exclusion chromatography, it is shown that the protein is monomeric in solution. Finally, limited proteolysis was employed tomore » demonstrate DTT-enhanced proteolytic digestion, indicating the existence of at least one intramolecular disulfide bridge or, alternatively, a requirement for a structural metal ion.« less

  7. Operative photo assimilation associated proteome modulations are critical for iron-dependent cadmium tolerance in Oryza sativa L.

    PubMed

    Sebastian, Abin; Prasad, M N V

    2015-09-01

    Iron-dependent Cd tolerance in Oryza sativa L. cv 7029 had been explored. Photo assimilatory process such as photosynthesis and nitrogen fixation found to be functional in the presence of excess Fe during Cd stress. Cd-inducible Fe deficiency demonstrated with upregulation of iron uptake gene families such as OsIRT and OsYSL was attributed as foremost reason for retardation of photo assimilation in the course of Cd treatment. Upholding of photo assimilation during Fe supplement was associated with proteome modulations. Monitoring of proteome responses in leaf and root revealed proteins imperative for alleviation of Cd stress. Specifically, proteins that take part in photosynthesis, glucose metabolism, nitrogen fixation, and abiotic stress tolerance played key role in Fe-dependent Cd detoxification. It is concluded that Fe supply help to operate photo assimilation which enable favorable proteome responses of Cd stress tolerance.

  8. Structure, allelic diversity and selection of Asr genes, candidate for drought tolerance, in Oryza sativa L. and wild relatives.

    PubMed

    Philippe, Romain; Courtois, Brigitte; McNally, Kenneth L; Mournet, Pierre; El-Malki, Redouane; Le Paslier, Marie Christine; Fabre, Denis; Billot, Claire; Brunel, Dominique; Glaszmann, Jean-Christophe; This, Dominique

    2010-08-01

    Asr (ABA, stress, ripening) genes represent a small gene family potentially involved in drought tolerance in several plant species. To analyze their interest for rice breeding for water-limited environments, this gene family was characterized further. Genomic organization of the gene family reveals six members located on four different chromosomes and with the same exon-intron structure. The maintenance of six members of the Asr gene family, which are the result of combination between tandem duplication and whole genome duplication, and their differential regulation under water stress, involves probably some sub-functionalization. The polymorphism of four members was studied in a worldwide collection of 204 accessions of Oryza sativa L. and 14 accessions of wild relatives (O. rufipogon and O. nivara). The nucleotide diversity of the Asr genes was globally low, but contrasted for the different genes, leading to different shapes of haplotype networks. Statistical tests for neutrality were used and compared to their distribution in a set of 111 reference genes spread across the genome, derived from another published study. Asr3 diversity exhibited a pattern concordant with a balancing selection at the species level and with a directional selection in the tropical japonica sub-group. This study provides a thorough description of the organization of the Asr family, and the nucleotide and haplotype diversity of four Asr in Oryza sativa species. Asr3 stood out as the best potential candidate. The polymorphism detected here represents a first step towards an association study between genetic polymorphisms of this gene family and variation in drought tolerance traits.

  9. Computational prediction of submergence responsive microRNA and their binding position within the genome of Oryza sativa

    PubMed Central

    Paul, Prosenjit; Chakraborty, Supriyo

    2013-01-01

    Background: MicroRNAs (miRNAs) are small noncoding RNAs which play crucial role in response to the adverse biotic and abiotic stress conditions at the post transcriptional level. The functions of the miRNAs are generally based on complementarity to their target region. Results: We used the online tool psRNA Target for the identification of submergence responsive miRNA using the gene expression profile related to the submergence condition. We wrote a perl script for the prediction of miRNA target gene. The position based feature of the script increases the overall specificity of the program. Our perl script performed well on the genomic data of Oryza sativa and produced significant results with their positions. These results were analyzed on the basis of complementarity and the statistical scores are used to find out the most probable binding regions. These predicted binding regions are aligned with their respective miRNAs to find out the consensus sequence. We scored the alignment using a position dependent, mismatch penalty system. We also identified the rate of conservation of bases at a particular position for all the predicted binding regions and it was found that all the predicted binding regions maintain above 70% rate of conservation of bases. Conclusion: Our approach provides a novel framework for screening the genome of Oryza sativa. It can be broadly applied to identify complementarity specific miRNA targets computationally by doing a little modification of the script depending on the type of the miRNA. PMID:24250112

  10. Red rice (Oryza sativa L.) emergence characteristics and influence on rice (O. sativa) yield at different planting dates

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Cultivated rice yield losses due to red rice infestation vary by cultivar, red rice density, and duration of interference. The competition effects of red rice could be influenced further by emergence characteristics, red rice biotype, and planting time of cultivated rice. We aimed to characterize th...

  11. Low pH-induced changes of antioxidant enzyme and ATPase activities in the roots of rice (Oryza sativa L.) seedlings.

    PubMed

    Zhang, Yi-Kai; Zhu, De-Feng; Zhang, Yu-Ping; Chen, Hui-Zhe; Xiang, Jing; Lin, Xian-Qing

    2015-01-01

    Soil acidification is the main problem in the current rice production. Here, the effects of low pH on the root growth, reactive oxygen species metabolism, plasma membrane functions, and the transcript levels of the related genes were investigated in rice seedlings (Oryza sativa L.) in a hydroponic system at pH 3.5, 4.5, and 5.5. There were two hybrid rice cultivars in this trial, including Yongyou 12 (YY12, a japonica hybrid) and Zhongzheyou 1 (ZZY1, an indica hybrid). Higher H+ activity markedly decreased root length, the proportion of fine roots, and dry matter production, but induced a significant accumulation of hydrogen peroxide (H2O2), and led to serious lipid peroxidation in the roots of the two varieties. The transcript levels of copper/zinc superoxide dismutase 1 (Cu/Zn SOD1), copper/zinc superoxide dismutase 2 (Cu/Zn SOD2), catalase A (CATA) and catalase B (CATB) genes in YY12 and ZZY1 roots were significantly down-regulated after low pH exposure for two weeks. Meanwhile, a significant decrease was observed in the expression of the P-type Ca2+-ATPases in roots at pH 3.5. The activities of antioxidant enzymes (SOD, CAT) and plasma membrane (PM) Ca2+-ATPase in the two varieties were dramatically inhibited by strong rhizosphere acidification. However, the expression levels of ascorbate peroxidase 1 (APX1) and PM H+-ATPase isoform 7 were up-regulated under H+ stress compared with the control. Significantly higher activities of APX and PM H+-ATPase could contribute to the adaptation of rice roots to low pH.

  12. Zinc absorption from low phytic acid genotypes of maize (Zea mays L.), Barley (Hordeum vulgare L.), and Rice (Oryza sativa L.) assessed in a suckling rat pup model.

    PubMed

    Lönnerdal, Bo; Mendoza, Concepcion; Brown, Kenneth H; Rutger, J Neil; Raboy, Victor

    2011-05-11

    Dietary phytic acid is a major causative factor for low Zn bioavailability in many cereal- and legume-based diets. The bioavailability of Zn in seed of low phytic acid (lpa) variants of maize ( Zea mays L.), rice ( Oryza sativa L.), and barley ( Hordeum vulgare L.) was evaluated using a suckling rat pup model. Suckling rat pups (14 days old, n = 6-8/treatment) were fasted for 6 h and intubated with (65)Zn-radiolabeled suspensions prepared using seed produced by either wild-type (normal phytic acid) or lpa genotypes of each cereal. Test solutions were radiolabeled overnight (all genotypes) or immediately prior to intubation (barley genotypes). Pups were killed 6 h postintubation and tissues removed and counted in a gamma counter. Zn absorption was low from wild-type genotypes of maize (21, 33%) and rice (26%), and phytic acid reduction resulted in significantly higher Zn absorption, 47-52 and 35-52%, respectively. Zn absorption from wild-type barley incubated overnight was high (86-91%), and phytate reduction did not improve Zn absorption (84-90%), which is likely due to endogenous phytase activity. When the wild-type barley solutions were prepared immediately before intubation, Zn absorption was significantly lower (63, 78%) than from the lpa cultivars (92, 96%). Variation in seed or flour phenolic acid levels did not affect Zn absorption. Differences in seed Zn levels did not substantially affect Zn absorption. Thus, when phytic acid is abundant in a diet, it has a larger effect on Zn absorption than the level of Zn. Therefore, reducing the phytic acid content of staple cereal grains may contribute to enhancing Zn nutrition of populations consuming these staple foods.

  13. The Effect of Green Synthesized CuO Nanoparticles on Callogenesis and Regeneration of Oryza sativa L.

    PubMed Central

    Anwaar, Sadaf; Maqbool, Qaisar; Jabeen, Nyla; Nazar, Mudassar; Abbas, Fazal; Nawaz, Bushra; Hussain, Talib; Hussain, Syed Z.

    2016-01-01

    In this study, we have investigated the effect of copper oxide nanoparticles (CuO-NPs) on callogenesis and regeneration of Oryza sativa L (Super Basmati, Basmati 2000, Basmati 370, and Basmati 385). In this regard, CuO-NPs have been bio-synthesized via Azadirachta indica leaf extract. Scanning electron microscope (SEM) analysis depicts average particle size of 40 ± 5 nm with highly homogenous and spherical morphology. X-ray diffraction (XRD) and Fourier transform infrared spectroscopy (FTIR) have been employed to confirm the phase purity of the synthesized NPs. It is found that CuO-NPs exhibit very promising results against callus induction. It is attributed to the fact that green synthesized CuO-NPs at optimum dosage possess very supportive effects on plant growth parameters. In contrast to callogenesis, differential regeneration pattern has been observed against all of the examined O. sativa L. indigenous verities. Overall observation concludes that CuO, being one of the essential plant nutrients, has greatly tailored the nutritive properties at nano-scale. PMID:27630655

  14. Purification, crystallization and preliminary X-ray diffraction analysis of pathogen-inducible oxygenase (PIOX) from Oryza sativa

    SciTech Connect

    Lloyd, Tracy; Krol, Adam; Campanaro, Danielle; Malkowski, Michael

    2006-04-01

    The heme-containing membrane-associated fatty-acid α-dioxygenase pathogen-inducible oxygenase (PIOX) from O. sativa has been crystallized and a data set collected to 3.0 Å using a rotating-anode generator and R-AXIS IV detector. Pathogen-inducible oxygenase (PIOX) is a heme-containing membrane-associated protein found in monocotyledon and dicotyledon plants that utilizes molecular oxygen to convert polyunsaturated fatty acids into their corresponding 2R-hydroperoxides. PIOX is a member of a larger family of fatty-acid α-dioxygenases that includes the mammalian cyclooxygenase enzymes cyclooxygenase 1 and 2 (COX-1 and COX-2). Single crystals of PIOX from rice (Oryza sativa) have been grown from MPD using recombinant protein expressed in Escherichia coli and subsequently extracted utilizing decyl maltoside as the solubilizing detergent. Crystals diffract to 3.0 Å resolution using a rotating-anode generator and R-AXIS IV detector, and belong to space group P1. Based on the Matthews coefficient and self-rotation function analyses, there are presumed to be four molecules in the asymmetric unit related by noncrystallographic 222 symmetry.

  15. N-glycan maturation is crucial for cytokinin-mediated development and cellulose synthesis in Oryza sativa.

    PubMed

    Fanata, Wahyu Indra Duwi; Lee, Kyoung Hwan; Son, Bo Hwa; Yoo, Jae Yong; Harmoko, Rikno; Ko, Ki Seong; Ramasamy, Nirmal Kumar; Kim, Kyung Hwa; Oh, Doo-Byoung; Jung, Hyun Suk; Kim, Jae-Yean; Lee, Sang Yeol; Lee, Kyun Oh

    2013-03-01

    To explore the physiological significance of N-glycan maturation in the plant Golgi apparatus, gnt1, a mutant with loss of N-acetylglucosaminyltransferase I (GnTI) function, was isolated in Oryza sativa. gnt1 exhibited complete inhibition of N-glycan maturation and accumulated high-mannose N-glycans. Phenotypic analyses revealed that gnt1 shows defective post-seedling development and incomplete cell wall biosynthesis, leading to symptoms such as failure in tiller formation, brittle leaves, reduced cell wall thickness, and decreased cellulose content. The developmental defects of gnt1 ultimately resulted in early lethality without transition to the reproductive stage. However, callus induced from gnt1 seeds could be maintained for periods, although it exhibited a low proliferation rate, small size, and hypersensitivity to salt stress. Shoot regeneration and dark-induced leaf senescence assays indicated that the loss of GnTI function results in reduced sensitivity to cytokinin in rice. Reduced expression of A-type O. sativa response regulators that are rapidly induced by cytokinins in gnt1 confirmed that cytokinin signaling is impaired in the mutant. These results strongly support the proposed involvement of N-glycan maturation in transport as well as in the function of membrane proteins that are synthesized via the endomembrane system.

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

    PubMed Central

    Meneses Martínez, Allan; Calvo, Amanda; Muñoz, Melania

    2016-01-01

    Wild crop relatives are an important source of genetic diversity for crop improvement. Diversity estimates are generally lacking for many wild crop relatives. The objective of the present study was to analyze how genetic diversity is distributed within and among populations of the wild rice species Oryza glumaepatula in Costa Rica. We also evaluated the likelihood of gene flow between wild and commercial rice species because the latter is commonly sympatric with wild rice populations. Introgression may change wild species by incorporating alleles from domesticated species, increasing the risk of losing original variation. Specimens from all known O. glumaepatula populations in Costa Rica were analyzed with 444 AFLP markers to characterize genetic diversity and structure. We also compared genetic diversity estimates between O. glumaepatula specimens and O. sativa commercial rice. Our results showed that O. glumaepatula populations in Costa Rica have moderately high levels of genetic diversity, comparable to those found in South American populations. Despite the restricted distribution of this species in Costa Rica, populations are fairly large, reducing the effects of drift on genetic diversity. We found a dismissible but significant structure (θ = 0.02 ± 0.001) among populations. A Bayesian structure analysis suggested that some individuals share a significant proportion of their genomes with O. sativa. These results suggest that gene flow from cultivated O. sativa populations may have occurred in the recent past. These results expose an important biohazard: recurrent hybridization may reduce the genetic diversity of this wild rice species. Introgression may transfer commercial traits into O. glumaepatula, which in turn could alter genetic diversity and increase the likelihood of local extinction. These results have important implications for in situ conservation strategies of the only wild populations of O. glumaepatula in Costa Rica. PMID:27077002

  17. Comparative transcriptome profiling of the early response to Magnaporthe oryzae in durable resistant vs susceptible rice (Oryza sativa L.) genotypes.

    PubMed

    Bagnaresi, Paolo; Biselli, Chiara; Orrù, Luigi; Urso, Simona; Crispino, Laura; Abbruscato, Pamela; Piffanelli, Pietro; Lupotto, Elisabetta; Cattivelli, Luigi; Valè, Giampiero

    2012-01-01

    Durable resistance to blast, the most significant fungal disease of rice, represents an agronomically relevant character. Gigante Vercelli (GV) and Vialone Nano (VN) are two old temperate japonica Italian rice cultivars with contrasting response to blast infection: GV displays durable and broad resistance while VN is highly susceptible. RNA-seq was used to dissect the early molecular processes deployed during the resistance response of GV at 24 h after blast inoculation. Differential gene expression analysis identified 1,070 and 1,484 modulated genes, of which 726 and 699 were up regulated in response to infection in GV and VN, respectively. Gene ontology (GO) enrichment analyses revealed a set of GO terms enriched in both varieties but, despite this commonality, the gene sets contributing to common GO enriched terms were dissimilar. The expression patterns of genes grouped in GV-specific enriched GO terms were examined in detail including at the transcript isoform level. GV exhibited a dramatic up-regulation of genes encoding diterpene phytoalexin biosynthetic enzymes, flavin-containing monooxygenase, class I chitinase and glycosyl hydrolase 17. The sensitivity and high dynamic range of RNA-seq allowed the identification of genes critically involved in conferring GV resistance during the early steps of defence perception-signalling. These included chitin oligosaccharides sensing factors, wall associated kinases, MAPK cascades and WRKY transcription factors. Candidate genes with expression patterns consistent with a potential role as GV-specific functional resistance (R) gene(s) were also identified. This first application of RNA-seq to dissect durable blast resistance supports a crucial role of the prompt induction of a battery of responses including defence-related genes as well as members of gene families involved in signalling and pathogen-related gene expression regulation.

  18. Genetic diversity and classification of Oryza sativa with emphasis on Chinese rice germplasm

    PubMed Central

    Wang, C-H; Zheng, X-M; Xu, Q; Yuan, X-P; Huang, L; Zhou, H-F; Wei, X-H; Ge, S

    2014-01-01

    Despite extensive studies on cultivated rice, the genetic structure and subdivision of this crop remain unclear at both global and local scales. Using 84 nuclear simple sequence repeat markers, we genotyped a panel of 153 global rice cultivars covering all previously recognized groups and 826 cultivars representing the diversity of Chinese rice germplasm. On the basis of model-based grouping, neighbour-joining tree and principal coordinate analysis, we confirmed the widely accepted five major groups of rice cultivars (indica, aus, aromatic, temperate japonica and tropical japonica), and demonstrated that rayada rice was unique in genealogy and should be treated as a new (the sixth) major group of rice germplasm. With reference to the global classification of rice cultivars, we identified three major groups (indica, temperate japonica and tropical japonica) in Chinese rice germplasm and showed that Chinese temperate japonica contained higher diversity than that of global samples, whereas Chinese indica and tropical japonica maintained slightly lower diversity than that present in the global samples. Particularly, we observed that all seasonal, drought-tolerant and endosperm types occurred within each of three major groups of Chinese cultivars, which does not support previous claims that seasonal differentiation exists in Indica and drought-tolerant differentiation is present in Japonica. It is most likely that differentiation of cultivar types arose multiple times stemming from artificial selection for adaptation to local environments. PMID:24326293

  19. Analysis of the genetic diversity of Chinese native Cannabis sativa cultivars by using ISSR and chromosome markers.

    PubMed

    Zhang, L G; Chang, Y; Zhang, X F; Guan, F Z; Yuan, H M; Yu, Y; Zhao, L J

    2014-12-12

    Hemp (Cannabis sativa) is an important fiber crop, and native cultivars exist widely throughout China. In the present study, we analyzed the genetic diversity of 27 important Chinese native hemp cultivars, by using inter-simple sequence repeats (ISSR) and chromosome markers. We determined the following chromosome formulas: 2n = 20 = 14m + 6sm; 2n = 20 = 20m; 2n = 20 = 18m + 2sm; 2n = 20 = 16m + 4sm; and 2n = 20 = 12m + 8sm. The results of our ISSR analysis revealed the genetic relationships among the 27 cultivars; these relationships were analyzed by using the unweighted pair-group method based on DNA polymorphism. Our results revealed that all of the native cultivars showed considerable genetic diversity. At a genetic distance of 0.324, the 27 varieties could be classified into five categories; this grouping corresponded well with the chromosome formulas. All of the investigated hemp cultivars represent relatively primitive types; moreover, the genetic distances show a geographical distribution, with a small amount of regional hybridity.

  20. Genetic architecture of cold tolerance in rice (Oryza sativa) determined through high resolution genome-wide analysis

    PubMed Central

    Shakiba, Ehsan; Edwards, Jeremy D.; Jodari, Farman; Duke, Sara E.; Baldo, Angela M.; Korniliev, Pavel; McCouch, Susan R.; Eizenga, Georgia C.

    2017-01-01

    Cold temperature is an important abiotic stress which negatively affects morphological development and seed production in rice (Oryza sativa L.). At the seedling stage, cold stress causes poor germination, seedling injury and poor stand establishment; and at the reproductive stage cold decreases seed yield. The Rice Diversity Panel 1 (RDP1) is a global collection of over 400 O. sativa accessions representing the five major subpopulations from the INDICA and JAPONICA varietal groups, with a genotypic dataset consisting of 700,000 SNP markers. The objectives of this study were to evaluate the RDP1 accessions for the complex, quantitatively inherited cold tolerance traits at the germination and reproductive stages, and to conduct genome-wide association (GWA) mapping to identify SNPs and candidate genes associated with cold stress at these stages. GWA mapping of the germination index (calculated as percent germination in cold divided by warm treatment) revealed 42 quantitative trait loci (QTLs) associated with cold tolerance at the seedling stage, including 18 in the panel as a whole, seven in temperate japonica, six in tropical japonica, 14 in JAPONICA, and nine in INDICA, with five shared across all subpopulations. Twenty-two of these QTLs co-localized with 32 previously reported cold tolerance QTLs. GWA mapping of cold tolerance at the reproductive stage detected 29 QTLs, including seven associated with percent sterility, ten with seed weight per panicle, 14 with seed weight per plant and one region overlapping for two traits. Fifteen co-localized with previously reported QTLs for cold tolerance or yield components. Candidate gene ontology searches revealed these QTLs were associated with significant enrichment for genes related to with lipid metabolism, response to stimuli, response to biotic stimuli (suggesting cross-talk between biotic and abiotic stresses), and oxygen binding. Overall the JAPONICA accessions were more tolerant to cold stress than INDICA

  1. Genetic dissection of ozone tolerance in rice (Oryza sativa L.) by a genome-wide association study

    PubMed Central

    Ueda, Yoshiaki; Frimpong, Felix; Qi, Yitao; Matthus, Elsa; Wu, Linbo; Höller, Stefanie; Kraska, Thorsten; Frei, Michael

    2015-01-01

    Tropospheric ozone causes various negative effects on plants and affects the yield and quality of agricultural crops. Here, we report a genome-wide association study (GWAS) in rice (Oryza sativa L.) to determine candidate loci associated with ozone tolerance. A diversity panel consisting of 328 accessions representing all subgroups of O. sativa was exposed to ozone stress at 60 nl l–1 for 7h every day throughout the growth season, or to control conditions. Averaged over all genotypes, ozone significantly affected biomass-related traits (plant height –1.0%, shoot dry weight –15.9%, tiller number –8.3%, grain weight –9.3%, total panicle weight –19.7%, single panicle weight –5.5%) and biochemical/physiological traits (symptom formation, SPAD value –4.4%, foliar lignin content +3.4%). A wide range of genotypic variance in response to ozone stress were observed in all phenotypes. Association mapping based on more than 30 000 single-nucleotide polymorphism (SNP) markers yielded 16 significant markers throughout the genome by applying a significance threshold of P<0.0001. Furthermore, by determining linkage disequilibrium blocks associated with significant SNPs, we gained a total of 195 candidate genes for these traits. The following sequence analysis revealed a number of novel polymorphisms in two candidate genes for the formation of visible leaf symptoms, a RING and an EREBP gene, both of which are involved in cell death and stress defence reactions. This study demonstrated substantial natural variation of responses to ozone in rice and the possibility of using GWAS in elucidating the genetic factors underlying ozone tolerance. PMID:25371505

  2. Evolution of microRNA genes in Oryza sativa and Arabidopsis thaliana: an update of the inverted duplication model.

    PubMed

    Zhang, Yun; Jiang, Wen-kai; Gao, Li-zhi

    2011-01-01

    The origin and evolution of microRNA (miRNA) genes, which are of significance in tuning and buffering gene expressions in a number of critical cellular processes, have long attracted evolutionary biologists. However, genome-wide perspectives on their origins, potential mechanisms of their de novo generation and subsequent evolution remain largely unsolved in flowering plants. Here, genome-wide analyses of Oryza sativa and Arabidopsis thaliana revealed apparently divergent patterns of miRNA gene origins. A large proportion of miRNA genes in O. sativa were TE-related and MITE-related miRNAs in particular, whereas the fraction of these miRNA genes much decreased in A. thaliana. Our results show that the majority of TE-related and pseudogene-related miRNA genes have originated through inverted duplication instead of segmental or tandem duplication events. Based on the presented findings, we hypothesize and illustrate the four likely molecular mechanisms to de novo generate novel miRNA genes from TEs and pseudogenes. Our rice genome analysis demonstrates that non-MITEs and MITEs mediated inverted duplications have played different roles in de novo generating miRNA genes. It is confirmed that the previously proposed inverted duplication model may give explanations for non-MITEs mediated duplication events. However, many other miRNA genes, known from the earlier proposed model, were rather arisen from MITE transpositions into target genes to yield binding sites. We further investigated evolutionary processes spawned from de novo generated to maturely-formed miRNA genes and their regulatory systems. We found that miRNAs increase the tunability of some gene regulatory systems with low gene copy numbers. The results also suggest that gene balance effects may have largely contributed to the evolution of miRNA regulatory systems.

  3. Genetic dissection of ozone tolerance in rice (Oryza sativa L.) by a genome-wide association study.

    PubMed

    Ueda, Yoshiaki; Frimpong, Felix; Qi, Yitao; Matthus, Elsa; Wu, Linbo; Höller, Stefanie; Kraska, Thorsten; Frei, Michael

    2015-01-01

    Tropospheric ozone causes various negative effects on plants and affects the yield and quality of agricultural crops. Here, we report a genome-wide association study (GWAS) in rice (Oryza sativa L.) to determine candidate loci associated with ozone tolerance. A diversity panel consisting of 328 accessions representing all subgroups of O. sativa was exposed to ozone stress at 60 nl l(-1) for 7h every day throughout the growth season, or to control conditions. Averaged over all genotypes, ozone significantly affected biomass-related traits (plant height -1.0%, shoot dry weight -15.9%, tiller number -8.3%, grain weight -9.3%, total panicle weight -19.7%, single panicle weight -5.5%) and biochemical/physiological traits (symptom formation, SPAD value -4.4%, foliar lignin content +3.4%). A wide range of genotypic variance in response to ozone stress were observed in all phenotypes. Association mapping based on more than 30 000 single-nucleotide polymorphism (SNP) markers yielded 16 significant markers throughout the genome by applying a significance threshold of P<0.0001. Furthermore, by determining linkage disequilibrium blocks associated with significant SNPs, we gained a total of 195 candidate genes for these traits. The following sequence analysis revealed a number of novel polymorphisms in two candidate genes for the formation of visible leaf symptoms, a RING and an EREBP gene, both of which are involved in cell death and stress defence reactions. This study demonstrated substantial natural variation of responses to ozone in rice and the possibility of using GWAS in elucidating the genetic factors underlying ozone tolerance.

  4. Cloning and characterization of the ONAC106 gene from Oryza sativa cultivar Kuku Belang

    NASA Astrophysics Data System (ADS)

    Basri, Khairunnisa; Sukiran, Noor Liyana; Zainal, Zamri

    2016-11-01

    Plants possess different mechanisms in stress response, where induction of stress-responsive genes provides tolerance to unfavorable conditions. Stress-responsive genes are characterized for functional and regulatory genes that help in overcoming stress by molecular, biochemical and morphological adaptations. NAC transcription factors are one of the regulatory proteins that involved in stress signaling pathway. A putative NAC transcription factor, ONAC016 was identified from drought transcriptomic data. Our data suggested that ONAC106 was induced by drought, but its function in abiotic stress is still unclear. In silico analysis of ONAC106 showed that this gene encodes 334 amino acids, and its protein consists of NAM (No Apical Meristem) domain. The orthologue of ONAC106 was present in several Poaceae family members, suggesting that ONAC106 is unique to monocot plants only. We found that ONAC106 was induced by salt and cold stresses, indicating that this gene involves in abiotic stress response. In addition, we also found that ONAC106 might function in defense response to pathogen invasion. The ABRE (Abscisic Acid Regulatory Element) cis-element was identified in the promoter region of ONAC106, suggesting that it may involve in the abscisic acid (ABA)-dependent signaling pathway. Based on this preliminary result, we hypothesize that ONAC106 may play a role in abiotic stress response by regulating ABA-responsive genes.

  5. Uptake, translocation and transformation of antimony in rice (Oryza sativa L.) seedlings.

    PubMed

    Cai, Fei; Ren, Jinghua; Tao, Shu; Wang, Xilong

    2016-02-01

    Antimony (Sb), as a toxic metalloid, has been gaining increasing research concerns due mainly to its severe pollution in many places. Rice has been identified to be the dominant intake route of Sb by residents close to the Sb mining areas. A hydroponic experiment was conducted to investigate the difference in uptake, translocation and transformation of Sb in rice seedlings of four cultivars exposed to 0.2 or 1.0 mg/L of Sb(V). The results showed that mass concentration of iron plaque (mg/kg FW) formed at the root surfaces of cultivar N was the highest among all tested cultivars at both low and high exposure levels of Sb(V). The accumulated Sb concentration in iron plaque significantly increased with an increase in mass concentration of iron plaque formed at the rice root. The total amount of iron plaque (mg/pot) at rice root generally increased with increasing exposed Sb(V) concentration, which was closely associated with the increasing lipid peroxidation in roots. Concentration percentage of Sb in rice root significantly reduced as the corresponding value in the iron plaque increased, suggesting that iron plaque formation strongly suppressed uptake of Sb by rice root. Sb concentration in rice tissues followed an order: root > stem, leaf. The japonica rice (cultivars N and Z) exhibited a stronger translocation tendency of Sb from root to stem than indica hybrid rice (cultivars F and G). Translocation of Sb from root of cultivar F to its stem and leaf was sharply enhanced with increasing Sb exposure concentration. Sb(V) could be reduced to Sb(III) in rice tissues, especially in stems (10-26% of the total Sb). For the sake of food safety, the difference in uptake, translocation and transformation of Sb in rice species planted in Sb-contaminated soils should be taken into consideration.

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

    PubMed Central

    2012-01-01

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

  7. CSN6, a subunit of the COP9 signalosome, is involved in early response to iron deficiency in Oryza sativa

    PubMed Central

    Tan, Song; Liu, Fang; Pan, Xiao-Xi; Zang, Yue-Peng; Jin, Fei; Zu, Wei-Xi; Qi, Xiao-Ting; Xiao, Wei; Yin, Li-Ping

    2016-01-01

    The COP9 signalosome (CSN) plays an important role in proteasome-mediated degradation by regulating CUL1 rubylation of the SCF ligase and is involved in many crucial biological processes. Here, we demonstrate a link between IDEF1 accumulation and the decline in COP9 derubylation activity in response to iron deficiency (-Fe) in rice (Oryza sativa). CSN6 expression is rapidly down-regulated during Fe depletion, contributing to reduced CSN activity, as judged by CSN5 and CUL1 expression, indicating CSN6 is involved in the early stage response of -Fe. In contrast to CSN6, the IDEF1 protein and expression of several iron uptake/utilisation-related genes are increased in response to -Fe. Thus, we constructed CSN6 transgenic sense and antisense lines and found that experimental depletion of CSN6 results in accumulation of the IDEF1 protein and up-regulation of several iron uptake/utilisation-related genes. Furthermore, IDEF1 can be decorated with K48-linked polyubiquitin and degraded via the 26S proteasome. Accumulated IDEF1 in antisense lines led to increased chlorophyll and Fe content in seedlings during -Fe. Collectively, the cellular CSN6 level is decreased during early stages of -Fe to ensure the rapid accumulation of IDEF1, which in turn up-regulates several iron uptake/utilisation-related genes to help overcome -Fe stress in rice. PMID:27137867

  8. Roles of plant hormones and anti-apoptosis genes during drought stress in rice (Oryza sativa L.).

    PubMed

    Ubaidillah, Mohammad; Safitri, Fika Ayu; Jo, Jun-Hyeon; Lee, Sang-Kyu; Hussain, Adil; Mun, Bong-Gyu; Chung, Il Kyung; Yun, Byung-Wook; Kim, Kyung-Min

    2016-12-01

    We previously identified the rice (Oryza sativa) senescence-associated gene OsSAP which encodes a highly conserved protein involved in anti-apoptotic activity. This novel Bax suppressor-related gene regulates tolerance to multiple stresses in yeast. Here, we show the effects of drought stress on leaf and root tissues of plants over-expressing OsSAP in relation to the levels of phytohormones, abscisic acid (ABA), jasmonic acid (JA), indole-3-carboxylic acid (ICA), gibberellic acid (GA3), and zeatin. Results showed that rice plants over-expressing SAP were tolerant to drought stress compared to wild type and the plants over-expressing AtBI-1, which is a homolog of the human Bax inhibitor-1 in Arabidopsis. ABA and JA levels in OsSAP and AtBI-1 transgenic plants consistently increased up to at least 3 days after drought treatment, whereas lower GA3 levels were recorded during early drought period. Comparison between control and transgenic plants overexpressing anti-apoptosis genes OsSAP and AtBI-1 resulted in different patterns of hormone levels, indicating that these genes are involved in the plant responses to drought stress and present an opportunity for further study on drought stress tolerance in rice and other plant species.

  9. Foliar uptake of radiocaesium from irrigation water by paddy rice (Oryza sativa): an overlooked pathway in contaminated environments.

    PubMed

    Uematsu, Shinichiro; Vandenhove, Hildegarde; Sweeck, Lieve; Hees, May Van; Wannijn, Jean; Smolders, Erik

    2017-04-01

    Flooded (paddy) rice (Oryza sativa) can take up ions from the irrigation water by foliar uptake via the exposed stem base. We hypothesised that the stem base uptake of radiocaesium (RCs) is a pathway for rice grown in RCs-contaminated environments. We developed a bi-compartmental device which discriminates the stem base from root RCs uptake from solutions, thereby using RCs isotopes ((137) Cs and (134) Cs) with < 2% solution leak between the compartments. Radiocaesium uptake was linear over time (0-24 h). Radiocaesium uptake to the entire plant, expressed per dry weight of the exposed parts, was sixfold higher for the roots than for the exposed stem base. At equal RCs concentrations in both compartments, the exposed stem base and root uptake contributed almost equally to the total shoot RCs concentrations. Reducing potassium supply to the roots not only increased the root RCs uptake but also increased RCs uptake by the stem base. This study was the first to experimentally demonstrate active and internally regulated RCs uptake by the stem base of rice. Scenario calculations for the Fukushima-affected area predict that RCs in irrigation water could be an important source of RCs in rice as indirectly suggested from field data.

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

    PubMed

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

    2016-07-01

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

  11. Oryza sativa H+-ATPase (OSA) is Involved in the Regulation of Dumbbell-Shaped Guard Cells of Rice.

    PubMed

    Toda, Yosuke; Wang, Yin; Takahashi, Akira; Kawai, Yuya; Tada, Yasuomi; Yamaji, Naoki; Feng Ma, Jian; Ashikari, Motoyuki; Kinoshita, Toshinori

    2016-06-01

    The stomatal apparatus consists of a pair of guard cells and regulates gas exchange between the leaf and atmosphere. In guard cells, blue light (BL) activates H(+)-ATPase in the plasma membrane through the phosphorylation of its penultimate threonine, mediating stomatal opening. Although this regulation is thought to be widely adopted among kidney-shaped guard cells in dicots, the molecular basis underlying that of dumbbell-shaped guard cells in monocots remains unclear. Here, we show that H(+)-ATPases are involved in the regulation of dumbbell-shaped guard cells. Stomatal opening of rice was promoted by the H(+)-ATPase activator fusicoccin and by BL, and the latter was suppressed by the H(+)-ATPase inhibitor vanadate. Using H(+)-ATPase antibodies, we showed the presence of phosphoregulation of the penultimate threonine in Oryza sativa H(+)-ATPases (OSAs) and localization of OSAs in the plasma membrane of guard cells. Interestingly, we identified one H(+)-ATPase isoform, OSA7, that is preferentially expressed among the OSA genes in guard cells, and found that loss of function of OSA7 resulted in partial insensitivity to BL. We conclude that H(+)-ATPase is involved in BL-induced stomatal opening of dumbbell-shaped guard cells in monocotyledon species.

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

    PubMed

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

    2014-03-01

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

  13. Elemental bioimaging of tissue level trace metal distributions in rice seeds (Oryza sativa L.) from a mining area in China.

    PubMed

    Basnet, Priyanka; Amarasiriwardena, Dulasiri; Wu, Fengchang; Fu, Zhiyou; Zhang, Tao

    2014-12-01

    Rice is a staple food and major source of nutrients, but it also bioaccumulates toxic elements. In this study, laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) was used to determine tissue-level trace metal spatial distribution in rice (Oryza sativa) seeds from the active Xikuangshan Sb mine area in China. Whole grain quantified elemental bioimages showed the highest concentration of Zn (1755 mg/kg) in the embryo andmicro zones of elevated Sb, As, Pb, Cd as high as 280, 57, 31 and 830 mg/kg, respectively on the husk/bran/endosperm tissues. Bioimages suggest that both Sb and Cd may be competing with Zn for binding sites. Both Sb(III) and Sb(V) species were detected in seeds from upstream and downstream fields indicating the presence of toxic Sb(III). Brown rice is a good source of Zn, but white rice is a safer option if rice is grown in a polluted area.

  14. γ-Aminobutyric acid addition alleviates ammonium toxicity by limiting ammonium accumulation in rice (Oryza sativa) seedlings.

    PubMed

    Ma, Xiaoling; Zhu, Changhua; Yang, Na; Gan, Lijun; Xia, Kai

    2016-12-01

    Excessive use of nitrogen (N) fertilizer has increased ammonium (NH4(+) ) accumulation in many paddy soils to levels that reduce rice vegetative biomass and yield. Based on studies of NH4(+) toxicity in rice (Oryza sativa, Nanjing 44) seedlings cultured in agar medium, we found that NH4(+) concentrations above 0.75 mM inhibited the growth of rice and caused NH4(+) accumulation in both shoots and roots. Use of excessive NH4(+) also induced rhizosphere acidification and inhibited the absorption of K, Ca, Mg, Fe and Zn in rice seedlings. Under excessive NH4(+) conditions, exogenous γ-aminobutyric acid (GABA) treatment limited NH4(+) accumulation in rice seedlings, reduced NH4(+) toxicity symptoms and promoted plant growth. GABA addition also reduced rhizosphere acidification and alleviated the inhibition of Ca, Mg, Fe and Zn absorption caused by excessive NH4(+) . Furthermore, we found that the activity of glutamine synthetase/NADH-glutamate synthase (GS; EC 6.3.1.2/NADH-GOGAT; EC1.4.1.14) in root increased gradually as the NH4(+) concentration increased. However, when the concentration of NH4(+) is more than 3 mM, GABA treatment inhibited NH4(+) -induced increases in GS/NADH-GOGAT activity. The inhibition of ammonium assimilation may restore the elongation of seminal rice roots repressed by high NH4(+) . These results suggest that mitigation of ammonium accumulation and assimilation is essential for GABA-dependent alleviation of ammonium toxicity in rice seedlings.

  15. Global Analysis of Lysine Acetylation Suggests the Involvement of Protein Acetylation in Diverse Biological Processes in Rice (Oryza sativa)

    PubMed Central

    Zhong, Xiaoxian; Tan, Feng; Mujahid, Hana; Zhang, Jian; Nanduri, Bindu; Peng, Zhaohua

    2014-01-01

    Lysine acetylation is a reversible, dynamic protein modification regulated by lysine acetyltransferases and deacetylases. Recent advances in high-throughput proteomics have greatly contributed to the success of global analysis of lysine acetylation. A large number of proteins of diverse biological functions have been shown to be acetylated in several reports in human cells, E.coli, and dicot plants. However, the extent of lysine acetylation in non-histone proteins remains largely unknown in monocots, particularly in the cereal crops. Here we report the mass spectrometric examination of lysine acetylation in rice (Oryza sativa). We identified 60 lysine acetylated sites on 44 proteins of diverse biological functions. Immunoblot studies further validated the presence of a large number of acetylated non-histone proteins. Examination of the amino acid composition revealed substantial amino acid bias around the acetylation sites and the amino acid preference is conserved among different organisms. Gene ontology analysis demonstrates that lysine acetylation occurs in diverse cytoplasmic, chloroplast and mitochondrial proteins in addition to the histone modifications. Our results suggest that lysine acetylation might constitute a regulatory mechanism for many proteins, including both histones and non-histone proteins of diverse biological functions. PMID:24586658

  16. Structural understanding of the recycling of oxidized ascorbate by dehydroascorbate reductase (OsDHAR) from Oryza sativa L. japonica.

    PubMed

    Do, Hackwon; Kim, Il-Sup; Jeon, Byoung Wook; Lee, Chang Woo; Park, Ae Kyung; Wi, Ah Ram; Shin, Seung Chul; Park, Hyun; Kim, Young-Saeng; Yoon, Ho-Sung; Kim, Han-Woo; Lee, Jun Hyuck

    2016-01-18

    Dehydroascorbate reductase (DHAR) is a key enzyme involved in the recycling of ascorbate, which catalyses the glutathione (GSH)-dependent reduction of oxidized ascorbate (dehydroascorbate, DHA). As a result, DHAR regenerates a pool of reduced ascorbate and detoxifies reactive oxygen species (ROS). In previous experiments involving transgenic rice, we observed that overexpression of DHAR enhanced grain yield and biomass. Since the structure of DHAR is not available, the enzymatic mechanism is not well-understood and remains poorly characterized. To elucidate the molecular basis of DHAR catalysis, we determined the crystal structures of DHAR from Oryza sativa L. japonica (OsDHAR) in the native, ascorbate-bound, and GSH-bound forms and refined their resolutions to 1.9, 1.7, and 1.7 Å, respectively. These complex structures provide the first information regarding the location of the ascorbate and GSH binding sites and their interacting residues. The location of the ascorbate-binding site overlaps with the GSH-binding site, suggesting a ping-pong kinetic mechanism for electron transfer at the common Cys20 active site. Our structural information and mutagenesis data provide useful insights into the reaction mechanism of OsDHAR against ROS-induced oxidative stress in rice.

  17. CSN6, a subunit of the COP9 signalosome, is involved in early response to iron deficiency in Oryza sativa

    NASA Astrophysics Data System (ADS)

    Tan, Song; Liu, Fang; Pan, Xiao-Xi; Zang, Yue-Peng; Jin, Fei; Zu, Wei-Xi; Qi, Xiao-Ting; Xiao, Wei; Yin, Li-Ping

    2016-05-01

    The COP9 signalosome (CSN) plays an important role in proteasome-mediated degradation by regulating CUL1 rubylation of the SCF ligase and is involved in many crucial biological processes. Here, we demonstrate a link between IDEF1 accumulation and the decline in COP9 derubylation activity in response to iron deficiency (-Fe) in rice (Oryza sativa). CSN6 expression is rapidly down-regulated during Fe depletion, contributing to reduced CSN activity, as judged by CSN5 and CUL1 expression, indicating CSN6 is involved in the early stage response of -Fe. In contrast to CSN6, the IDEF1 protein and expression of several iron uptake/utilisation-related genes are increased in response to -Fe. Thus, we constructed CSN6 transgenic sense and antisense lines and found that experimental depletion of CSN6 results in accumulation of the IDEF1 protein and up-regulation of several iron uptake/utilisation-related genes. Furthermore, IDEF1 can be decorated with K48-linked polyubiquitin and degraded via the 26S proteasome. Accumulated IDEF1 in antisense lines led to increased chlorophyll and Fe content in seedlings during -Fe. Collectively, the cellular CSN6 level is decreased during early stages of -Fe to ensure the rapid accumulation of IDEF1, which in turn up-regulates several iron uptake/utilisation-related genes to help overcome -Fe stress in rice.

  18. Proteomic analyses of Oryza sativa mature pollen reveal novel proteins associated with pollen germination and tube growth.

    PubMed

    Dai, Shaojun; Li, Lei; Chen, Taotao; Chong, Kang; Xue, Yongbiao; Wang, Tai

    2006-04-01

    As a highly reduced organism, pollen performs specialized functions to generate and carry sperm into the ovule by its polarily growing pollen tube. Yet the molecular genetic basis of these functions is poorly understood. Here, we identified 322 unique proteins, most of which were not reported previously to be in pollen, from mature pollen of Oryza sativa L. ssp japonica using a proteomic approach, 23% of them having more than one isoform. Functional classification reveals that an overrepresentation of the proteins was related to signal transduction (10%), wall remodeling and metabolism (11%), and protein synthesis, assembly and degradation (14%), as well as carbohydrate and energy metabolism (25%). Further, 11% of the identified proteins are functionally unknown and do not contain any conserved domain associated with known activities. These analyses also identified 5 novel proteins by de novo sequencing and revealed several important proteins, mainly involved in signal transduction (such as protein kinases, receptor kinase-interacting proteins, guanosine 5'-diphosphate dissociation inhibitors, C2 domain-containing proteins, cyclophilins), protein synthesis, assembly and degradation (such as prohibitin, mitochondrial processing peptidase, putative UFD1, AAA+ ATPase), and wall remodeling and metabolism (such as reversibly glycosylated polypeptides, cellulose synthase-like OsCsLF7). The study is the first close investigation, to our knowledge, of protein complement in mature pollen, and presents useful molecular information at the protein level to further understand the mechanisms underlying pollen germination and tube growth.

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

    PubMed

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

    2017-03-16

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

  20. Genome-wide association study of rice (Oryza sativa L.) leaf traits with a high-throughput leaf scorer

    PubMed Central

    Yang, Wanneng; Guo, Zilong; Huang, Chenglong; Wang, Ke; Jiang, Ni; Feng, Hui; Chen, Guoxing; Liu, Qian; Xiong, Lizhong

    2015-01-01

    Leaves are the plant’s solar panel and food factory, and leaf traits are always key issues to investigate in plant research. Traditional methods for leaf trait measurement are time-consuming. In this work, an engineering prototype has been established for high-throughput leaf scoring (HLS) of a large number of Oryza sativa accessions. The mean absolute per cent of errors in traditional measurements versus HLS were below 5% for leaf number, area, shape, and colour. Moreover, HLS can measure up to 30 leaves per minute. To demonstrate the usefulness of HLS in dissecting the genetic bases of leaf traits, a genome-wide association study (GWAS) was performed for 29 leaf traits related to leaf size, shape, and colour at three growth stages using HLS on a panel of 533 rice accessions. Nine associated loci contained known leaf-related genes, such as Nal1 for controlling the leaf width. In addition, a total of 73, 123, and 177 new loci were detected for traits associated with leaf size, colour, and shape, respectively. In summary, after evaluating the performance with a large number of rice accessions, the combination of GWAS and high-throughput leaf phenotyping (HLS) has proven a valuable strategy to identify the genetic loci controlling rice leaf traits. PMID:25796084

  1. Salicylic acid modulates arsenic toxicity by reducing its root to shoot translocation in rice (Oryza sativa L.).

    PubMed

    Singh, Amit P; Dixit, Garima; Mishra, Seema; Dwivedi, Sanjay; Tiwari, Manish; Mallick, Shekhar; Pandey, Vivek; Trivedi, Prabodh K; Chakrabarty, Debasis; Tripathi, Rudra D

    2015-01-01

    Arsenic (As) is posing serious health concerns in South East Asia where rice, an efficient accumulator of As, is prominent crop. Salicylic acid (SA) is an important signaling molecule and plays a crucial role in resistance against biotic and abiotic stress in plants. In present study, ameliorative effect of SA against arsenate (As(V)) toxicity has been investigated in rice (Oryza sativa L.). Arsenate stress hampered the plant growth in terms of root, shoots length, and biomass as well as it enhanced the level of H2O2 and MDA in dose dependent manner in shoot. Exogenous application of SA, reverted the growth, and oxidative stress caused by As(V) and significantly decreased As translocation to the shoots. Level of As in shoot was positively correlated with the expression of OsLsi2, efflux transporter responsible for root to shoot translocation of As in the form of arsenite (As(III)). SA also overcame As(V) induced oxidative stress and modulated the activities of antioxidant enzymes in a differential manner in shoots. As treatment hampered the translocation of Fe in the shoot which was compensated by the SA treatment. The level of Fe in root and shoot was positively correlated with the transcript level of transporters responsible for the accumulation of Fe, OsNRAMP5, and OsFRDL1, in the root and shoot, respectively. Co-application of SA was more effective than pre-treatment for reducing As accumulation as well as imposed toxicity.

  2. OsSLI1, a homeodomain containing transcription activator, involves abscisic acid related stress response in rice (Oryza sativa L.).

    PubMed

    Huang, Xi; Duan, Min; Liao, Jiakai; Yuan, Xi; Chen, Hui; Feng, Jiejie; Huang, Ji; Zhang, Hong-Sheng

    2014-01-01

    Homeodomain-leucine zipper type I (HD-Zip I) proteins are involved in the regulation of plant development and response to environmental stresses. In this study, OsSLI1 (Oryza sativa stress largely induced 1), encoding a member of the HD-Zip I subfamily, was isolated from rice. The expression of OsSLI1 was dramatically induced by multiple abiotic stresses and exogenous abscisic acid (ABA). In silico sequence analysis discovered several cis-acting elements including multiple ABREs (ABA-responsive element binding factors) in the upstream promoter region of OsSLI1. The OsSLI1-GFP fusion protein was localized in the nucleus of rice protoplast cells and the transcriptional activity of OsSLI1 was confirmed by the yeast hybrid system. Further, it was found that OsSLI1 expression was enhanced in an ABI5-Like1 (ABL1) deficiency rice mutant abl1 under stress conditions, suggesting that ABL1 probably negatively regulates OsSLI1 gene expression. Moreover, it was found that OsSLI1 was regulated in panicle development. Taken together, OsSLI1 may be a transcriptional activator regulating stress-responsive gene expression and panicle development in rice.

  3. Oryza sativa H+-ATPase (OSA) is Involved in the Regulation of Dumbbell-Shaped Guard Cells of Rice

    PubMed Central

    Toda, Yosuke; Wang, Yin; Takahashi, Akira; Kawai, Yuya; Tada, Yasuomi; Yamaji, Naoki; Feng Ma, Jian; Ashikari, Motoyuki; Kinoshita, Toshinori

    2016-01-01

    The stomatal apparatus consists of a pair of guard cells and regulates gas exchange between the leaf and atmosphere. In guard cells, blue light (BL) activates H+-ATPase in the plasma membrane through the phosphorylation of its penultimate threonine, mediating stomatal opening. Although this regulation is thought to be widely adopted among kidney-shaped guard cells in dicots, the molecular basis underlying that of dumbbell-shaped guard cells in monocots remains unclear. Here, we show that H+-ATPases are involved in the regulation of dumbbell-shaped guard cells. Stomatal opening of rice was promoted by the H+-ATPase activator fusicoccin and by BL, and the latter was suppressed by the H+-ATPase inhibitor vanadate. Using H+-ATPase antibodies, we showed the presence of phosphoregulation of the penultimate threonine in Oryza sativa H+-ATPases (OSAs) and localization of OSAs in the plasma membrane of guard cells. Interestingly, we identified one H+-ATPase isoform, OSA7, that is preferentially expressed among the OSA genes in guard cells, and found that loss of function of OSA7 resulted in partial insensitivity to BL. We conclude that H+-ATPase is involved in BL-induced stomatal opening of dumbbell-shaped guard cells in monocotyledon species. PMID:27048369

  4. Association mapping and genetic dissection of nitrogen use efficiency-related traits in rice (Oryza sativa L.).

    PubMed

    Liu, Zhiyi; Zhu, Chengsong; Jiang, Yue; Tian, Yunlu; Yu, Jun; An, Hongzhou; Tang, Weijie; Sun, Juan; Tang, Jianpeng; Chen, Gaoming; Zhai, Huqu; Wang, Chunming; Wan, Jianmin

    2016-05-01

    The increases in the usage of nitrogen fertilizer result in deleterious impacts on the environment; thus, there is an urgent need to improve nitrogen use efficiency (NUE) in crops including rice (Oryza sativa L.). Attentions have focused on quantitative trait loci (QTL) mapping of NUE-related traits using single experimental population, but to date, very few studies have taken advantage of association mapping to examine hundreds of lines for identifying potentially novel QTLs in rice. Here, we conducted association analysis on NUE-related traits using a population containing 184 varieties, which were genotyped with 157 genome-wide simple sequence repeat (SSR) markers. We detected eight statistically significant marker loci associating with NUE-related traits, of which two QTLs at RM5639 and RM3628 harbored known NUE-related genes GS1;2 and AspAt3, respectively. At a novel NUE-related locus RM5748, we developed Kompetitive Allele Specific PCR (KASP) single nucleotide polymorphism (SNP) markers and searched for putative NUE-related genes which are close to the associated SNP marker. Based on a transcriptional map of N stress responses constructed by our lab, we evaluated expressions of the NUE-related genes in this region and validated their effect on NUE. Meanwhile, we analyzed NUE-related alleles of the eight loci that could be utilized in marker-assisted selection. Moreover, we estimated breeding values of all the varieties through genomic prediction approach that could be beneficial for rice NUE enhancement.

  5. Interactive effects of different inorganic As and Se species on their uptake and translocation by rice (Oryza sativa L.) seedlings.

    PubMed

    Hu, Ying; Duan, Gui-Lan; Huang, Yi-Zong; Liu, Yun-Xia; Sun, Guo-Xin

    2014-03-01

    There is a lack of information on the interactive relationship of absorption and transformation between two inorganic arsenic (As) species and two inorganic selenium (Se) species in rice grown under hydroponic condition. Interactive effects of inorganic As (As(III)) and (As(V)) and Se (Se(IV)and Se(VI)) species on their uptake, accumulation, and translocation in rice (Oryza sativa L.) seedlings were investigated in hydroponic culture. The results clearly showed the interactive effects of inorganic As and Se on their uptake by rice. The presence of Se reduced the sum of As species in the rice shoots regardless of Se speciation. If Se is present as Se(IV), then is it is accompanied by a corresponding increase of the sum of As species, but if Se is present as Se(VI), then there is no change in the sum of As species in rice roots. These effects are observed regardless of initial As speciation. When the rice plants are exposed to Se(IV), the presence of As increases the sum of Se species in the roots, and decreases the sum of Se species in the corresponding shoots. This effect is more pronounced for As(III) than for As(V). There is no effect on Se during exposure to Se(VI). Co-existence of As also increased SeMet in rice roots.

  6. Identification of OsbHLH133 as a regulator of iron distribution between roots and shoots in Oryza sativa.

    PubMed

    Wang, Lu; Ying, Yinghui; Narsai, Reena; Ye, Lingxiao; Zheng, Luqing; Tian, Jingluan; Whelan, James; Shou, Huixia

    2013-01-01

    Iron (Fe) is an essential micronutrient element for plant growth. Regulation of Fe-deficiency signalling networks is one of the many functions reported for basic helix-loop-helix (bHLH) transcription factors in plants. In the present study, OsbHLH133 was found to be induced by Fe-deficiency conditions in Oryza sativa. Insertional inactivation of OsbHLH133 (bhlh133) resulted in growth retardation, with enhanced Fe concentration seen in shoots, and reduced Fe concentration in roots. Overexpression of OsbHLH133 had the opposite effect, that is resulted in an enhanced Fe concentration in roots and reduced Fe concentration in shoots and also in xylem sap. Microarray analysis showed that some of the genes encoding Fe-related functions were up-regulated under Fe-sufficient conditions, in bhlh133 mutant plants compared to wild-type plants. Significant differential expression of a number of signalling pathways, including calcium signalling, was also seen in bhlh133 plants compared to wild-type plants, independent of Fe conditions.

  7. Alteration of leaf metabolism in Bt-transgenic rice (Oryza sativa L.) and its wild type under insecticide stress.

    PubMed

    Zhou, Jia; Zhang, Lei; Chang, Yuwei; Lu, Xin; Zhu, Zhen; Xu, Guowang

    2012-08-03

    Insecticide is always used to control the damage from pests, while the potential influence on plants is rarely known. Time-course metabolic changes of wild and Bacillus thuringiensis (Bt) transgenic rice (Oryza sativa L.) plants after insecticide treatment were investigated by using gas chromatography-mass spectrometry (GC-MS). A combined statistical strategy of 2-way ANOVA and multivariate analyses (principal component analysis and hierarchal cluster analysis) was performed to find the stress-associated effects. The results reveal that a wide range of metabolites were dynamically varied in both varieties as a response to insecticide, in multiple metabolic pathways, such as biosynthesis and metabolism of amino acids, carbohydrates, fatty acids, TCA cycle, and the shikimate/phenylpropanoid pathway, and most of the changes were correlated with the exposure time and dependent on the variety. A set of stress defenses were activated, including phytohormone signaling pathway, antioxidant defense system, shikimate-mediated secondary metabolism, and so on. In particular, insecticide led to much stronger regulations of signaling molecules (salicylate and the precursor of jasmonate) and antioxidants (α-tocopherol and dehydroascorbate/ascorbate) in Bt-transgenic variety at the early stage. Our results demonstrated that the Bt-transgenic rice had a more acute and drastic response to insecticide stress than its non-transgenic counterpart in antioxidant system and signaling regulation.

  8. Functional characterization of heat-shock protein 90 from Oryza sativa and crystal structure of its N-terminal domain.

    PubMed

    Raman, Swetha; Suguna, Kaza

    2015-06-01

    Heat-shock protein 90 (Hsp90) is an ATP-dependent molecular chaperone that is essential for the normal functioning of eukaryotic cells. It plays crucial roles in cell signalling, cell-cycle control and in maintaining proteome integrity and protein homeostasis. In plants, Hsp90s are required for normal plant growth and development. Hsp90s are observed to be upregulated in response to various abiotic and biotic stresses and are also involved in immune responses in plants. Although there are several studies elucidating the physiological role of Hsp90s in plants, their molecular mechanism of action is still unclear. In this study, biochemical characterization of an Hsp90 protein from rice (Oryza sativa; OsHsp90) has been performed and the crystal structure of its N-terminal domain (OsHsp90-NTD) was determined. The binding of OsHsp90 to its substrate ATP and the inhibitor 17-AAG was studied by fluorescence spectroscopy. The protein also exhibited a weak ATPase activity. The crystal structure of OsHsp90-NTD was solved in complex with the nonhydrolyzable ATP analogue AMPPCP at 3.1 Å resolution. The domain was crystallized by cross-seeding with crystals of the N-terminal domain of Hsp90 from Dictyostelium discoideum, which shares 70% sequence identity with OsHsp90-NTD. This is the second reported structure of a domain of Hsp90 from a plant source.

  9. Overexpression of wheat gene TaMOR improves root system architecture and grain yield in Oryza sativa

    PubMed Central

    Li, Bo; Liu, Dan; Li, Qiaoru; Mao, Xinguo; Li, Ang; Wang, Jingyi; Chang, Xiaoping; Jing, Ruilian

    2016-01-01

    Improved root architecture is an effective strategy to increase crop yield. We demonstrate that overexpression of transcription factor gene MORE ROOT (TaMOR) from wheat (Triticum aestivum L.) results in more roots and higher grain yield in rice (Oryza sativa). TaMOR, encoding a plant-specific transcription factor belonging to the ASYMMETRIC LEAVES2/LATERAL ORGAN BOUNDARIES (AS2/LOB) protein family, is highly conserved in wheat and its wild relatives. In this study, tissue expression patterns indicated that TaMOR mainly localizes to root initiation sites. The consistent gene expression pattern suggests that TaMOR is involved in root initiation. Exogenous auxin treatment induced TaMOR expression without de novo protein biosynthesis. Both in vivo and in vitro experiments demonstrated that TaMOR interacts with TaMOR-related protein TaMRRP, which contains a four-tandem-pentatricopeptide repeat motif. Overexpression of TaMOR led to more lateral roots in Arabidopsis thaliana, and TaMOR-overexpressing rice plants had more crown roots, a longer main panicle, a higher number of primary branches on the main panicle, a higher grain number per plant, and higher yield per plant than the plants of wild type. In general, TaMOR-D-overexpressing lines had larger root systems in Arabidopsis and rice, and produce a higher grain yield per plant. TaMOR therefore offers an opportunity to improve root architecture and increase yield in crop plants. PMID:27229732

  10. Structural understanding of the recycling of oxidized ascorbate by dehydroascorbate reductase (OsDHAR) from Oryza sativa L. japonica

    PubMed Central

    Do, Hackwon; Kim, Il-Sup; Jeon, Byoung Wook; Lee, Chang Woo; Park, Ae Kyung; Wi, Ah Ram; Shin, Seung Chul; Park, Hyun; Kim, Young-Saeng; Yoon, Ho-Sung; Kim, Han-Woo; Lee, Jun Hyuck

    2016-01-01

    Dehydroascorbate reductase (DHAR) is a key enzyme involved in the recycling of ascorbate, which catalyses the glutathione (GSH)-dependent reduction of oxidized ascorbate (dehydroascorbate, DHA). As a result, DHAR regenerates a pool of reduced ascorbate and detoxifies reactive oxygen species (ROS). In previous experiments involving transgenic rice, we observed that overexpression of DHAR enhanced grain yield and biomass. Since the structure of DHAR is not available, the enzymatic mechanism is not well-understood and remains poorly characterized. To elucidate the molecular basis of DHAR catalysis, we determined the crystal structures of DHAR from Oryza sativa L. japonica (OsDHAR) in the native, ascorbate-bound, and GSH-bound forms and refined their resolutions to 1.9, 1.7, and 1.7 Å, respectively. These complex structures provide the first information regarding the location of the ascorbate and GSH binding sites and their interacting residues. The location of the ascorbate-binding site overlaps with the GSH-binding site, suggesting a ping-pong kinetic mechanism for electron transfer at the common Cys20 active site. Our structural information and mutagenesis data provide useful insights into the reaction mechanism of OsDHAR against ROS-induced oxidative stress in rice. PMID:26775680

  11. Internal aeration of paddy field rice (Oryza sativa) during complete submergence---importance of light and floodwater O2.

    PubMed

    Winkel, Anders; Colmer, Timothy D; Ismail, Abdelbagi M; Pedersen, Ole

    2013-03-01

    Flash floods can submerge paddy field rice (Oryza sativa), with adverse effects on internal aeration, sugar status and survival. Here, we investigated the in situ aeration of roots of rice during complete submergence, and elucidated how underwater photosynthesis and floodwater pO(2) influence root aeration in anoxic soil. In the field, root pO(2) was measured using microelectrodes during 2 d of complete submergence. Leaf gas films that formed on the superhydrophobic leaves were left intact, or experimentally removed, to elucidate their effect on internal aeration. In darkness, root pO(2) declined to very low concentrations (0.24 kPa) and was strongly correlated with floodwater pO(2). In light, root pO(2) was high (14 kPa) and primarily a function of the incident light determining the rates of underwater net photosynthesis. Plants with intact leaf gas films maintained higher underwater net photosynthesis relative to plants without gas films when the submerged shoots were in light. During complete submergence, internal aeration of rice in the field relies on underwater photosynthesis during the day and entry of O(2) from the floodwater during the night. Leaf gas films enhance photosynthesis during submergence leading to improved O(2) production and sugar status, and therefore contribute to the submergence tolerance of rice.

  12. Improved expression, purification and crystallization of a putative N-acetyl-γ-glutamyl-phosphate reductase from rice (Oryza sativa)

    SciTech Connect

    Miura-Ohnuma, Jun; Nonaka, Tsuyoshi; Katoh, Shizue; Murata, Katsuyoshi; Kita, Akiko; Miki, Kunio

    2005-12-01

    Crystals of OsAGPR were obtained using the sitting-drop vapour-diffusion method at 293 K and diffract X-rays to at least 1.8 Å resolution. They belong to the hexagonal space group P6{sub 1}, with unit-cell parameters a = 86.11, c = 316.3 Å. N-Acetyl-γ-glutamyl-phosphate reductase (AGPR) catalyzes the third step in an eight-step arginine-biosynthetic pathway that starts with glutamate. This enzyme converts N-acetyl-γ-glutamyl phosphate to N-acetylglutamate-γ-semialdehyde by an NADPH-dependent reductive dephosphorylation. AGPR from Oryza sativa (OsAGPR) was expressed in Escherichia coli at 291 K as a soluble fusion protein with an upstream thioredoxin-hexahistidine [Trx-(His){sub 6}] extension. OsAGPR(Ala50–Pro366) was purified and crystals were obtained using the sitting-drop vapour-diffusion method at 293 K and diffract X-rays to at least 1.8 Å resolution. They belong to the hexagonal space group P6{sub 1}, with unit-cell parameters a = 86.11, c = 316.3 Å.

  13. The promoting effects of alginate oligosaccharides on root development in Oryza sativa L. mediated by auxin signaling.

    PubMed

    Zhang, Yunhong; Yin, Heng; Zhao, Xiaoming; Wang, Wenxia; Du, Yuguang; He, Ailing; Sun, Kegang

    2014-11-26

    Alginate oligosaccharides (AOS), which are marine oligosaccharides, are involved in regulating plant root growth, but the promotion mechanism for AOS remains unclear. Here, AOS (10-80 mg/L) induced the expression of auxin-related gene (OsYUCCA1, OsYUCCA5, OsIAA11 and OsPIN1) in rice (Oryza sativa L.) tissues to accelerate auxin biosynthesis and transport, and reduced indole-3-acetic acid (IAA) oxidase activity in rice roots. These changes resulted in the increase of 37.8% in IAA concentration in rice roots, thereby inducing the expression of root development-related genes, promoting root growth in a dose-dependent manner, which were inhibited by auxin transport inhibitor 2,3,5-triiodo benzoic acid (TIBA) and calcium-chelating agent ethylene glycol bis (2-aminoethyl) tetraacetic acid (EGTA). AOS also induced calcium signaling generation in rice roots. Those results indicated that auxin mediated AOS regulation of root development, and calcium signaling may act mainly in the upstream of auxin in the regulation of AOS on rice root development.

  14. Chloroplast downsizing under nitrate nutrition restrained mesophyll conductance and photosynthesis in rice (Oryza sativa L.) under drought conditions.

    PubMed

    Li, Yong; Ren, Binbin; Yang, Xiuxia; Xu, Guohua; Shen, Qirong; Guo, Shiwei

    2012-05-01

    The phenomenon whereby ammonium enhances the tolerance of rice seedlings (Oryza sativa L., cv. 'Shanyou 63' hybrid indica China) to water stress has been reported in previous studies. To study the intrinsic mechanism of biomass synthesis related to photosynthesis, hydroponic experiments supplying different nitrogen (N) forms were conducted; water stress was simulated by the addition of polyethylene glycol. Water stress decreased leaf water potential (Ψ(leaf)) under nitrate nutrition, while it had no negative effect under ammonium nutrition. The decreased Ψ(leaf) under nitrate nutrition resulted in chloroplast downsizing and subsequently decreased mesophyll conductance to CO(2) (g(m)). The decreased g(m) and stomatal conductance (g(s)) under nitrate nutrition with water stress restrained the CO(2) supply to the chloroplast and Rubisco. The relatively higher distribution of leaf N to Rubisco under ammonium nutrition might also be of benefit for photosynthesis under water stress. In conclusion, chloroplast downsizing induced a decline in g(m), a relatively higher decrease in g(s) under nitrate nutrition with water stress, restrained the CO(2) supply to Rubisco and finally decreased the photosynthetic rate.

  15. Identification of a stable quantitative trait locus for percentage grains with white chalkiness in rice (Oryza sativa).

    PubMed

    Guo, Tao; Liu, Xiaolu; Wan, Xiangyuan; Weng, Jianfeng; Liu, Shijia; Liu, Xi; Chen, Mingjiang; Li, Jingjing; Su, Ning; Wu, Fuqing; Cheng, Zhijun; Guo, Xiuping; Lei, Cailin; Wang, Jiulin; Jiang, Ling; Wan, Jianmin

    2011-08-01

    High chalkiness is a major problem in many rice-producing areas of the world, especially in hybrid rice (Oryza sativa L.) in China. We previously showed a major quantitative trait locus for the percentage of grains with white chalkiness (QTLqPGWC-8) in the interval G1149-R727 on chromosome 8 using a chromosome segment substitution line (CSSL). Here, we selected the line-CSSL50 harboring the QTLqPGWC-8 allele from the CSSLs derived from a cross between Asominori (as a recurrent parent) and IR24 (as a donor parent), which had higher percentage chalkiness, markedly different from that of Asominori. There were also significant differences in starch granules, appearance of amylose content (AAC) and milling qualities between Asominori and CSSL50, but not in grain size or thousand grain weight (TGW). The BC(4) F(2) and BC(4) F(3) populations from a cross between CSSL50 and Asominori were used for fine mapping of qPGWC-8. We narrowed down the location of this QTL to a 142 kb region between Indel markers 8G-7 and 8G-9. QTLqPGWC-8 accounted for 50.9% of the difference in PGWC between the parents. The markers tightly linked to qPGWC-8 should facilitate cloning of the gene underlying this QTL and will be of value for marker-assisted selection in breeding rice varieties with better grain quality.

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

    PubMed

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

    2012-05-30

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

  17. Comparative transcriptome analysis of transporters, phytohormone and lipid metabolism pathways in response to arsenic stress in rice (Oryza sativa).

    PubMed

    Yu, Lu-jun; Luo, Ying-feng; Liao, Bin; Xie, Li-juan; Chen, Liang; Xiao, Shi; Li, Jin-tian; Hu, Song-nian; Shu, Wen-sheng

    2012-07-01

    • Arsenic (As) contamination of rice (Oryza sativa) is a worldwide concern and elucidating the molecular mechanisms of As accumulation in rice may provide promising solutions to the problem. Previous studies using microarray techniques to investigate transcriptional regulation of plant responses to As stress have identified numerous differentially expressed genes. However, little is known about the metabolic and regulatory network remodelings, or their interactions with microRNA (miRNA) in plants upon As(III) exposure. • We used Illumina sequencing to acquire global transcriptome alterations and miRNA regulation in rice under As(III) treatments of varying lengths of time and dosages. • We found that the response of roots was more distinct when the dosage was varied, whereas that of shoots was more distinct when the treatment time was varied. In particular, the genes involved in heavy metal transportation, jasmonate (JA) biosynthesis and signaling, and lipid metabolism were closely related to responses of rice under As(III) stress. Furthermore, we discovered 36 new As(III)-responsive miRNAs, 14 of which were likely involved in regulating gene expression in transportation, signaling, and metabolism. • Our findings highlight the significance of JA signaling and lipid metabolism in response to As(III) stress and their regulation by miRNA, which provides a foundation for subsequent functional research.

  18. OsMPK6 plays a critical role in cell differentiation during early embryogenesis in Oryza sativa

    PubMed Central

    Yi, Jakyung; Lee, Yang-Seok; Lee, Dong-Yeon; Cho, Man-Ho; Jeon, Jong-Seong; An, Gynheung

    2016-01-01

    The formation of body axes is the basis of morphogenesis during plant embryogenesis. We identified embryo-lethal mutants of rice (Oryza sativa) in which T-DNAs were inserted in OsMPK6. Embryonic organs were absent because their development was arrested at the globular stage. Similar to observations made with gle4, shootless, and organless, the osmpk6 mutations affected the initial step of cell differentiation. Expression of an apical–basal axis marker gene, OSH1, was reduced in the mutant embryos while that of the radial axes marker genes OsSCR and OsPNH1 was not detected. The signal for ROC1, a protodermal cell marker, was weak at the globular stage and gradually disappeared. Transcript levels of auxin and gibberellin biosynthesis genes were diminished in osmpk6 embryos. In addition, phytoalexin biosynthesis genes were down-regulated in osmpk6 and a major diterpene phytoalexin, momilactone A, did not accumulate in the mutant embryos. These results indicate that OsMPK6 begins to play a critical role during early embryogenesis, especially when the L1 radial axis is being formed. PMID:26912801

  19. Genome-wide association study of rice (Oryza sativa L.) leaf traits with a high-throughput leaf scorer.

    PubMed

    Yang, Wanneng; Guo, Zilong; Huang, Chenglong; Wang, Ke; Jiang, Ni; Feng, Hui; Chen, Guoxing; Liu, Qian; Xiong, Lizhong

    2015-09-01

    Leaves are the plant's solar panel and food factory, and leaf traits are always key issues to investigate in plant research. Traditional methods for leaf trait measurement are time-consuming. In this work, an engineering prototype has been established for high-throughput leaf scoring (HLS) of a large number of Oryza sativa accessions. The mean absolute per cent of errors in traditional measurements versus HLS were below 5% for leaf number, area, shape, and colour. Moreover, HLS can measure up to 30 leaves per minute. To demonstrate the usefulness of HLS in dissecting the genetic bases of leaf traits, a genome-wide association study (GWAS) was performed for 29 leaf traits related to leaf size, shape, and colour at three growth stages using HLS on a panel of 533 rice accessions. Nine associated loci contained known leaf-related genes, such as Nal1 for controlling the leaf width. In addition, a total of 73, 123, and 177 new loci were detected for traits associated with leaf size, colour, and shape, respectively. In summary, after evaluating the performance with a large number of rice accessions, the combination of GWAS and high-throughput leaf phenotyping (HLS) has proven a valuable strategy to identify the genetic loci controlling rice leaf traits.

  20. Differential morphological, cytological and biochemical responses of two rice cultivars to coumarin

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Plants are often exposed to allelochemicals in the environment produced by neighboring plants. Coumarin is a common allelochemical produced by many higher plants. Two cultivars (susceptible BS-2000 and less susceptible BR-41) of rice (Oryza sativa L.) were selected to compare their differential root...

  1. Molecular analysis of an additional case of hybrid sterility in rice (Oryza sativa L.).

    PubMed

    Zhao, Z G; Zhu, S S; Zhang, Y H; Bian, X F; Wang, Y; Jiang, L; Liu, X; Chen, L M; Liu, S J; Zhang, W W; Ikehashi, H; Wan, J M

    2011-03-01

    Hybrid sterility hinders the exploitation of the heterosis displayed by japonica × indica rice hybrids. The variation in pollen semi-sterility observed among hybrids between the japonica recipient cultivar and each of two sets of chromosome segment substitution lines involving introgression from an indica cultivar was due to a factor on chromosome 5 known to harbor the gene S24. S24 was fine mapped to a 42 kb segment by analyzing a large F(2) population bred from the cross S24-NIL × Asominori, while the semi-sterility shown by the F(1) hybrid was ascribable to mitotic failure at the early bicellular pollen stage. Interestingly, two other pollen sterility genes (f5-Du and Sb) map to the same region (Li et al. in Chin Sci Bull 51:675-680, 2006; Wang et al. in Theor Appl Genet 112:382-387, 2006), allowing a search for candidate genes in the 6.4 kb overlap between the three genes. By sequencing the overlapped fragment in wild rice, indica cultivars and japonica cultivars, a protein ankyrin-3 encoded by the ORF2 was identified as the molecular base for S24. A cultivar Dular was found to have a hybrid-sterility-neutral allele, S24-n, in which an insertion of 30 bp was confirmed. Thus, it was possible to add one more case of molecular bases for the hybrid sterility. No gamete abortion is caused on heterozygous maternal genotype with an impaired sequence from the hybrid-sterility-neutral genotype. This result will be useful in understanding of wide compatibility in rice breeding.

  2. Genomewide survey and characterization of metacaspase gene family in rice (Oryza sativa).

    PubMed

    Wang, Likai; Zhang, Hua

    2014-04-01

    Metacaspases (MCs), which are cysteine-dependent proteases found in plants, fungi, and protozoa, may be involved in programmed cell death processes, being distant relatives of metazoan caspases. In this study, we analysed the structures, phylogenetic relationship, genome localizations, expression patterns and domestic selections of eight MC genes identified in rice (OsMC). Alignment analysis of the corresponding protein sequences suggested OsMC proteins can be classified into two subtypes. The expression profiles of eight OsMC genes were analysed in 27 tissues covering the whole life cycle of rice. There are four OsMC genes uniquely expressed in mature tissues, indicating that these genes might play certain roles in senescence. Under abiotic and biotic stresses, four OsMC genes were expressed with treatments of one or more of Magnaporthe oryzae (M. oryzae) infected, pest damaged, cold stress and drought stress, indicating they might be involved in plant defense. In addition, gene trees and genetic diversity (π) were performed to measure whether candidate genes were selected during rice domestication. The results suggested that all the type I genes could not be domestication genes. However, two of five type II OsMC genes showed strong evidence for selective sweep, suggesting that these genes might be involved in cultivated rice domestication. These results provide a foundation for future functional genomic studies of this family in rice.

  3. Reactive oxygen species, ascorbate-glutathione pool, and enzymes of their metabolism in drought-sensitive and tolerant indica rice (Oryza sativa L.) seedlings subjected to progressing levels of water deficit.

    PubMed

    Pyngrope, Samantha; Bhoomika, Kumari; Dubey, R S

    2013-04-01

    Water deficit for rice is a worldwide concern, and to produce drought-tolerant varieties, it is essential to elucidate molecular mechanisms associated with water deficit tolerance. In the present study, we investigated the differential responses of nonenzymatic antioxidants ascorbate (AsA), glutathione (GSH), and their redox pool as well as activity levels of enzymes of ascorbate-glutathione cycle in seedlings of drought-sensitive rice (Oryza sativa L.) cv. Malviya-36 and drought-tolerant cv. Brown Gora subjected to water deficit treatment of -1.0 and -2.1 MPa for 24-72 h using PEG-6000 in sand cultures. Water deficit caused increased production of reactive oxygen species such as O2[Symbol: see text](-), H2O2, and HO[Symbol: see text] in the tissues, and the level of production was higher in the sensitive than the tolerant cultivar. Water deficit caused reduction in AsA and GSH and decline in their redox ratios (AsA/DHA and GSH/GSSG) with lesser decline in tolerant than the sensitive seedlings. With progressive level of water deficit, the activities of monodehydroascorbate reductase, dehydroascorbate reductase, ascorbate peroxidase (APX), and glutathione transferase increased in the seedlings of both rice cultivars, but the increased activity levels were higher in the seedlings of drought-tolerant cv. Brown Gora compared to the sensitive cv. Malviya-36. Greater accumulation of proline was observed in stressed seedlings of tolerant than the sensitive cultivar. In-gel activity staining of APX revealed varying numbers of their isoforms and their differential expression in sensitive and tolerant seedlings under water deficit. Results suggest that an enhanced oxidative stress tolerance by a well-coordinated cellular redox state of ascorbate and glutathione in reduced forms and induction of antioxidant defense system by elevated activity levels of enzymes of ascorbate-glutathione cycle is associated with water deficit tolerance in rice.

  4. Uptake and transport mechanisms of decabromodiphenyl ether (BDE-209) by rice (Oryza sativa).

    PubMed

    Chow, Ka Lai; Man, Yu Bon; Tam, Nora Fung Yee; Liang, Yan; Wong, Ming Hung

    2015-01-01

    The extensive industrial use of brominated flame retardants has aroused rapidly growing public concerns about their ubiquity in the environment. The feasibility of uptake and translocation of decabromodiphenyl ether (BDE-209) by three rice cultivars, namely Fengmeizhan, Hefengzhan and Guangyinzhan, and the uptake mechanisms of BDE-209 into rice roots, were investigated by employing a partition-limited model. Uptake of BDE-209 by the rice cultivars (Fengmeizhan, Hefengzhan and Guangyinzhan) was examined by a 60-day cultivation in sterilized BDE-209 spiked sand, followed by Soxhlet extraction and gas chromatography-mass spectrometry (GC-MS) analysis. A partition-limited model was applied for estimating and describing the approach of the uptake of BDE-209 by rice in sand. The average quasi-equilibrium factor (αpt) of BDE-209 in root uptake in sand was 0.112×10(-3) for three rice cultivars in the present study (<1), implying a non-equilibrium movement of molecules and a dominated passive transport uptake. According to the results of sorption analysis of dead and fresh roots, apoplastic pathway likely dominated the transport of BDE-209 into roots cells.

  5. Assessment of gene flow from a herbicide-resistant indica rice (Oryza sativa L.) to the Costa Rican weedy rice (Oryza sativa) in Tropical America: factors affecting hybridization rates and characterization of F1 hybrids.

    PubMed

    Olguin, Elena R Sanchez; Arrieta-Espinoza, Griselda; Lobo, Jorge A; Espinoza-Esquivel, Ana M

    2009-08-01

    Herbicide-resistant rice cultivars allow selective weed control. A glufosinate indica rice has been developed locally. However, there is concern about weedy rice becoming herbicide resistant through gene flow. Therefore, assessment of gene flow from indica rice cultivars to weedy rice is crucial in Tropical America. A field trial mimicking crop-weed growing patterns was established to assess the rate of hybridization between a Costa Rican glufosinate-resistant rice line (PPT-R) and 58 weedy rice accessions belonging to six weedy rice morphotypes. The effects of overlapping anthesis, morphotype, weedy accession/PPT-R percentage, and the particular weedy accession on hybridization rates were evaluated. Weedy rice accessions with short overlapping anthesis (4-9 days) had lower average hybridization rates (0.1%) than long anthesis overlapping (10-14 days) accessions (0.3%). Hybridization also varied according to weedy rice morphotype and accession. Sativa-like morphotypes (WM-020, WM-120) hybridized more readily than intermediate (WM-023, WM-073, WM-121) and rufipogon-like (WM-329) morphotypes. No hybrids were identified in 11 of the 58 accessions analyzed, 21 accessions had hybridization rates from 0.01% to 0.09%, 21 had rates from 0.1% to 0.9%, and 5 had frequencies from 1% to 2.3%. Another field trial was established to compare the weedy rice-PPT-R F(1) hybrids with their parental lines under noncompetitive conditions. F(1) hybrids had a greater phenotypic variation. They had positive heterosis for vegetative trait and reproductive potential (number of spikelets and panicle length) traits, but negative heterosis for seed set. This study demonstrated the complexity of factors affecting hybridization rates in Tropical America and suggested that the phenotype of F(1) hybrids facilitate their identification in the rice fields.

  6. Analysis of simple sequence repeat markers linked with blast disease resistance genes in a segregating population of rice (Oryza sativa).

    PubMed

    Ashkani, S; Rafii, M Y; Sariah, M; Siti Nor Akmar, A; Rusli, I; Abdul Rahim, H; Latif, M A

    2011-07-06

    Among 120 simple sequence repeat (SSR) markers, 23 polymorphic markers were used to identify the segregation ratio in 320 individuals of an F(2) rice population derived from Pongsu Seribu 2, a resistant variety, and Mahsuri, a susceptible rice cultivar. For phenotypic study, the most virulent blast (Magnaporthe oryzae) pathotype, P7.2, was used in screening of F(2) population in order to understand the inheritance of blast resistance as well as linkage with SSR markers. Only 11 markers showed a good fit to the expected segregation ratio (1:2:1) for the single gene model (d.f. = 1.0, P < 0.05) in chi-square (χ(2)) analyses. In the phenotypic data analysis, the F(2) population segregated in a 3:1 (R:S) ratio for resistant and susceptible plants, respectively. Therefore, resistance to blast pathotype P7.2 in Pongsu Seribu 2 is most likely controlled by a single nuclear gene. The plants from F(2) lines that showed resistance to blast pathotype P7.2 were linked to six alleles of SSR markers, RM168 (116 bp), RM8225 (221 bp), RM1233 (175 bp), RM6836 (240 bp), RM5961 (129 bp), and RM413 (79 bp). These diagnostic markers could be used in marker assisted selection programs to develop a durable blast resistant variety.

  7. Functional Characterization of Endophytic Fungal Community Associated with Oryza sativa L. and Zea mays L.

    PubMed Central

    Potshangbam, Momota; Devi, S. Indira; Sahoo, Dinabandhu; Strobel, Gary A.

    2017-01-01

    In a natural ecosystem, the plant is in a symbiotic relationship with beneficial endophytes contributing huge impact on its host plant. Therefore, exploring beneficial endophytes and understanding its interaction is a prospective area of research. The present work aims to characterize the fungal endophytic communities associated with healthy maize and rice plants and to study the deterministic factors influencing plant growth and biocontrol properties against phytopathogens, viz, Pythium ultimum, Sclerotium oryzae, Rhizoctonia solani, and Pyricularia oryzae. A total of 123 endophytic fungi was isolated using the culture-dependent approach from different tissue parts of the plant. Most dominating fungal endophyte associated with both the crops belong to genus Fusarium, Sarocladium, Aspergillus, and Penicillium and their occurrence was not tissue specific. The isolates were screened for in vitro plant growth promotion, stress tolerance, disease suppressive mechanisms and based on the results, each culture from both the cereal crops was selected for further study. Acremonium sp. (ENF 31) and Penicillium simplicisssum (ENF22), isolated from maize and rice respectively could potentially inhibit the growth of all the tested pathogens with 46.47 ± 0.16 mm to 60.09 ± 0.04 mm range zone of inhibition for ENF31 and 35.48 ± 0.14 to 62.29 ± 0.15 mm for ENF22. Both significantly produce the defensive enzymes, ENF31 could tolerate a wide range of pH from 2 to 12, very important criteria, for studying plant growth in different soil types, especially acidic as it is widely prevalent here, making more land unsuitable for cultivation. ENF22 grows in pH range 3–12, with 10% salt tolerating ability, another factor of consideration. Study of root colonization during 7th to 30th days of growth phase reveals that ENF31 could colonize pleasantly in rice, though a maize origin, ranging from 1.02 to 1.21 log10 CFU/g root and in maize, it steadily colonizes ranging from 0.95 to 1

  8. 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.

  9. Association between QTLs and morphological traits toward sheath blight resistance in rice (Oryza sativa L.).

    PubMed

    Hossain, Md Kamal; Jena, Kshirod Kumar; Bhuiyan, Md Atiqur Rahman; Wickneswari, Ratnam

    2016-09-01

    Sheath blight is considered the most significant disease of rice and causes enormous yield losses over the world. Breeding for resistant varieties is the only viable option to combat the disease efficiently. Seventeen diverged rice genotypes along with 17 QTL-linked SSR markers were evaluated under greenhouse conditions. Pearson's correlation showed only the flag leaf angle had a significant correlation with sheath blight resistance under greenhouse screening. Multivariate analysis based on UPGMA clustering and principal component analysis (PCA) indicated that the flag leaf angle, flag leaf length, and plant compactness were significantly associated with the following SSR marker alleles: RM209 (116,130), RM202 (176), RM224 (126), RM257 (156), RM426 (175), and RM6971 (196), which are linked to the SB QTLs: QRlh11, qSBR11-3, qSBR11-1, qSBR9-1, qShB3-2, and qSB-9. A Mantel test suggested a weak relationship between the observed phenotypes and allelic variation patterns, implying the independent nature of morphological and molecular variations. Teqing and Tetep were found to be the most resistant cultivars. IR65482-4-136-2-2, MR219-4, and MR264 showed improved resistance potentials. These results suggest that the morphological traits and QTLs which have been found to associate with sheath blight resistance are a good choice to enhance resistance through pyramiding either 2 QTLs or QTLs and traits in susceptible rice cultivars.

  10. Association between QTLs and morphological traits toward sheath blight resistance in rice (Oryza sativa L.)

    PubMed Central

    Hossain, Md Kamal; Jena, Kshirod Kumar; Bhuiyan, Md Atiqur Rahman; Wickneswari, Ratnam

    2016-01-01

    Sheath blight is considered the most significant disease of rice and causes enormous yield losses over the world. Breeding for resistant varieties is the only viable option to combat the disease efficiently. Seventeen diverged rice genotypes along with 17 QTL-linked SSR markers were evaluated under greenhouse conditions. Pearson’s correlation showed only the flag leaf angle had a significant correlation with sheath blight resistance under greenhouse screening. Multivariate analysis based on UPGMA clustering and principal component analysis (PCA) indicated that the flag leaf angle, flag leaf length, and plant compactness were significantly associated with the following SSR marker alleles: RM209 (116,130), RM202 (176), RM224 (126), RM257 (156), RM426 (175), and RM6971 (196), which are linked to the SB QTLs: QRlh11, qSBR11-3, qSBR11-1, qSBR9-1, qShB3-2, and qSB-9. A Mantel test suggested a weak relationship between the observed phenotypes and allelic variation patterns, implying the independent nature of morphological and molecular variations. Teqing and Tetep were found to be the most resistant cultivars. IR65482-4-136-2-2, MR219-4, and MR264 showed improved resistance potentials. These results suggest that the morphological traits and QTLs which have been found to associate with sheath blight resistance are a good choice to enhance resistance through pyramiding either 2 QTLs or QTLs and traits in susceptible rice cultivars. PMID:27795687

  11. Cloning and characterization of the serotonin N-acetyltransferase-2 gene (SNAT2) in rice (Oryza sativa).

    PubMed

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

    2016-09-01

    The penultimate enzyme in melatonin synthesis is serotonin N-acetyltransferase (SNAT), which exists as a single copy in mammals and plants. Our recent studies of the Arabidopsis snat-knockout mutant and SNAT RNAi rice (Oryza sativa) plants predicted the presence of at least one other SNAT isogene in plants; that is, the snat-knockout mutant of Arabidopsis and the SNAT RNAi rice plants still produced melatonin, even in the absence or the suppression of SNAT expression. Here, we report a molecular cloning of an SNAT isogene (OsSNAT2) from rice. The mature amino acid sequences of SNAT proteins indicated that OsSNAT2 and OsSNAT1 proteins had 39% identity values and 60% similarity. The Km and Vmax values of the purified recombinant OsSNAT2 were 371 μm and 4700 pmol/min/mg protein, respectively; the enzyme's optimal activity temperature was 45°C. Confocal microscopy showed that the OsSNAT2 protein was localized to both the cytoplasm and chloroplasts. The in vitro enzyme activity of OsSNAT2 was severely inhibited by melatonin, but the activities of sheep SNAT (OaSNAT) and rice OsSNAT1 proteins were not. The enzyme activity of OsSNAT2 was threefold higher than that of OsSNAT1, but 232-fold lower than that of OaSNAT. The OsSNAT1 and OsSNAT2 transcripts were similarly suppressed in rice leaves during the melatonin induction after cadmium treatment. Phylogenetic analyses indicated that OsSNAT1 and OsSNAT2 are distantly related, suggesting that they evolved independently from Cyanobacteria prior to the endosymbiosis event.

  12. SET DOMAIN GROUP 708, a histone H3 lysine 36-specific methyltransferase, controls flowering time in rice (Oryza sativa).

    PubMed

    Liu, Bing; Wei, Gang; Shi, Jinlei; Jin, Jing; Shen, Ting; Ni, Ting; Shen, Wen-Hui; Yu, Yu; Dong, Aiwu

    2016-04-01

    As a key epigenetic modification, the methylation of histone H3 lysine 36 (H3K36) modulates chromatin structure and is involved in diverse biological processes. To better understand the language of H3K36 methylation in rice (Oryza sativa), we chose potential histone methylation enzymes for functional exploration. In particular, we characterized rice SET DOMAIN GROUP 708 (SDG708) as an H3K36-specific methyltransferase possessing the ability to deposit up to three methyl groups on H3K36. Compared with the wild-type, SDG708-knockdown rice mutants displayed a late-flowering phenotype under both long-day and short-day conditions because of the down-regulation of the key flowering regulatory genes Heading date 3a (Hd3a), RICE FLOWERING LOCUS T1 (RFT1), and Early heading date 1 (Ehd1). Chromatin immunoprecipitation experiments indicated that H3K36me1, H3K36me2, and H3K36me3 levels were reduced at these loci in SDG708-deficient plants. More importantly, SDG708 was able to directly target and effect H3K36 methylation on specific flowering genes. In fact, knockdown of SDG708 led to misexpression of a set of functional genes and a genome-wide decrease in H3K36me1/2/3 levels during the early growth stages of rice. SDG708 is a methyltransferase that catalyses genome-wide deposition of all three methyl groups on H3K36 and is involved in many biological processes in addition to flowering promotion.

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

    PubMed

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

    2017-02-01

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

  14. Epistasis underlying female sterility detected in hybrid breakdown in a Japonica-Indica cross of rice (Oryza sativa L.).

    PubMed

    Kubo, Takahiko; Yoshimura, Atsushi

    2005-01-01

    Epistasis is considered to be a primary genetic basis of hybrid breakdown. We found novel epistatic genes causing hybrid breakdown in an intraspecific cross of cultivated rice (Oryza sativa L.). F2 progeny derived from a cross between a Japonica variety, Asominori, and an Indica variety, IR24, showed segregation of high sterility for seeds, even though the reciprocal F1 hybrids showed about 60% seed fertility. Backcross populations (BC3F2, BC3F3), obtained from repeated backcrossing with Asominori, showed the segregation of causal genes in a simple Mendelian fashion. Using these populations, we identified that this sterility was hybrid breakdown caused by interaction among three nuclear genes distributed on the both parental genomes. These new genes, designated as hsa1, hsa2, and hsa3, were found to be involved in female gamete development by histological examination. The Indica parent IR24 has a sterile allele, hsa1-IR, which was located at near RFLP marker G148 on chromosome 12, whereas the Japonica parent Asominori has two sterile alleles, hsa2-As on chromosome 8 (close to G104) and hsa3-As on chromosome 9 (close to RM285). Female gametes carrying the hsa1-IR, hsa2-As, and hsa3-As alleles aborted in hsa1-IR homozygous plant, leading to seed sterility and selective elimination of the specific allelic combination. This study provides direct evidence that hybrid breakdown is attributed to epistatic interaction of genes from both parents and suggests that complicated mechanisms has been developed for hybrid breakdown during the evolution of rice.

  15. Rubidium chloride tolerant callus cultures of rice (Oryza sativa L.) accumulate more potassium and cross tolerate to other salts.

    PubMed

    Naga Amrutha, R; Jogeswar, G; Srilaxmi, P; Kavi Kishor, P B

    2007-09-01

    Callus cultures from salt tolerant (CSR-10) and susceptible (Swarnadhan) varieties of Oryza sativa L. were established in Murashige and Skoog's (MS) medium containing lethal concentrations (50 mM) of rubidium chloride (RbCl) as a selective agent. While 95-100% cells were viable in callus cultures grown without RbCl, viability was 75% in 50 mM RbCl selected cultures. Growth of RbCl selected calli in presence of salt was comparable to that of callus grown without it. Cells tolerant to RbCl showed more vacuoles and accumulated more K(+) in comparison with their corresponding controls. Suspension cultures were established and uptake of (86)Rb(+) was measured at 10 and 20 min intervals, which revealed a linear relationship between the absorption of K(+) and time. Callus cultures (560-day-old) tolerant to 50 mM RbCl regenerated shoots with 35-40% frequencies in both the varieties, but the same age-old callus grown in the medium devoid of RbCl did not show any organogenesis. Callus cultures that are tolerant to 50 mM RbCl when exposed to 25 mM LiCl, 50 mM NaCl, 50 mM KCl and 25 mM CsCl also exhibited cross tolerance in both the varieties. This is the first time that a callus line of rice resistant to RbCl was raised and shown to accumulate a major cation K(+ )and also an increased influx of it.

  16. 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.

  17. Mechanism of Safening Action of Dymuron and Its Two Monomethyl Analogues against Bensulfuron-methyl Injury to Rice (Oryza sativa)

    PubMed

    Omokawa; Wu; Hatzios

    1996-05-01

    The comparative efficacy and mechanism of action of the herbicide dymuron and its two optically active monomethyl analogues, (R)-1-(alpha-methylbenzyl)-3-(p-tolylurea) (R-MBTU) and S-MBTU, as safeners of rice against injury from bensulfuron-methyl were investigated. Bioassays using etiolated seedlings of rice (Oryza sativa L., cv. Lemont), grown either in agar or in liquid media containing bensulfuron-methyl, showed that this sulfonylurea herbicide is a potent inhibitor of rice root growth (I50 = 120 nM). Similar studies with the herbicide dymuron and its two optically active monomethyl analogues (R-MTBU and S-MTBU) showed that at 10 μM, dymuron and R-MBTU reduced rice root length by 25 and 17%, respectively, whereas S-MBTU had no effect on root growth of Lemont rice. Combined treatments with bensulfuron-methyl and dymuron or each of its two analogues confirmed that S-MTBU is an excellent safener of rice against bensulfuron-methyl, far more effective than either dymuron or R-MTBU. The protective action of S-MTBU appeared to result mainly from a drastic reduction in the uptake of bensulfuron-methyl by safened rice seedlings. Dymuron and R-MTBU reduced also the uptake of bensulfuron-methyl by rice seedlings, but to a lesser extent than S-MTBU. Quantitative changes in the metabolism of bensulfuron-methyl by safened rice seedlings were also observed, but did not appear to support the involvement of enhanced herbicide metabolism in the safening action of S-MBTU, R-MBTU, and dymuron. The major metabolites of bensulfuron-methyl detected in both safened and unsafened rice seedlings were tentatively identified as methyl-(4-hydroxy-6-methoxypyrimidin-2-yl-carbamoylsulfamoyl)-o-toluate; methyl-(aminosulfonyl)-o-toluate; and 1H-2,3-benzothiazin-4-(3H)-one-2,2-dioxide.

  18. Activation of the Oryza sativa non-symbiotic haemoglobin-2 promoter by the cytokinin-regulated transcription factor, ARR1.

    PubMed

    Ross, Emily J H; Stone, Julie M; Elowsky, Christian G; Arredondo-Peter, Raul; Klucas, Robert V; Sarath, Gautam

    2004-08-01

    Using in silico methods, several putative phytohormone-responsive cis-elements in the Oryza sativa non-symbiotic haemoglobin (NSHB) 1-4 and Arabidopsis thaliana NSHB1-2 promoters have been identified. An OsNSHB2 promoter::GUS reporter gene fusion shows tissue-specific expression in A. thaliana. GUS expression was observed in roots, the vasculature of young leaves, in flowers, and in the pedicel/stem junction. In transient assays, activity of the OsNSHB2 promoter was significantly up-regulated in the presence of the cytokinin, 6-benzylaminopurine (BA). Deletion analyses indicated that the full-length promoter was required for maximal trans-activation in the presence of cytokinin. Mutation of the single cytokinin-regulated ARR1-binding element abolished promoter activation in response to cytokinin. Constitutive expression of ARR1 under the control of the 35S cauliflower mosaic virus promoter enhanced wild-type OsNSHB2 promoter activity, but had no effect on the activity of the mutated promoter in the absence of cytokinin. However, overexpression of ARR1 in the presence of cytokinin resulted in super-activation of the wild-type promoter. The mutated promoter was only moderately activated in the presence of cytokinin and ARR1, indicating that the OsNSHB2 promoter can be regulated by the ARR1 protein, but requires other cytokinin-induced factors for optimal activation. This is the first report that identifies a trans-acting factor involved in the activation of a NSHB gene.

  19. Salicylic acid modulates arsenic toxicity by reducing its root to shoot translocation in rice (Oryza sativa L.)

    PubMed Central

    Singh, Amit P.; Dixit, Garima; Mishra, Seema; Dwivedi, Sanjay; Tiwari, Manish; Mallick, Shekhar; Pandey, Vivek; Trivedi, Prabodh K.; Chakrabarty, Debasis; Tripathi, Rudra D.

    2015-01-01

    Arsenic (As) is posing serious health concerns in South East Asia where rice, an efficient accumulator of As, is prominent crop. Salicylic acid (SA) is an important signaling molecule and plays a crucial role in resistance against biotic and abiotic stress in plants. In present study, ameliorative effect of SA against arsenate (AsV) toxicity has been investigated in rice (Oryza sativa L.). Arsenate stress hampered the plant growth in terms of root, shoots length, and biomass as well as it enhanced the level of H2O2 and MDA in dose dependent manner in shoot. Exogenous application of SA, reverted the growth, and oxidative stress caused by AsV and significantly decreased As translocation to the shoots. Level of As in shoot was positively correlated with the expression of OsLsi2, efflux transporter responsible for root to shoot translocation of As in the form of arsenite (AsIII). SA also overcame AsV induced oxidative stress and modulated the activities of antioxidant enzymes in a differential manner in shoots. As treatment hampered the translocation of Fe in the shoot which was compensated by the SA treatment. The level of Fe in root and shoot was positively correlated with the transcript level of transporters responsible for the accumulation of Fe, OsNRAMP5, and OsFRDL1, in the root and shoot, respectively. Co-application of SA was more effective than pre-treatment for reducing As accumulation as well as imposed toxicity. PMID:26042132

  20. Molecular cloning and characterization of gravity specific cDNA in rice (Oryza sativa L.) suspension callus.

    PubMed

    Kwon, S T; Kikuchi, S; Oono, K

    1992-08-01

    Rice (Oryza sativa L. var. Nipponbare) suspension callus was exposed to gravity stress at 450,000 g for 2 hours, after which poly(A)+RNA was isolated and a cDNA library was constructed. Three different gravity specific cDNAs, namely, GSC 128, GSC 233 and GSC 381 of 0.67, 0.60 and 0.68 kilobase pairs and transcripts of 1.9, 1.6 and 2.0 kb, respectively, were isolated by differential screening and Northern hybridization. The maximum level of transcript was achieved after 4 hours of exposure to gravity at 450,000 g for GSC 128, 2 hours for GSC 233 and 8 hours for GSC 381 followed by a gradual decrease to undetectable levels with the extension of gravitation time. Callus (GSC 128), shoot and callus (GSC 381) and root and callus (GSC 233) specific expression of transcripts was identified. Although the protection of callus by treatment with ABA, kinetin and sucrose extended the period of expression of mRNA in suspension callus after gravity exposure, the expression of gravity-inducible mRNA was exclusively regulated by the degree of callus viability or survival after the stress. In addition, we demonstrated that the level of GSC 381 transcript was markedly increased by exposing the cell to periodical gravity stress, suggesting that this mRNA is expressed and translated into special proteins which are closely related to the survival of the cell against gravity stress. The sequence of GSC 233 and GSC 381, consisting of 417 and 531 base pairs of the longest open reading frames, encode polypeptides with calculated molecular weights of 15.29 and 19.47 kDa, respectively. A sequence homology search against a data bank revealed that GSC 233 and GSC 381 differed from other stress inducible genes in terms of the coding sequence and expression characteristics.

  1. Stable mercury isotope variation in rice plants (Oryza sativa L.) from the Wanshan mercury mining district, SW China.

    PubMed

    Yin, Runsheng; Feng, Xinbin; Meng, Bo

    2013-03-05

    To study the sources and transformations of Hg in the rice plant ( Oryza sativa L.), stable Hg isotope variations in different tissues (foliage, root, stem, and seed) of rice which were collected from the Wanshan mercury mine (WSMM, Guizhou province, SW China) were investigated by multicollector inductively coupled plasma mass spectrometry (MC-ICP-MS). In comparison, Hg isotope compositions of paddy soil, lichen, and direct ambient air samples in WSMM were also analyzed. We observed that mass dependent fractionation (MDF) of Hg differed by up to ∼ 3.0‰ in δ(202)Hg values and that mass independent fractionation (MIF) of Hg isotopes affected the odd Hg isotopes to produce a ∼ 0.40‰ range in Δ(199)Hg (and Δ(201)Hg) values in tissues of rice plant. The 1:1 Δ(199)Hg/Δ(201)Hg ratio in tissues of rice supported the hypothesis that a fraction of Hg in tissues of rice plants has undergone a photoreduction process prior to being accumulated by rice plants. We suggest that the variation of MIF represents a mixing between soil Hg and atmospheric Hg in rice plants. The estimated fraction of atmospheric Hg (f) in tissues of rice followed the trend of f leaf > f stem > f seed > f root. Finally, we demonstrated a significant MDF of >1.0‰ in δ(202)Hg during the processes of absorption of atmospheric Hg by leaf tissues and of absorption of soil Hg by roots. Our study demonstrated that Hg isotopes may represent an important contribution both to the study of Hg transportation in plants and to the understanding of sources of Hg contamination to critical food crops.

  2. Prediction of evapotranspiration and grain yield of rice ( Oryza sativa L. cv Thriveni) in a humid tropical climate

    NASA Astrophysics Data System (ADS)

    Rao, A. S.; Alexander, D.

    1988-06-01

    In a humid tropical climate at Pattambi (10° 48' N, 76° 12' E), the evapotranspiration (ET) rates of rice ( Oryza sativa L. cv. Thriveni) were 2.8 5.7 mm/day during the first crop season (May September) and 6.2 9.1 mm/day during the second crop season (September January). The crop was grown at the Station in the irrigated lowlands on sandy soils with average yields of 3025 and 2925 kg/ha in the first and second cropping seasons, respectively. The seasonal ET, water requirements, water use efficiency and field water use efficiency of the crop were 400 mm, 1150 mm, 7.56 and 2.63 kg/ha per mm in the first crop season and 650 mm, 1500 mm, 4.50 and 1.95 kg/ha per millimetre in the second crop season. Using the reference crop ET computed by Blaney-Criddle, Radiation, and Penman methods and measured evaporation from class A pan, Colorado and GGI 3000 pans, the crop coefficients were worked out. Correlations between weather parameters and the biomass of rice were obtained. The grain yield (Y, in kg/ha) of the crop was predicted using the equation Y=1.71 Y 0-56 S+85 F-2430 ( N=8, r=0.920), where Y 0 is the sample of biomass of the rice at flowering in kg/ha, S and F are the duration of sunshine hours and maximum air temperatures (°C) between the 46th day of transplanting and maturity.

  3. Improvement of efficient in vitro regeneration potential of mature callus induced from Malaysian upland rice seed (Oryza sativa cv. Panderas)

    PubMed Central

    Mohd Din, Abd Rahman Jabir; Iliyas Ahmad, Fauziah; Wagiran, Alina; Abd Samad, Azman; Rahmat, Zaidah; Sarmidi, Mohamad Roji

    2015-01-01

    A new and rapid protocol for optimum callus production and complete plant regeneration has been assessed in Malaysian upland rice (Oryza sativa) cv. Panderas. The effect of plant growth regulator (PGR) on the regeneration frequency of Malaysian upland rice (cv. Panderas) was investigated. Mature seeds were used as a starting material for callus induction experiment using various concentrations of 2,4-D and NAA. Optimal callus induction frequency at 90% was obtained on MS media containing 2,4-D (3 mg L−1) and NAA (2 mg L−1) after 6 weeks while no significant difference was seen on tryptophan and glutamine parameters. Embryogenic callus was recorded as compact, globular and light yellowish in color. The embryogenic callus morphology was further confirmed with scanning electron microscopy (SEM) analysis. For regeneration, induced calli were treated with various concentrations of Kin (0.5–1.5 mg L−1), BAP, NAA and 0.5 mg L−1 of TDZ. The result showed that the maximum regeneration frequency (100%) was achieved on MS medium containing BAP (0.5 mg L−1), Kin (1.5 mg L−1), NAA (0.5 mg L−1) and TDZ (0.5 mg L−1) within four weeks. Developed shoots were successfully rooted on half strength MS free hormone medium and later transferred into a pot containing soil for acclimatization. This cutting-edge finding is unique over the other existing publishable data due to the good regeneration response by producing a large number of shoots. PMID:26858569

  4. Selenium ameliorates arsenic induced oxidative stress through modulation of antioxidant enzymes and thiols in rice (Oryza sativa L.).

    PubMed

    Kumar, Amit; Singh, Rana Pratap; Singh, Pradyumna Kumar; Awasthi, Surabhi; Chakrabarty, Debasis; Trivedi, Prabodh Kumar; Tripathi, Rudra Deo

    2014-09-01

    Arsenic (As) contamination of rice is a major problem for South-East Asia. In the present study, the effect of selenium (Se) on rice (Oryza sativa L.) plants exposed to As was studied in hydroponic culture. Arsenic accumulation, plant growth, thiolic ligands and antioxidative enzyme activities were assayed after single (As and Se) and simultaneous supplementations (As + Se). The results indicated that the presence of Se (25 µM) decreased As accumulation by threefold in roots and twofold in shoots as compared to single As (25 µM) exposed plants. Arsenic induced oxidative stress in roots and shoots was significantly ameliorated by Se supplementation. The observed positive response was found associated with the increased activities of ascorbate peroxidase (APX; EC 1.11.1.11), catalase (CAT; EC 1.11.1.6) and glutathione peroxidase (GPx; EC 1.11.1.9) and induced levels of non-protein thiols (NPTs), glutathione (GSH) and phytochelatins (PCs) in As + Se exposed plants as compared to single As treatment. Selenium supplementation modulated the thiol metabolism enzymes viz., γ-glutamylcysteine synthetase (γ-ECS; EC 6.3.2.2), glutathione-S-transferase (GST; EC 2.5.1.18) and phytochelatin synthase (PCS; EC 2.3.2.15). Gene expression analysis of several metalloid responsive genes (LOX, SOD and MATE) showed upregulation during As stress, however, significant downregulation during As + Se exposure as compared to single As treatment. Gene expressions of enzymes of antioxidant and GSH and PC biosynthetic systems, such as APX, CAT, GPx, γ-ECS and PCS were found to be significantly positively correlated with their enzyme activities. The findings suggested that Se supplementation could be an effective strategy to reduce As accumulation and toxicity in rice plants.

  5. Root aquaporins contribute to whole plant water fluxes under drought stress in rice (Oryza sativa L.).

    PubMed

    Grondin, Alexandre; Mauleon, Ramil; Vadez, Vincent; Henry, Amelia

    2016-02-01

    Aquaporin activity and root anatomy may affect root hydraulic properties under drought stress. To better understand the function of aquaporins in rice root water fluxes under drought, we studied the root hydraulic conductivity (Lpr) and root sap exudation rate (Sr) in the presence or absence of an aquaporin inhibitor (azide) under well-watered conditions and following drought stress in six diverse rice varieties. Varieties varied in Lpr and Sr under both conditions. The contribution of aquaporins to Lpr was generally high (up to 79% under well-watered conditions and 85% under drought stress) and differentially regulated under drought. Aquaporin contribution to Sr increased in most varieties after drought, suggesting a crucial role for aquaporins in osmotic water fluxes during drought and recovery. Furthermore, root plasma membrane aquaporin (PIP) expression and root anatomical properties were correlated with hydraulic traits. Three chromosome regions highly correlated with hydraulic traits of the OryzaSNP panel were identified, but did not co-locate with known aquaporins. These results therefore highlight the importance of aquaporins in the rice root radial water pathway, but emphasize the complex range of additional mechanisms related to root water fluxes and drought response.

  6. 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

  7. Population structure analysis and association mapping of blast resistance in indica rice (Oryza sativa L.) landraces.

    PubMed

    Wu, Y Y; He, J B; Li, A H; Fang, N Y; He, W W; Dang, L L; Zeng, G Y; Huang, J; Bao, Y M; Zhang, H S

    2016-08-12

    Rice blast caused by Magnaporthe oryzae is one of the most devastating rice diseases worldwide. To understand the genetic diversity of indica landrace accessions and identify simple sequence repeat (SSR) markers that are associated with blast resistance, a population of 276 indica landraces from across the world was constructed. This population was then used to evaluate the blast-resistance phenotype through artificial inoculation under controlled conditions in 2012 and 2013. The genetic diversity and association of the population with resistance were analyzed by examining the phenotype for 160 SSR markers distributed on 12 rice chromosomes. The 276 accessions were classified into seven groups using model- and distance-based cluster analyses. Associations between SSR markers and blast resistance showed that 26 SSR markers were significantly associated with blast resistance in 2012 and 2013 (P < 0.01) and that the phenotypic variation ranged from 2.68 to 13.11%. Nineteen of the markers associated with blast resistance were located in regions where genes or quantitative trait loci (QTLs) have been previously reported, and seven were newly identified in this study. These results indicate that marker-trait association has potential advantages over classical linkage analysis and QTL mapping, and that these markers could be used for marker-assisted selection in rice blast-resistance-breeding programs.

  8. Molecular cytogenetic analysis of monoecious hemp (Cannabis sativa L.) cultivars reveals its karyotype variations and sex chromosomes constitution.

    PubMed

    Razumova, Olga V; Alexandrov, Oleg S; Divashuk, Mikhail G; Sukhorada, Tatiana I; Karlov, Gennady I

    2016-05-01

    Hemp (Cannabis sativa L., 2n = 20) is a dioecious plant. Sex expression is controlled by an X-to-autosome balance system consisting of the heteromorphic sex chromosomes XY for males and XX for females. Genetically monoecious hemp offers several agronomic advantages compared to the dioecious cultivars that are widely used in hemp cultivation. The male or female origin of monoecious maternal plants is unknown. Additionally, the sex chromosome composition of monoecious hemp forms remains unknown. In this study, we examine the sex chromosome makeup in monoecious hemp using a cytogenetic approach. Eight monoecious and two dioecious cultivars were used. The DNA of 210 monoecious plants was used for PCR analysis with the male-associated markers MADC2 and SCAR323. All monoecious plants showed female amplification patterns. Fluorescence in situ hybridization (FISH) with the subtelomeric CS-1 probe to chromosomes plates and karyotyping revealed a lack of Y chromosome and presence of XX sex chromosomes in monoecious cultivars with the chromosome number 2n = 20. There was a high level of intra- and intercultivar karyotype variation detected. The results of this study can be used for further analysis of the genetic basis of sex expression in plants.

  9. Germinated Pigmented Rice (Oryza Sativa L. cv. Superhongmi) Improves Glucose and Bone Metabolisms in Ovariectomized Rats

    PubMed Central

    Chung, Soo Im; Ryu, Su Noh; Kang, Mi Young

    2016-01-01

    The effect of germinated Superhongmi, a reddish brown pigmented rice cultivar, on the glucose profile and bone turnover in the postmenopausal-like model of ovariectomized rats was determined. The ovariectomized Sprague-Dawley rats were randomly divided into three dietary groups (n = 10): normal control diet (NC) and normal diet supplemented with non-germinated Superhongmi (SH) or germinated Superhongmi (GSH) rice powder. After eight weeks, the SH and GSH groups showed significantly lower body weight, glucose and insulin concentrations, levels of bone resorption markers and higher glycogen and 17-β-estradiol contents than the NC group. The glucose metabolism improved through modulation of adipokine production and glucose-regulating enzyme activities. The GSH rats exhibited a greater hypoglycemic effect and lower bone resorption than SH rats. These results demonstrate that germinated Superhongmi rice may potentially be useful in the prevention and management of postmenopausal hyperglycemia and bone turnover imbalance. PMID:27775654

  10. Development of genetic markers linked to straighthead resistance through fine mapping in rice (Oryza sativa L.).

    PubMed

    Pan, Xuhao; Zhang, Qijun; Yan, Wengui; Jia, Melissa; Jackson, Aaron; Li, Xiaobai; Jia, Limeng; Huang, Bihu; Xu, Peizhou; Correa-Victoria, Fernando; Li, Shigui

    2012-01-01

    Straighthead, a physiological disorder characterized by sterile florets and distorted spikelets, causes significant yield losses in rice, and occurs in many countries. The current control method of draining paddies early in the season stresses plants, is costly, and wastes water. Development of resistant cultivar is regarded as the most efficient way for its control. We mapped a QTL for straighthead resistance using two recombinant inbred line (RIL) F(9) populations that were phenotyped over two years using monosodium methanearsonate (MSMA) to induce the symptoms. One population of 170 RILs was genotyped with 136 SSRs and the other population of 91 RILs was genotyped with 159 SSRs. A major QTL qSH-8 was identified in an overlapping region in both populations, and explained 46% of total variation in one and 67% in another population for straighthead resistance. qSH-8 was fine mapped from 1.0 Mbp to 340 kb using 7 SSR markers and further mapped to 290 kb in a population between RM22573 and InDel 27 using 4 InDel markers. SSR AP3858-1 and InDel 11 were within the fine mapped region, and co-segregated with straighthead resistance in both RIL populations, as well as in a collection of diverse global accessions. These results demonstrate that AP3858-1 and InDel 11 can be used for marker-assisted selection (MAS) for straighthead resistant cultivars, which is especially important because there is no effective way to directly evaluate straighthead resistance.

  11. Unraveling the Complex Trait of Harvest Index with Association Mapping in Rice (Oryza sativa L.)

    PubMed Central

    Li, Xiaobai; Yan, Wengui; Agrama, Hesham; Jia, Limeng; Jackson, Aaron; Moldenhauer, Karen; Yeater, Kathleen; McClung, Anna; Wu, Dianxing

    2012-01-01

    Harvest index is a measure of success in partitioning assimilated photosynthate. An improvement of harvest index means an increase in the economic portion of the plant. Our objective was to identify genetic markers associated with harvest index traits using 203 O. sativa accessions. The phenotyping for 14 traits was conducted in both temperate (Arkansas) and subtropical (Texas) climates and the genotyping used 154 SSRs and an indel marker. Heading, plant height and weight, and panicle length had negative correlations, while seed set and grain weight/panicle had positive correlations with harvest index across both locations. Subsequent genetic diversity and population structure analyses identified five groups in this collection, which corresponded to their geographic origins. Model comparisons revealed that different dimensions of principal components analysis (PCA) affected harvest index traits for mapping accuracy, and kinship did not help. In total, 36 markers in Arkansas and 28 markers in Texas were identified to be significantly associated with harvest index traits. Seven and two markers were consistently associated with two or more harvest index correlated traits in Arkansas and Texas, respectively. Additionally, four markers were constitutively identified at both locations, while 32 and 24 markers were identified specifically in Arkansas and Texas, respectively. Allelic analysis of four constitutive markers demonstrated that allele 253 bp of RM431 had significantly greater effect on decreasing plant height, and 390 bp of RM24011 had the greatest effect on decreasing panicle length across both locations. Many of these identified markers are located either nearby or flanking the regions where the QTLs for harvest index have been reported. Thus, the results from this association mapping study complement and enrich the information from linkage-based QTL studies and will be the basis for improving harvest index directly and indirectly in rice. PMID:22291889

  12. 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.

  13. Inheritance of Gelatinization Temperature and Gel Consistency in Rice (Oryza sativa L.)

    NASA Astrophysics Data System (ADS)

    Kiani; Sh.; Ranjbar, G. A.; Kazemitabar, S. K.; Jelodar, N. B.; Nowrozi, M.; Bagheri, N.

    Gelatinization Temperature (GT) and Gel Consistency (GC) are important traits in determination of rice quality. In present study four rice cultivars namely Sang-e-Tarrom, Gerdeh, IR229 and IRRI2 have been utilized in hybridization as parents. In order to know about genetic characteristics and inheritance of the related traits, direct and reciprocal crosses have been conducted between parents Sang-e-Tarrom and Gerdeh and between IR229 and IRRI2. Inheritance of related traits have been studied in direct and reciprocal hybridizations for hard, intermediate and soft GC, low and high GT. For these evaluations P1, P2, F1, F2, BC1, BC2 generations and their reciprocal crosses have been utilized in present study. Results showed that gene hard GC dominates on intermediate and soft and also intermediate GT dominates on low. From direct and reciprocal crosses Gerdeh x Sang-e-Tarrom and IR229 x IRRI2 have been illustrated that GC and GT expressions are under monogenic control of one major gene corresponding with several modifier genes. Gene dosage effects play a tremendously important and effective role in segregation production among traits. Regarding to the obtained results selections can effectively be performed in later segregation generations for GC and in early generations for GT.

  14. Fine mapping of the lesion mimic and early senescence 1 (lmes1) in rice (Oryza sativa).

    PubMed

    Li, Zhi; Zhang, Yingxin; Liu, Lin; Liu, Qunen; Bi, Zhenzhen; Yu, Ning; Cheng, Shihua; Cao, Liyong

    2014-07-01

    A novel rice mutant, lesion mimic and early senescence 1 (lmes1), was induced from the rice 93-11 cultivar in a γ-ray field. This mutant exhibited spontaneous disease-like lesions in the absence of pathogen attack at the beginning of the tillering stage. Moreover, at the booting stage, lmes1 mutants exhibited a significantly increased MDA but decreased chlorophyll content, soluble protein content and photosynthetic rate in the leaves, which are indicative of an early senescence phenotype. The lmes1 mutant was significantly more resistant than 93-11 against rice bacterial blight infection, which was consistent with a marked increase in the expression of three resistance-related genes. Here, we employed a map-based cloning approach to finely map the lmes1 gene. In an initial mapping with 94 F2 individuals derived from a cross between the lmes1 mutant and Nipponbare, the lmes1 gene was located in a 10.6-cM region on the telomere of the long arm of chromosome 7 using simple sequence repeat (SSR) markers. To finely map lmes1, we derived two F2 populations with 940 individuals from two crosses between the lmes1 mutant and two japonica rice varieties, Nipponbare and 02428. Finally, the lmes1 gene was mapped to an 88-kb region between two newly developed inDel markers, Zl-3 and Zl-22, which harbored 15 ORFs.

  15. Establishment of an in vitro fertilization system in rice (Oryza sativa L.).

    PubMed

    Uchiumi, Takao; Uemura, Isao; Okamoto, Takashi

    2007-08-01

    In vitro fertilization (IVF) systems using isolated male and female gametes have been utilized to dissect fertilization-induced events in angiosperms, such as egg activation, zygote development and early embryogenesis, as the female gametophytes of plants are deeply embedded within ovaries. In this study, a rice IVF system was established to take advantage of the abundant resources stemming from rice research for investigations into the mechanisms of fertilization and early embryogenesis. Fusion of gametes was performed using a modified electrofusion method, and the fusion product, a zygote, formed cell wall and an additional nucleolus. The zygote divided into a two-celled embryo 15-24 h after fusion, and developed into a globular-like embryo consisting of an average of 15-16 cells by 48 h after fusion. Comparison of the developmental processes of zygotes produced by IVF with those of zygotes generated in planta suggested that zygotes produced by IVF develop and grow into early globular stage embryos in a highly similar manner to those in planta. Although the IVF-produced globular embryos did not develop into late globular-stage or differentiated embryos, but into irregularly shaped cell masses, fertile plants were regenerated from the cell masses and the seeds harvested from these plants germinated normally. The rice IVF system reported here will be a powerful tool for studying the molecular mechanisms involved in the early embryogenesis of angiosperms and for making new cultivars.

  16. Allele Mining Strategies: Principles and Utilisation for Blast Resistance Genes in Rice (Oryza sativa L.).

    PubMed

    Ashkani, Sadegh; Yusop, Mohd Rafii; Shabanimofrad, Mahmoodreza; Azady, Amin; Ghasemzadeh, Ali; Azizi, Parisa; Latif, Mohammad Abdul

    2015-01-01

    Allele mining is a promising way to dissect naturally occurring allelic variants of candidate genes with essential agronomic qualities. With the identification, isolation and characterisation of blast resistance genes in rice, it is now possible to dissect the actual allelic variants of these genes within an array of rice cultivars via allele mining. Multiple alleles from the complex locus serve as a reservoir of variation to generate functional genes. The routine sequence exchange is one of the main mechanisms of R gene evolution and development. Allele mining for resistance genes can be an important method to identify additional resistance alleles and new haplotypes along with the development of allele-specific markers for use in marker-assisted selection. Allele mining can be visualised as a vital link between effective utilisation of genetic and genomic resources in genomics-driven modern plant breeding. This review studies the actual concepts and potential of mining approaches for the discovery of alleles and their utilisation for blast resistance genes in rice. The details provided here will be important to provide the rice breeder with a worthwhile introduction to allele mining and its methodology for breakthrough discovery of fresh alleles hidden in hereditary diversity, which is vital for crop improvement.

  17. Traditional and modern plant breeding methods with examples in rice (Oryza sativa L.).

    PubMed

    Breseghello, Flavio; Coelho, Alexandre Siqueira Guedes

    2013-09-04

    Plant breeding can be broadly defined as alterations caused in plants as a result of their use by humans, ranging from unintentional changes resulting from the advent of agriculture to the application of molecular tools for precision breeding. The vast diversity of breeding methods can be simplified into three categories: (i) plant breeding based on observed variation by selection of plants based on natural variants appearing in nature or within traditional varieties; (ii) plant breeding based on controlled mating by selection of plants presenting recombination of desirable genes from different parents; and (iii) plant breeding based on monitored recombination by selection of specific genes or marker profiles, using molecular tools for tracking within-genome variation. The continuous application of traditional breeding methods in a given species could lead to the narrowing of the gene pool from which cultivars are drawn, rendering crops vulnerable to biotic and abiotic stresses and hampering future progress. Several methods have been devised for introducing exotic variation into elite germplasm without undesirable effects. Cases in rice are given to illustrate the potential and limitations of different breeding approaches.

  18. A novel 5-enolpyruvoylshikimate-3-phosphate (EPSP) synthase transgene for glyphosate resistance stimulates growth and fecundity in weedy rice (Oryza sativa) without herbicide.

    PubMed

    Wang, Wei; Xia, Hui; Yang, Xiao; Xu, Ting; Si, Hong Jiang; Cai, Xing Xing; Wang, Feng; Su, Jun; Snow, Allison A; Lu, Bao-Rong

    2014-04-01

    Understanding evolutionary interactions among crops and weeds can facilitate effective weed management. For example, gene flow from crops to their wild or weedy relatives can lead to rapid evolution in recipient populations. In rice (Oryza sativa), transgenic herbicide resistance is expected to spread to conspecific weedy rice (Oryza sativa f. spontanea) via hybridization. Here, we studied fitness effects of transgenic over-expression of a native 5-enolpyruvoylshikimate-3-phosphate synthase (epsps) gene developed to confer glyphosate resistance in rice. Controlling for genetic background, we examined physiological traits and field performance of crop-weed hybrid lineages that segregated for the presence or absence of this novel epsps transgene. Surprisingly, we found that transgenic F2 crop-weed hybrids produced 48-125% more seeds per plant than nontransgenic controls in monoculture- and mixed-planting designs without glyphosate application. Transgenic plants also had greater EPSPS protein levels, tryptophan concentrations, photosynthetic rates, and per cent seed germination compared with nontransgenic controls. Our findings suggest that over-expression of a native rice epsps gene can lead to fitness advantages, even without exposure to glyphosate. We hypothesize that over-expressed epsps may be useful to breeders and, if deployed, could result in fitness benefits in weedy relatives following transgene introgression.

  19. A novel 5-enolpyruvoylshikimate-3-phosphate (EPSP) synthase transgene for glyphosate resistance stimulates growth and fecundity in weedy rice (Oryza sativa) without herbicide

    PubMed Central

    Wang, Wei; Xia, Hui; Yang, Xiao; Xu, Ting; Si, Hong Jiang; Cai, Xing Xing; Wang, Feng; Su, Jun; Snow, Allison A; Lu, Bao-Rong

    2014-01-01

    Understanding evolutionary interactions among crops and weeds can facilitate effective weed management. For example, gene flow from crops to their wild or weedy relatives can lead to rapid evolution in recipient populations. In rice (Oryza sativa), transgenic herbicide resistance is expected to spread to conspecific weedy rice (Oryza sativa f. spontanea) via hybridization. Here, we studied fitness effects of transgenic over-expression of a native 5-enolpyruvoylshikimate-3-phosphate synthase (epsps) gene developed to confer glyphosate resistance in rice. Controlling for genetic background, we examined physiological traits and field performance of crop–weed hybrid lineages that segregated for the presence or absence of this novel epsps transgene. Surprisingly, we found that transgenic F2 crop–weed hybrids produced 48–125% more seeds per plant than nontransgenic controls in monoculture- and mixed-planting designs without glyphosate application. Transgenic plants also had greater EPSPS protein levels, tryptophan concentrations, photosynthetic rates, and per cent seed germination compared with nontransgenic controls. Our findings suggest that over-expression of a native rice epsps gene can lead to fitness advantages, even without exposure to glyphosate. We hypothesize that over-expressed epsps may be useful to breeders and, if deployed, could result in fitness benefits in weedy relatives following transgene introgression. PMID:23905647

  20. 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.

  1. Allelopathic Activity of Extracts from Different Brazilian Peanut (Arachis hypogaea L.) Cultivars on Lettuce (Lactuca sativa) and Weed Plants

    PubMed Central

    Garcia, R.; Simas, N. K.

    2017-01-01

    Peanut (Arachis hypogaea L.) is the fourth most consumed oleaginous plant in the world, producing seeds with high contents of lipids, proteins, vitamins, and carbohydrates. Biological activities of different extracts of this species have already been evaluated by many researchers, including antioxidant, antitumoral, and antibacterial. In this work, the allelopathic activity of extracts from different Brazilian peanut cultivars against lettuce (Lactuca sativa) and two weed plants (Commelina benghalensis and Ipomoea nil) was studied. Aerial parts, roots, seeds, and seed coats were used for the preparation of crude extracts. Seed extract partitioning was performed with n-hexane, dichloromethane, ethyl acetate, n-butanol, and aqueous residue. Germination and growth of hypocotyls and rootlets were evaluated after one and five days of incubation with plant extracts, respectively. Crude seed extract and its dichloromethanic partition displayed highest allelopathic activity. These results contribute for the study of new potential natural herbicides.

  2. Comparison of power output by rice (Oryza sativa) and an associated weed (Echinochloa glabrescens) in vascular plant bio-photovoltaic (VP-BPV) systems.

    PubMed

    Bombelli, Paolo; Iyer, Durgaprasad Madras Rajaraman; Covshoff, Sarah; McCormick, Alistair J; Yunus, Kamran; Hibberd, Julian M; Fisher, Adrian C; Howe, Christopher J

    2013-01-01

    Vascular plant bio-photovoltaics (VP-BPV) is a recently developed technology that uses higher plants to harvest solar energy and the metabolic activity of heterotrophic microorganisms in the plant rhizosphere to generate electrical power. In the present study, electrical output and maximum power output variations were investigated in a novel VP-BPV configuration using the crop plant rice (Oryza sativa L.) or an associated weed, Echinochloa glabrescens (Munro ex Hook. f.). In order to compare directly the physiological performances of these two species in VP-BPV systems, plants were grown in the same soil and glasshouse conditions, while the bio-electrochemical systems were operated in the absence of additional energy inputs (e.g. bias potential, injection of organic substrate and/or bacterial pre-inoculum). Diurnal oscillations were clearly observed in the electrical outputs of VP-BPV systems containing the two species over an 8-day growth period. During this 8-day period, O. sativa generated charge ∼6 times faster than E. glabrescens. This greater electrogenic activity generated a total charge accumulation of 6.75 ± 0.87 Coulombs for O. sativa compared to 1.12 ± 0.16 for E. glabrescens. The average power output observed over a period of about 30 days for O. sativa was significantly higher (0.980 ± 0.059 GJ ha(-1) year(-1)) than for E. glabrescens (0.088 ± 0.008 GJ ha(-1) year(-1)). This work indicates that electrical power can be generated in both VP-BPV systems (O. sativa and E. glabrescens) when bacterial populations are self-forming. Possible reasons for the differences in power outputs between the two plant species are discussed.

  3. Evaluations of allelopathic effect of Echinochloa colona weed on rice (Oryza sativa L. 'Vandana').

    PubMed

    Swain, D; Paroha, Seema; Singh, Monika; Subudhi, H N

    2012-09-01

    Echinochloa colona (L.) Link is a very problematic weed in up land and medium land rice causing significant reduction in yield. In the present investigation, laboratory and field experiments were conducted to evaluate the nature of interaction E. colona on germination and growth of the up land rice cultivar 'Vandana'. The effects of decomposing and decomposed aqueous leachates (1-10% w/v) obtained from the dried biomass of 20, 30, 40 and 60 days old Ecolona plants were studied on rice using petridish bioassay technique with three different types of culture media like filter paper, soil, and soil + activated charcoal. The decomposing leachates of E. colona showed strong toxic effect on root and shoot growth of rice, the highest being noted with 10% leachates of 60 days old plant residue. It inhibited root and shoot growth by 100% and 43.9% respectively as compared to control. The corresponding decomposed leachates inhibited rice germination by 90% and root and shoot growth by 70 and 25% respectively. These toxic effects of leachates showed in filter paper medium were significantly reduced in soil and soil plus activated charcoal media proving their allelopathic nature. In a field experiment, E. colona and rice were grown in proportions of 1:1, 1: 2 and 1:4, the total plant density being maintained at 100 pants m(-2). The height and dry matter of rice were adversely affected with increasing in E. colona population. From another similar field trial, data on dry matter of 20, 30, 40, and 60 days old plants were taken and their plant relative yield (PRY) and relative yield total (RYT) values were calculated. The PRY and RYT values were found to be less than unit (< 1) throughout the growth period studied which suggested the presence of severe antagonistic interspecific interaction between rice and E. colona due to allelopathy.

  4. Analysis of population structure and genetic diversity of Egyptian and exotic rice (Oryza sativa L.) genotypes.

    PubMed

    Salem, Khaled F M; Sallam, Ahmed

    2016-01-01

    Understanding the population structure and genetic diversity is a very important goal to improve the economic value of crops. In rice, a loss of genetic diversity in the last few centuries is observed. To address this challenge, a set of 22 lines from three different regions - India (two), and Philippines (six), and Egypt (14) - were used to assess the genetic diversity and the features of population structure. These genotypes were analyzed using 106 SSR alleles that showed a clear polymorphism among the lines. Genetic diversity was estimated based on the number of different alleles, polymorphism information content (PIC), and gene diversity. A total of 106 SSR alleles was identified from the 23 SSR loci and used to study the population structure and carry out a cluster analysis. All SSR loci showed a wide range of the number of different alleles extended from two (one loci) to seven alleles (three loci). Five and eight loci showed high PIC and gene diversity (≥0.70), respectively. The results of population structure are in agreement with cluster analysis results. Both analyses revealed two different subpopulations (G1 and G2) with different genetic properties in number of private alleles, number of different alleles (Na), number of effective alleles (Ne), expected heterozygosity (He), and Shannon's Information Index (SII). Our findings indicate that five SSR loci (RM 111, RM 307, RM 22, RM 19, and RM 271) could be used in breeding programs to enhance the marker-assisted selection through QTL mapping and association studies. A high genetic diversity found between genotypes which can be exploited to improve and produce rice cultivars for important traits (e.g. high agronomic features and tolerance to biotic or/and abiotic stresses).

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

    PubMed

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

    2010-01-01

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

  6. Joint Mapping and Allele Mining of the Rolled Leaf Trait in Rice (Oryza sativa L.)

    PubMed Central

    Wang, Chunchao; Nafisah; Joseph, Charles; Zhang, Wenzhong; Xu, Jianlong; Li, Zhikang

    2016-01-01

    The rolled leaf trait, long considered to be a key component of plant architecture, represents an important target trait for improving plant architecture at the population level. We therefore performed linkage mapping using a set of 262 highly variable RILs from two rice cultivars (Minghui 63 and 02428) with minor differences in leaf rolling index (LRI) in conjunction with GWAS mapping of a random subset of the 1127 germplasms from the 3K Rice Genomes Project (3K Rice). A total of seven main-effect loci were found to underlie the transgressive segregation of progenies from parents with minor differences in LRI. Five of these loci were previously identified and two (qRl7b and qRl9b) are newly reported with additional evidence from GWAS mapping for qRl7b. A total of 18 QTLs were identified by GWAS, including four newly identified QTLs. Six QTLs were confirmed by linkage mapping with the above RIL population, and 83.3% were found to be consistent with previously reported loci based on comparative mapping. We also performed allele mining with representative SNPs and identified the elite germplasms for the improvement of rolled leaf trait. Most favorable alleles at the detected loci were contributed by various 3K Rice germplasms. By a re-scanning of the candidate region with more saturated SNP markers, we dissected the region harboring gRl4-2 into three subregions, in which the average effect on LRI was 3.5% with a range from 2.4 to 4.1% in the third subregion, suggesting the presence of a new locus or loci within this region. The representative SNPs for favorable alleles in the reliable QTLs which were consistently identified in both bi-parental mapping and GWAS, such as qRl4, qRl5, qRl6, qRl7a, and qRl7b will be useful for future molecular breeding programs for ideal plant type in rice. PMID:27441398

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Background: Lettuce (Lactuca sativa L.) is the major vegetable from the group of leafy vegetables. Several types of molecular markers were developed that are effictively used in lettuce breeding and genetic studies. However only a very limited number of microsattelite-based markers are publicly avai...

  8. Seed Dormancy in Red Rice (Oryza sativa) (IX. Embryo Fructose-2,6-Bisphosphate during Dormancy Breaking and Subsequent Germination).

    PubMed Central

    Footitt, S.; Cohn, M. A.

    1995-01-01

    Fructose-2,6-bisphosphate (Fru-2,6-bisP) was evaluated as a potential marker for the dormancy-breaking phase or the germination phase before pericarp splitting in red rice (Oryza sativa). During 4 h of imbibition at 30[deg]C, Fru-2,6-bisP of dehulled dormant and nondormant seeds increased to 0.26 and 0.38 pmol embryo-1, respectively. In nondormant seeds, embryo Fru-2,6-bisP content remained stable until the onset of pericarp splitting (12 h) and increased rapidly thereafter. In dormant seeds, Fru-2,6-bisP declined to 0.09 pmol embryo-1 at 24 h. Embryo Fru-2,6-bisP was correlated with O2 uptake of dormant and nondormant seeds. A 24-h exposure of dehulled, water-imbibed, dormant seeds to treatments yielding >90% germination (sodium nitrite [4 mM], propionic acid [22 mM], methyl propionate [32 mM], propanol [75 mM], and propionaldehyde [40 mM]) led to changes in embryo Fru-2,6-bisP that were unrelated to the final germination percentages. Furthermore, a 2-h pulse of propionaldehyde increased Fru-2,6-bisP 4-fold but did not break dormancy. Whereas nitrite and propionaldehyde increased Fru-2,6-bisP to 0.33 pmol embryo-1 after 2 h of contact, propionic acid and methyl propionate did not increase Fru-2,6-bisP above the untreated control. In all cases, further increases in Fru-2,6-bisP occurred after pericarp splitting. However, the plateau Fru-2,6-bisP attained during chemical contact was inversely correlated with elapsed time to 30% germination (r = -0.978). Therefore, although Fru-2,6-bisP is not a universal marker for dormancy release, its rapid increase during nitrite and propionaldehyde treatments suggests that events associated with dormancy breaking can occur within 2 h of chemical treatment. PMID:12228440

  9. Gene Space Dynamics During the Evolution of Aegilops tauschii, Brachypodium distachyon, Oryza sativa, and Sorghum bicolor Genomes

    PubMed Central

    Massa, A. N.; Wanjugi, H.; Deal, K. R.; O'Brien, K.; You, F. M.; Maiti, R.; Chan, A. P.; Gu, Y. Q.; Luo, M. C.; Anderson, O. D.; Rabinowicz, P. D.; Dvorak, J.; Devos, K. M.

    2011-01-01

    Nine different regions totaling 9.7 Mb of the 4.02 Gb Aegilops tauschii genome were sequenced using the Sanger sequencing technology and compared with orthologous Brachypodium distachyon, Oryza sativa (rice), and Sorghum bicolor (sorghum) genomic sequences. The ancestral gene content in these regions was inferred and used to estimate gene deletion and gene duplication rates along each branch of the phylogenetic tree relating the four species. The total gene number in the extant Ae. tauschii genome was estimated to be 36,371. The gene deletion and gene duplication rates and total gene numbers in the four genomes were used to estimate the total gene number in each node of the phylogenetic tree. The common ancestor of the Brachypodieae and Triticeae lineages was estimated to have had 28,558 genes, and the common ancestor of the Panicoideae, Ehrhartoideae, and Pooideae subfamilies was estimated to have had 27,152 or 28,350 genes, depending on the ancestral gene scenario. Relative to the Brachypodieae and Triticeae common ancestor, the gene number was reduced in B. distachyon by 3,026 genes and increased in Ae. tauschii by 7,813 genes. The sum of gene deletion and gene duplication rates, which reflects the rate of gene synteny loss, was correlated with the rate of structural chromosome rearrangements and was highest in the Ae. tauschii lineage and lowest in the rice lineage. The high rate of gene space evolution in the Ae. tauschii lineage accounts for the fact that, contrary to the expectations, the level of synteny between the phylogenetically more related Ae. tauschii and B. distachyon genomes is similar to the level of synteny between the Ae. tauschii genome and the genomes of the less related rice and sorghum. The ratio of gene duplication to gene deletion rates in these four grass species closely parallels both the total number of genes in a species and the overall genome size. Because the overall genome size is to a large extent a function of the repeated

  10. Gene space dynamics during the evolution of Aegilops tauschii, Brachypodium distachyon, Oryza sativa, and Sorghum bicolor genomes.

    PubMed

    Massa, A N; Wanjugi, H; Deal, K R; O'Brien, K; You, F M; Maiti, R; Chan, A P; Gu, Y Q; Luo, M C; Anderson, O D; Rabinowicz, P D; Dvorak, J; Devos, K M

    2011-09-01

    Nine different regions totaling 9.7 Mb of the 4.02 Gb Aegilops tauschii genome were sequenced using the Sanger sequencing technology and compared with orthologous Brachypodium distachyon, Oryza sativa (rice), and Sorghum bicolor (sorghum) genomic sequences. The ancestral gene content in these regions was inferred and used to estimate gene deletion and gene duplication rates along each branch of the phylogenetic tree relating the four species. The total gene number in the extant Ae. tauschii genome was estimated to be 36,371. The gene deletion and gene duplication rates and total gene numbers in the four genomes were used to estimate the total gene number in each node of the phylogenetic tree. The common ancestor of the Brachypodieae and Triticeae lineages was estimated to have had 28,558 genes, and the common ancestor of the Panicoideae, Ehrhartoideae, and Pooideae subfamilies was estimated to have had 27,152 or 28,350 genes, depending on the ancestral gene scenario. Relative to the Brachypodieae and Triticeae common ancestor, the gene number was reduced in B. distachyon by 3,026 genes and increased in Ae. tauschii by 7,813 genes. The sum of gene deletion and gene duplication rates, which reflects the rate of gene synteny loss, was correlated with the rate of structural chromosome rearrangements and was highest in the Ae. tauschii lineage and lowest in the rice lineage. The high rate of gene space evolution in the Ae. tauschii lineage accounts for the fact that, contrary to the expectations, the level of synteny between the phylogenetically more related Ae. tauschii and B. distachyon genomes is similar to the level of synteny between the Ae. tauschii genome and the genomes of the less related rice and sorghum. The ratio of gene duplication to gene deletion rates in these four grass species closely parallels both the total number of genes in a species and the overall genome size. Because the overall genome size is to a large extent a function of the repeated

  11. Suppression of OsRAD51D results in defects in reproductive development in rice (Oryza sativa L.).

    PubMed

    Byun, Mi Young; Kim, Woo Taek

    2014-07-01

    The cellular roles of RAD51 paralogs in somatic and reproductive growth have been extensively described in a wide range of animal systems and, to a lesser extent, in Arabidopsis, a dicot model plant. Here, the OsRAD51D gene was identified and characterized in rice (Oryza sativa L.), a monocot model crop. In the rice genome, three alternative OsRAD51D mRNA splicing variants, OsRAD51D.1, OsRAD51D.2, and OsRAD51D.3, were predicted. Yeast two-hybrid studies, however, showed that only OsRAD51D.1 interacted with OsRAD51B and OsRAD51C paralogs, suggesting that OsRAD51D.1 is a functional OsRAD51D protein in rice. Loss-of-function osrad51d mutant rice plants displayed normal vegetative growth. However, the mutant plants were defective in reproductive growth, resulting in sterile flowers. Homozygous osrad51d mutant flowers exhibited impaired development of lemma and palea and contained unusual numbers of stamens and stigmas. During early meiosis, osrad51d pollen mother cells (PMCs) failed to form normal homologous chromosome pairings. In subsequent meiotic progression, mutant PMCs represented fragmented chromosomes. The osrad51d pollen cells contained numerous abnormal micro-nuclei that resulted in malfunctioning pollen. The abnormalities of heterozygous mutant and T2 Ubi:RNAi-OsRAD51D RNAi-knock-down transgenic plants were intermediate between those of wild type and homozygous mutant plants. The osrad51d and Ubi:RNAi-OsRAD51D plants contained longer telomeres compared with wild type plants, indicating that OsRAD51D is a negative factor for telomere lengthening. Overall, these results suggest that OsRAD51D plays a critical role in reproductive growth in rice. This essential function of OsRAD51D is distinct from Arabidopsis, in which AtRAD51D is not an essential factor for meiosis or reproductive development.

  12. Effects of timing and severity of salinity stress on rice (Oryza sativa L.) yield, grain composition, and starch functionality.

    PubMed

    Thitisaksakul, Maysaya; Tananuwong, Kanitha; Shoemaker, Charles F; Chun, Areum; Tanadul, Orn-u-ma; Labavitch, John M; Beckles, Diane M

    2015-03-04

    The aim of this work was to examine agronomic, compositional, and functional changes in rice (Oryza sativa L. cv. Nipponbare) grains from plants grown under low-to-moderate salinity stress in the greenhouse. Plants were grown in sodium chloride-containing soil (2 or 4 dS/m(2) electrical conductivity), which was imposed 4-weeks after transplant (called Seedling EC2 and EC4) or after the appearance of the anthers (called Anthesis EC2 and EC4). The former simulates field conditions while the latter permits observation of the isolated effect of salt on grain filling processes. Key findings of this study are the following: (i) Plants showed adaptive responses to prolonged salt treatment with no negative effects on grain weight or fertility. Seedling EC2 plants had more panicles and enhanced caryopsis dimensions, while surprisingly, Seedling EC4 plants did not differ from the control group in the agronomic parameters measured. (ii) Grain starch increased in Seedling EC4 (32.6%) and Anthesis EC2 (39%), respectively, suggesting a stimulatory effect of salt on starch accumulation. (iii) The salinity treatment of 2 dS/m(2) was better tolerated at anthesis than the 4 dS/m(2) treatment as the latter led to reduced grain weight (28.8%) and seed fertility (19.4%) and compensatory increases in protein (20.1%) and nitrogen (19.8%) contents. (iv) Although some salinity treatments led to changes in starch content, these did not alter starch fine structure, morphology, or composition. We observed no differences in reducing sugar and amylose content or starch granule size distribution among any of the treatments. The only alterations in starch were limited to small changes in thermal properties and glucan chain distribution, which were only seen in the Anthesis EC4 treatment. This similarity of compositional and functional features was supported by multivariate analysis of all variables measured, which suggested that differences due to treatments were minimal. Overall, this study

  13. De novo Transcriptome Assembly of Phomopsis liquidambari Provides Insights into Genes Associated with Different Lifestyles in Rice (Oryza sativa L.).

    PubMed

    Zhou, Jun; Li, Xin; Chen, Yan; Dai, Chuan-Chao

    2017-01-01

    The mechanisms that trigger the switch from endophytic fungi to saprophytic fungi are largely unexplored. Broad host range Phomopsis liquidambari is established in endophytic and saprophytic systems with rice (Oryza sativa L.). Endophytic P. liquidambari promotes rice growth, increasing rice yield and improving the efficiency of nitrogen fertilizer. This species's saprophytic counterpart can decompose rice litterfall, promoting litter organic matter cycling and the release of nutrients and improving the soil microbial environment. Fluorescence microscopy, confocal laser scanning microscopy and quantitative PCR investigated the colonization dynamics and biomass of P. liquidambari in rice in vivo. P. liquidambari formed infection structures similar to phytopathogens with infected vascular tissues that systematically spread to acrial parts. However, different from pathogenic infection, P. liquidambari colonization exhibits space restriction and quantity restriction. Direct comparison of a fungal transcriptome under three different habitats provided a better understanding of lifestyle conversion during plant-fungi interactions. The isolated total RNA of Ck (pure culture), EP (endophytic culture) and FP (saprophytic culture) was subjected to Illumina transcriptome sequencing. To the best of our knowledge, this study is the first to investigate Phomopsis sp. using RNA-seq technology to obtain whole transcriptome information. A total of 27,401,258 raw reads were generated and 22,700 unigenes were annotated. Functional annotation indicated that carbohydrate metabolism and biosynthesis of secondary metabolites played important roles. There were 2522 differentially expressed genes (DEGs) between the saprophytic and endophytic lifestyles. Quantitative PCR analysis validated the DEGs of RNA-seq. Analysis of DEGs between saprophytic and endophytic lifestyles revealed that most genes from amino acids metabolism, carbohydrate metabolism, fatty acid biosynthesis, secondary

  14. Constitutive expression of a plant ferredoxin-like protein (pflp) enhances capacity of photosynthetic carbon assimilation in rice (Oryza sativa).

    PubMed

    Chang, Hsiang; Huang, Hsiang-En; Cheng, Chin-Fu; Ho, Mei-Hsuan; Ger, Mang-Jye

    2017-04-01

    The plant ferredoxin-like protein (PFLP) gene, cloned from sweet peppers predicted as an electron carrier in photosynthesis, shows high homology to the Fd-I sequence of Arabidopsis thaliana, Lycopersicon esculentum, Oryza sativa and Spinacia oleracea. Most of pflp related studies focused on anti-pathogenic effects, while less understanding for the effects in photosynthesis with physiological aspects, such as photosynthesis rate, and levels of carbohydrate metabolites. This project focuses on the effects of pflp overexpression on photosynthesis by physiological evaluations of carbon assimilation with significant higher levels of carbohydrates with higher photosynthesis efficiency. In this report, two independent transgenic lines of rice plants (designated as pflp-1 and pflp-2) were generated from non-transgenic TNG67 rice plant (WT). Both transgenic pflp rice plants exhibited enhanced photosynthesis efficiency, and gas exchange rates of photosynthesis were 1.3- and 1.2-fold higher for pflp-1 and pflp-2 than WT respectively. Significantly higher electron transport rates of pflp rice plants were observed. Moreover, photosynthetic products, such as fructose, glucose, sucrose and starch contents of pflp transgenic lines were increased accordingly. Molecular evidences of carbohydrate metabolism related genes activities (osHXK5, osHXK6, osAGPL3, osAGPS2α, osSPS, ospFBPase, oscFBPase, and osSBPase) in transgenic lines were higher than those of WT. For performance of crop production, 1000-grain weight for pflp-1 and pflp-2 rice plants were 52.9 and 41.1 g that were both significantly higher than 31.6 g for WT, and panicles weights were 1.4- and 1.2-fold higher than WT. Panicle number, tiller number per plants for pflp rice plants were all significantly higher compared with those of WT where there was no significant difference observed between two pflp rice plants. Taken altogether; this study demonstrated that constitutive pflp expression can improve rice production by

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

    PubMed Central

    2012-01-01

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

  16. De novo Transcriptome Assembly of Phomopsis liquidambari Provides Insights into Genes Associated with Different Lifestyles in Rice (Oryza sativa L.)

    PubMed Central

    Zhou, Jun; Li, Xin; Chen, Yan; Dai, Chuan-Chao

    2017-01-01

    The mechanisms that trigger the switch from endophytic fungi to saprophytic fungi are largely unexplored. Broad host range Phomopsis liquidambari is established in endophytic and saprophytic systems with rice (Oryza sativa L.). Endophytic P. liquidambari promotes rice growth, increasing rice yield and improving the efficiency of nitrogen fertilizer. This species's saprophytic counterpart can decompose rice litterfall, promoting litter organic matter cycling and the release of nutrients and improving the soil microbial environment. Fluorescence microscopy, confocal laser scanning microscopy and quantitative PCR investigated the colonization dynamics and biomass of P. liquidambari in rice in vivo. P. liquidambari formed infection structures similar to phytopathogens with infected vascular tissues that systematically spread to acrial parts. However, different from pathogenic infection, P. liquidambari colonization exhibits space restriction and quantity restriction. Direct comparison of a fungal transcriptome under three different habitats provided a better understanding of lifestyle conversion during plant-fungi interactions. The isolated total RNA of Ck (pure culture), EP (endophytic culture) and FP (saprophytic culture) was subjected to Illumina transcriptome sequencing. To the best of our knowledge, this study is the first to investigate Phomopsis sp. using RNA-seq technology to obtain whole transcriptome information. A total of 27,401,258 raw reads were generated and 22,700 unigenes were annotated. Functional annotation indicated that carbohydrate metabolism and biosynthesis of secondary metabolites played important roles. There were 2522 differentially expressed genes (DEGs) between the saprophytic and endophytic lifestyles. Quantitative PCR analysis validated the DEGs of RNA-seq. Analysis of DEGs between saprophytic and endophytic lifestyles revealed that most genes from amino acids metabolism, carbohydrate metabolism, fatty acid biosynthesis, secondary

  17. 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.

  18. Influence of Location, Host Cultivar, and Inoculation on the Composition of Naturalized Populations of Rhizobium meliloti in Medicago sativa Nodules †

    PubMed Central

    Bromfield, E. S. P.; Sinha, Indu B.; Wolynetz, M. S.

    1986-01-01

    A phage typing system was used to evaluate the composition of indigenous populations of Rhizobium meliloti inhabiting nodules of Medicago sativa cultivars grown with and without inoculation at two field sites during 1983 and 1984. Soil at both locations contained established populations of R. meliloti at planting. Analysis of 1,920 nodule isolates revealed 55 unique phage types of indigenous R. meliloti at one site and 65 indigenous types at the other location. The distributions of phage types differed markedly between locations. At one site, the nodule population was dominated by two phage types; seven others occurred consistently but at lower frequency, and the remainder were encountered infrequently. No indigenous types predominated at the other location, although nine occurred more frequently than the remaining types. Indigenous R. meliloti predominated in nodules from inoculated plots at both sites, with inoculant recovery varying between 10 and 38% in each of two years. The frequency of occurrence of particular phage types at one location was significantly influenced by both M. sativa cultivar and inoculation. At this location, the interaction of cultivar and inoculation on the incidence of phage types suggests that the presence of an inoculant strain differentially affected nodule occupancy of M. sativa cultivars by members of the indigenous R. meliloti population. At both sites, the frequency of specific phage types differed between years. The data emphasize the importance of understanding the ecology and characteristics of indigenous Rhizobium populations as a prerequisite for elucidating problems of inoculant establishment and persistence in competitive situations. Images PMID:16347054

  19. Molecular progress on the mapping and cloning of functional genes for blast disease in rice (Oryza sativa L.): current status and future considerations.

    PubMed

    Ashkani, S; Rafii, M Y; Shabanimofrad, M; Ghasemzadeh, A; Ravanfar, S A; Latif, M A

    2016-01-01

    Rice blast disease, which is caused by the fungal pathogen Magnaporthe oryzae, is a recurring problem in all rice-growing regions of the world. The use of resistance (R) genes in rice improvement breeding programmes has been considered to be one of the best options for crop protection and blast management. Alternatively, quantitative resistance conferred by quantitative trait loci (QTLs) is also a valuable resource for the improvement of rice disease resistance. In the past, intensive efforts have been made to identify major R-genes as well as QTLs for blast disease using molecular techniques. A review of bibliographic references shows over 100 blast resistance genes and a larger number of QTLs (∼500) that were mapped to the rice genome. Of the blast resistance genes, identified in different genotypes of rice, ∼22 have been cloned and characterized at the molecular level. In this review, we have summarized the reported rice blast resistance genes and QTLs for utilization in future molecular breeding programmes to introgress high-degree resistance or to pyramid R-genes in commercial cultivars that are susceptible to M. oryzae. The goal of this review is to provide an overview of the significant studies in order to update our understanding of the molecular progress on rice and M. oryzae. This information will assist rice breeders to improve the resistance to rice blast using marker-assisted selection which continues to be a priority for rice-breeding programmes.

  20. Genome-wide Association Mapping of Quantitative Trait Loci (QTLs) for Contents of Eight Elements in Brown Rice (Oryza sativa L.).

    PubMed

    Nawaz, Zarqa; Kakar, Kaleem U; Li, Xiao-bai; Li, Shan; Zhang, Bin; Shou, Hui-xia; Shu, Qing-yao

    2015-09-16

    An association mapping of quantitative trait loci (QTLs) regulating the concentrations of eight elements in brown rice (Oryza sativa L.) was performed using USDA mini-core subset cultivated in two different environments. In addition, correlation between the grain elemental concentrations was also studied. A total of 60 marker loci associated with 8 grain elemental concentrations were identified, and these loci were clustered into 37 genomic regions. Twenty new QTLs were found to be associated with important elements such as Zn, Fe, and P, along with others. Fe concentration was associated with the greatest number of markers in two environments. In addition, several important elemental/metal transporter genes were identified in a few mapped regions. Positive correlation was observed within all grain elemental concentrations. In summary, the results provide insight into the genetic basis of rice grain element accumulation and may help in the identification of genes associated with the accumulation of Zn, Fe, and other essential elements in rice.

  1. Plant architecture and grain yield are regulated by the novel DHHC-type zinc finger protein genes in rice (Oryza sativa L.).

    PubMed

    Zhou, Bo; Lin, Jian Zhong; Peng, Dan; Yang, Yuan Zhu; Guo, Ming; Tang, Dong Ying; Tan, Xiaofeng; Liu, Xuan Ming

    2017-01-01

    In many plants, architecture and grain yield are affected by both the environment and genetics. In rice, the tiller is a vital factor impacting plant architecture and regulated by many genes. In this study, we cloned a novel DHHC-type zinc finger protein gene Os02g0819100 and its alternative splice variant OsDHHC1 from the cDNA of rice (Oryza sativa L.), which regulate plant architecture by altering the tiller in rice. The tillers increased by about 40% when this type of DHHC-type zinc finger protein gene was over-expressed in Zhong Hua 11 (ZH11) rice plants. Moreover, the grain yield of transgenic rice increased approximately by 10% compared with wild-type ZH11. These findings provide an important genetic engineering approach for increasing rice yields.

  2. Sulfur (S)-induced enhancement of iron plaque formation in the rhizosphere reduces arsenic accumulation in rice (Oryza sativa L.) seedlings.

    PubMed

    Hu, Zheng-Yi; Zhu, Yong-Guan; Li, Min; Zhang, Li-Gan; Cao, Zhi-Hong; Smith, F Andrew

    2007-05-01

    The effects of two sulfur (S) sources (SO(4)(2-), S(0)), and three rates of S application (0, 30, 120 mgS/kg) on the formation of iron plaque in the rhizosphere, and on the root surface of rice, and As (arsenic) uptake into rice (Oryza sativa L.) were studied in a combined soil-sand culture experiment. Significant differences in As uptake into rice between +S and -S treatments were observed in relation to S sources, and rates of S application. Concentrations of As in rice shoots decreased with increasing rates of S application. The mechanism could be ascribed to sulfur, induced the formation of iron plaque, since concentrations of Fe in iron plaque on quartz sands in the rhizosphere, and on the root surface of rice increased with increasing rates of S application. The results suggest that sulfur fertilization may be important for the development approaches to reducing As accumulation in rice.

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

    PubMed

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

    2013-01-01

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

  4. The pleiotropic SEPALLATA-like gene OsMADS34 reveals that the 'empty glumes' of rice (Oryza sativa) spikelets are in fact rudimentary lemmas.

    PubMed

    Lin, Xuelei; Wu, Feng; Du, Xiaoqiu; Shi, Xiaowei; Liu, Yuan; Liu, Shujun; Hu, Yuxin; Theißen, Günter; Meng, Zheng

    2014-04-01

    The single floret of the rice (Oryza sativa) spikelet is subtended by a pair of enigmatic organs usually termed 'empty glumes' or 'sterile lemmas'. As the identity of these organs remains essentially unknown, we refer to them as 'organs of unknown identity' (OUIs). Here we present a novel mutant of the rice SEPALLATA-like gene OsMADS34 which develops, in addition to disorganized branches and sterile seeds, elongated OUIs. The function and evolution of OsMADS34 were studied. Morphological and molecular markers indicate that the elongated OUIs have adopted lemma identity. Evolutionary analyses show that the ancestral genes of the OsM34 subclade evolved under positive selection, and that three specific motifs occur in the C-terminal region of proteins in the OsM34 subclade. Yeast two-hybrid assays revealed that the C-terminal region of OsMADS34 plays a crucial role in mediating protein interactions. Sequence analyses for the wild rice Oryza grandiglumis which has elongated OUIs revealed the association of OsMADS34 functionality with OUI identity. Our findings support the hypothesis that OUIs originated from the lemmas of degenerate florets under the negative control of OsMADS34. As OUIs neither are homologues to glumes nor have the identity of lemmas any more, but originated from these organs, we suggest calling them 'rudimentary lemmas'.

  5. Two linked genes on rice chromosome 2 for F1 pollen sterility in a hybrid between Oryza sativa and O. glumaepatula.

    PubMed

    Sakata, Mitsukazu; Yamagata, Yoshiyuki; Doi, Kazuyuki; Yoshimura, Atsushi

    2014-12-01

    Hybrid incompatibility plays an important role in establishment of post-zygotic reproductive isolation. To unveil genetic basis of hybrid incompatibilities between diverged species of genus Oryza AA genome species, we conducted genetic dissection of hybrid sterility loci, S22(t), which had been identified in backcross progeny derived from Oryza sativa ssp. japonica (recurrent parent) and South American wild rice O. glumaepatula near the end of the short arm of chromosome 2. The S22(t) region was found to be composed of two loci, designated S22A and S22B, that independently induce F1 pollen sterility. Pollen grains containing either of the sterile alleles (S22A-glum (s) or S22B-glum (s) ) were sterile if produced on a heterozygous plant. No transmission of the S22A-glum (s) allele via pollen was observed, whereas a low frequency of transmission of S22B-glum (s) was observed. Cytological analysis showed that the sterile pollen grains caused by S22A could reach the bicellular or tricellular stage, and the nearly-sterile pollen grains caused by S22B could reach the tricellular stage. Our genetic analysis showed repulsion linkage effect is possible to induce strong reproductive barrier by high pollen sterility based on recombination value and transmission ratio of hybrid sterility gene to the progeny was influenced by frequency of competitors on fertilization.

  6. Two linked genes on rice chromosome 2 for F1 pollen sterility in a hybrid between Oryza sativa and O. glumaepatula

    PubMed Central

    Sakata, Mitsukazu; Yamagata, Yoshiyuki; Doi, Kazuyuki; Yoshimura, Atsushi

    2014-01-01

    Hybrid incompatibility plays an important role in establishment of post-zygotic reproductive isolation. To unveil genetic basis of hybrid incompatibilities between diverged species of genus Oryza AA genome species, we conducted genetic dissection of hybrid sterility loci, S22(t), which had been identified in backcross progeny derived from Oryza sativa ssp. japonica (recurrent parent) and South American wild rice O. glumaepatula near the end of the short arm of chromosome 2. The S22(t) region was found to be composed of two loci, designated S22A and S22B, that independently induce F1 pollen sterility. Pollen grains containing either of the sterile alleles (S22A-glums or S22B-glums) were sterile if produced on a heterozygous plant. No transmission of the S22A-glums allele via pollen was observed, whereas a low frequency of transmission of S22B-glums was observed. Cytological analysis showed that the sterile pollen grains caused by S22A could reach the bicellular or tricellular stage, and the nearly-sterile pollen grains caused by S22B could reach the tricellular stage. Our genetic analysis showed repulsion linkage effect is possible to induce strong reproductive barrier by high pollen sterility based on recombination value and transmission ratio of hybrid sterility gene to the progeny was influenced by frequency of competitors on fertilization. PMID:25914585

  7. A gene for a Class II DNA photolyase from Oryza sativa: cloning of the cDNA by dilution-amplification.

    PubMed

    Hirouchi, T; Nakajima, S; Najrana, T; Tanaka, M; Matsunaga, T; Hidema, J; Teranishi, M; Fujino, T; Kumagai, T; Yamamoto, K

    2003-07-01

    Ultraviolet radiation induces the formation of two classes of photoproducts in DNA-the cyclobutane pyrimidine dimer (CPD) and the pyrimidine [6-4] pyrimidone photoproduct (6-4 product). Many organisms produce enzymes, termed photolyases, which specifically bind to these lesions and split them via a UV-A/blue light-dependent mechanism, thereby reversing the damage. These photolyases are specific for either CPDs or 6-4 products. Two classes of photolyases (class I and class II) repair CPDs. A gene that encodes a protein with class II CPD photolyase activity in vitro has been cloned from several plants including Arabidopsis thaliana, Cucumis sativus and Chlamydomonas reinhardtii. We report here the isolation of a homolog of this gene from rice (Oryza sativa), which was cloned on the basis of sequence similarity and PCR-based dilution-amplification. The cDNA comprises a very GC-rich (75%) 5; region, while the 3; portion has a GC content of 50%. This gene encodes a protein with CPD photolyase activity when expressed in E. coli. The CPD photolyase gene encodes at least two types of mRNA, formed by alternative splicing of exon 5. One of the mRNAs encodes an ORF for 506 amino acid residues, while the other is predicted to code for 364 amino acid residues. The two RNAs occur in about equal amounts in O. sativa cells.

  8. The durably resistant rice cultivar Digu activates defence gene expression before the full maturation of Magnaporthe oryzae appressorium.

    PubMed

    Li, Weitao; Liu, Ya; Wang, Jing; He, Min; Zhou, Xiaogang; Yang, Chao; Yuan, Can; Wang, Jichun; Chern, Mawsheng; Yin, Junjie; Chen, Weilan; Ma, Bingtian; Wang, Yuping; Qin, Peng; Li, Shigui; Ronald, Pamela; Chen, Xuewei

    2016-04-01

    Rice blast caused by the fungal pathogen Magnaporthe oryzae is one of the most destructive diseases worldwide. Although the rice-M. oryzae interaction has been studied extensively, the early molecular events that occur in rice before full maturation of the appressorium during M. oryzae invasion are unknown. Here, we report a comparative transcriptomics analysis of the durably resistant rice variety Digu and the susceptible rice variety Lijiangxintuanheigu (LTH) in response to infection by M. oryzae (5, 10 and 20 h post-inoculation, prior to full development of the appressorium). We found that the transcriptional responses differed significantly between these two rice varieties. Gene ontology and pathway analyses revealed that many biological processes, including extracellular recognition and biosynthesis of antioxidants, terpenes and hormones, were specifically activated in Digu shortly after infection. Forty-eight genes encoding receptor kinases (RKs) were significantly differentially regulated by M. oryzae infection in Digu. One of these genes, LOC_Os08g10300, encoding a leucine-rich repeat RK from the LRR VIII-2 subfamily, conferred enhanced resistance to M. oryzae when overexpressed in rice. Our study reveals that a multitude of molecular events occur in the durably resistant rice Digu before the full maturation of the appressorium after M. oryzae infection and that membrane-associated RKs play important roles in the early response.

  9. Primary and secondary metabolite composition of kernels from three cultivars of Portuguese chestnut (Castanea sativa Mill.) at different stages of industrial transformation.

    PubMed

    Do Carmo Barbosa Mendes De Vasconcelos, Maria; Bennett, Richard N; Rosa, Eduardo A S; Ferreira Cardoso, Jorge Ventura

    2007-05-02

    Chestnut (Castanea sativa) is an important basic food in rural diets and a major starch crop used in a similar way to potatoes. Chestnuts are a fundamental economic resource in the "chestnut regions" not only for the fruit but also for the chestnut wood. Chestnuts have become increasingly important with respect to human health, for example, as an alternative gluten-free flour source. Chestnuts are also a rich source of other beneficial compounds, but there have been few studies on the composition during processing. In this study, we analyzed the chemical composition of three Portuguese cultivars at different stages of industrial processing. The chestnut cultivars were Longal, Judia, and Martaínha. All three cultivars had high moisture contents but were low in ash, crude fat, and crude protein contents, with high starch and low fiber contents. The free amino acid contents, including various essential amino acids, varied depending on the cultivar. All three cultivars also had a significant content of polyphenolics with gallic acid; ellagic acid was predominant among hydrolyzable and condensed tannins. Many of these compounds are known to exert significant positive effects on human health. The one-way analysis of variance for fresh chestnut shows significant differences among the three cultivars for most of the studied parameters. The same statistical analysis applied to each one of the two cultivars (Judia and Longal) sampled for the four processing steps analyzed indicates a significant effect of this factor in practically all of the constituents. On the other hand, the two-way analysis of variance shows that, besides the residual, the processing step and the interaction cultivar x processing step were the factors that more contributed for the total variation observed in the constituents analyzed, while the contribution of cultivar was much less significant.

  10. Polyphenolic Compounds and Antioxidant Activity of Cold-Pressed Seed Oil from Finola Cultivar of Cannabis sativa L.

    PubMed

    Smeriglio, Antonella; Galati, Enza M; Monforte, Maria T; Lanuzza, Francesco; D'Angelo, Valeria; Circosta, Clara

    2016-08-01

    The aim of this study was to characterize the polyphenolic compounds and antioxidant activity of cold-pressed seed oil from Finola cultivar of industrial hemp (Cannabis sativa L.). Several methodologies have been employed to evaluate the in vitro antioxidant activity of Finola hempseed oil (FHSO) and both lipophilic (LF) and hydrophilic fractions (HF). The qualitative and quantitative composition of the phenolic fraction of FHSO was performed by HPLC analyses. From the results is evident that FHSO has high antioxidative activity, as measured by DPPH radical (146.76 mmol of TE/100 g oil), inhibited β-carotene bleaching, quenched a chemically generated peroxyl radical in vitro and showed high ferrous ion chelating activity. Reactivity towards 2,2'-azino-bis (3-ethylbenzothiazoline-6-sulfonic acid) radical cation and ferric-reducing antioxidant power values were 695.2 µmol of TE/100g oil and 3690.6 µmol of TE/100 g oil respectively. FHSO contains a significant amount of phenolic compounds of which 2780.4 mg of quercetin equivalent/100 g of total flavonoids. The whole oil showed higher antioxidant activity compared with LF and HF. Our findings indicate that the significant antioxidant properties shown from Finola seed oil might generally depend on the phenolic compounds, especially flavonoids, such as flavanones, flavonols, flavanols and isoflavones. Copyright © 2016 John Wiley & Sons, Ltd.

  11. Genotype variations in cadmium and lead accumulations of leafy lettuce (Lactuca sativa L.) and screening for pollution-safe cultivars for food safety.

    PubMed

    Zhang, Kun; Yuan, Jiangang; Kong, Wei; Yang, Zhongyi

    2013-06-01

    Heavy-metals in polluted soils can accumulate in plants and threaten crop safety. To evaluate the risk of heavy-metal pollution in leafy lettuce (Lactuca sativa L.), two pot experiments were conducted to investigate Cd and Pb accumulation and transfer potential in 28 cultivars of lettuce and to screen for low-Cd and low-Pb accumulative cultivars. In the three treatments, 5.2-fold, 4.8-fold and 4.8-fold differences in the shoot Cd concentration were observed between the cultivars with the highest and the lowest Cd concentrations, respectively. This genotype variation was sufficiently large to identify low-Cd accumulative genotypes to reduce Cd contamination in food. Cadmium accumulation in the low-Cd accumulative genotypes was significantly positively correlated with Pb accumulation. At the cultivar level, Cd and Pb accumulation in lettuce was stable and genotype-dependent. High Pb soil levels did not affect shoot Cd accumulation in lettuce. Lettuce was concluded to be at high risk for Cd pollution and low risk for Pb pollution. Among the tested cultivars, cvs. SJGT, YLGC, N518, and KR17 had the lowest Cd and Pb accumulation abilities in shoots and are thus important parental material for breeding pollution-safe cultivars to minimize Cd and Pb accumulation.

  12. Characteristics of grains and oils of four different oats (Avena sativa L.) cultivars growing in Turkey.

    PubMed

    Musa Ozcan, M; Ozkan, Gülcan; Topal, Ali

    2006-01-01

    Some physical and chemical properties of four oat (Avena sativa L.) varieties (BDMY-6, BDMY-7, Che-Chois and Y-2330) harvested from Konya in Turkey were investigated. The weight of the grain, moisture, crude protein, crude ash, crude fibre, crude energy, crude oil and water-soluble extract contents of all oat variety grains were analysed. Contents of aluminium, calcium, cadmium, phosphorus, magnesium, zinc, lead, potassium and manganese were also determined in the oat grains. The specific gravity, refractive index, free fatty acids, peroxide value, saponification number and unsaponifiable matter were determined in the grain oil. Tocopherol contents of these four oat grain oils were measured. Palmitic acid (15.72%), oleic acid (33.97-51.26%) and linoleic acid (22.80-35.90%) were found to be rich in protein, oil, fibre, unsaturated fatty acids and minerals, suggesting that they may be valuable for food uses. Due to high nutritive values, it is recommended to process for healthy food products.

  13. Molecular mapping of a novel gene, Grh5, conferring resistance to green rice leafhopper (Nephotettix cincticeps Uhler) in rice, Oryza sativa L.

    PubMed

    Fujita, Daisuke; Doi, Kazuyuki; Yoshimura, Atsushi; Yasui, Hideshi

    2006-08-01

    The green rice leafhopper (GRH), Nephotettix cincticeps Uhler, is one of the most serious insect pests affecting cultivated rice (Oryza sativa L.) in temperate regions of East Asia. An accession of the wild rice species, Oryza rufipogon Griff. (W1962), was found to be highly resistant to GRH by an antibiosis test. To understand the genetic basis of the GRH resistance, a BC1F1 population derived from a cross between a susceptible Japonica variety, Taichung 65 (T65), and a highly resistant accession W1962 was analyzed by quantitative trait loci (QTL) mapping. A single major QTL for GRH resistance was detected on rice chromosome 8. A nearly isogenic population containing segments of the targeted QTL region derived from W1962 was then developed through advanced backcrossing with marker-assisted selection. Further molecular mapping using a BC4F2 population revealed that a new resistance gene, designated as Green rice leafhopper resistance 5 (Grh5), was located on the distal region of the long arm of chromosome 8 and tightly linked to the simple sequence repeat markers RM3754 and RM3761. A nearly isogenic line (NIL) carrying Grh5 was subsequently developed in the progeny of the mapping population. The resistance level of Grh5-NIL was compared with those of developed NILs for GRH resistance and was found to have the highest resistance. The DNA markers found to be closely linked to Grh5 would be useful for marker-assisted selection for the improvement of resistance to GRH in rice.

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

    NASA Astrophysics Data System (ADS)

    Hamim, Hamim; Banon, Sri; Dorly, Dorly

    2016-01-01

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

  15. Agrobacterium-mediated transformation of oat (Avena sativa L.) cultivars via immature embryo and leaf explants.

    PubMed

    Gasparis, Sebastian; Bregier, Cezary; Orczyk, Waclaw; Nadolska-Orczyk, Anna

    2008-11-01

    This paper reports on the successful Agrobacterium-mediated transformation of oat, and on some factors influencing this process. In the first step of the experiments, three cultivars, two types of explant, and three combinations of strain/vectors, which were successfully used for transformation of other cereals were tested. Transgenic plants were obtained from the immature embryos of cvs. Bajka, Slawko and Akt and from leaf base explants of cv. Bajka after transformation with A. thumefaciens strain LBA4404(pTOK233). The highest transformation rate (12.3%) was obtained for immature embryos of cv. Bajka. About 79% of the selected plants proved to be transgenic; however, only 14.3% of the T(0) plants and 27.5% of the T(1) showed GUS expression. Cell competence of both types of explant differed in terms of their transformation ability and transgene expression. The next step of the study was to test the suitability for oat transformation of the pGreen binary vector combined with different selection cassettes: nptII or bar under the nos or 35S promoter. Transgenic plants were selected in combinations transformed with nos::nptII, 35S::nptII and nos::bar. The highest transformation efficiency (5.3%) was obtained for cv. Akt transformed with nos::nptII. A detailed analysis of the T(0) plants selected from a given callus line and their progeny revealed that they were the mixture of transgenic, chimeric-transgenic and non-transgenic individuals. Southern blot analysis of T(0) and T(1) showed simple integration pattern with the low copy number of the introduced transgenes.

  16. Molecular phylogenetic study and expression analysis of ATP-binding cassette transporter gene family in Oryza sativa in response to salt stress.

    PubMed

    Saha, Jayita; Sengupta, Atreyee; Gupta, Kamala; Gupta, Bhaskar

    2015-02-01

    ATP-binding cassette (ABC) transporter is a large gene superfamily that utilizes the energy released from ATP hydrolysis for transporting myriad of substrates across the biological membranes. Although many investigations have been done on the structural and functional analysis of the ABC transporters in Oryza sativa, much less is known about molecular phylogenetic and global expression pattern of the complete ABC family in rice. In this study, we have carried out a comprehensive phylogenetic analysis constructing neighbor-joining and maximum-likelihood trees based on various statistical methods of different ABC protein subfamily of five plant lineages including Chlamydomonas reinhardtii (green algae), Physcomitrella patens (moss), Selaginella moellendorffii (lycophyte), Arabidopsis thaliana (dicot) and O. sativa (monocot) to explore the origin and evolutionary patterns of these ABC genes. We have identified several conserved motifs in nucleotide binding domain (NBD) of ABC proteins among all plant lineages during evolution. Amongst the different ABC protein subfamilies, 'ABCE' has not yet been identified in lower plant genomes (algae, moss and lycophytes). The result indicated that gene duplication and diversification process acted upon these genes as a major operative force creating new groups and subgroups and functional divergence during evolution. We have demonstrated that rice ABCI subfamily consists of only half size transporters that represented highly dynamic members showing maximum sequence variations among the other rice ABC subfamilies. The evolutionary and the expression analysis contribute to a deep insight into the evolution and diversity of rice ABC proteins and their roles in response to salt stress that facilitate our further understanding on rice ABC transporters.

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

    PubMed Central

    Nassirou, Tondi Yacouba; Zhou, Wei; Yin, Yilong; Dong, Xilong; Rao, Quanqin; Shi, Han; Zhao, Wubin; Efisue, Andrew; Jin, Deming

    2016-01-01

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

  18. Salicylic acid mediates antioxidant defense system and ABA pathway related gene expression in Oryza sativa against quinclorac toxicity.

    PubMed

    Wang, Jian; Lv, Mengting; Islam, Faisal; Gill, Rafaqat A; Yang, Chong; Ali, Basharat; Yan, Guijun; Zhou, Weijun

    2016-11-01

    The auxin herbicide quinclorac is widely used for controlling weeds in transplanted and direct-seeded rice fields. However, its phytotoxic responses on rice are still unknown. Therefore, in the present investigation we studied the effects of different concentrations (0, 0.1 and 0.5g/L) of quinclorac herbicide on the physiological and biochemical changes of two rice cultivars (XS 134 and ZJ 88) and further analyzed the ameliorating role of salicylic acid (SA) on quinclorac toxicity in rice plants. The results revealed that exogenous application of SA significantly increased plant biomass and total chlorophyll contents in herbicide stressed plants. The lipid peroxidation and ROS (H2O2, O2(-.), (-)OH) production were significantly increased in roots and leaves of both rice cultivars under quinclorac stress, demonstrating an oxidative burst in rice plants. Whereas, application of SA significantly lowered ROS contents under quinclorac stress. Further, exogenous SA treatment significantly modulated antioxidant enzymes and enhanced GSH concentration in stress plants. Anatomical observations of leaf and root revealed that herbicide affected internal structures, while SA played a vital role in protection from toxic effects. Expression analysis of stress hormone ABA genes (OsABA8oxs, OsNCEDs) revealed that quinclorac application enhanced stress condition in cultivar ZJ 88, while SA treatment downregulated ABA genes more in cultivar XS 134, which correlated with the enhanced tolerance to quinclorac induced oxidative stress in this cultivar. The present study delineated that SA played a critical role under quinclorac stress in both rice cultivars by regulating antioxidant defense system, reducing ROS formation and preventing the degradation of internal cell organelles.

  19. Comparative Genomic Analysis of the GRF Genes in Chinese Pear (Pyrus bretschneideri Rehd), Poplar (Populous), Grape (Vitis vinifera), Arabidopsis and Rice (Oryza sativa)

    PubMed Central

    Cao, Yunpeng; Han, Yahui; Jin, Qing; Lin, Yi; Cai, Yongping

    2016-01-01

    Growth-regulating factors (GRFs) are plant-specific transcription factors that have important functions in regulating plant growth and development. Previous studies on GRF family members focused either on a single or a small set of genes. Here, a comparative genomic analysis of the GRF gene family was performed in poplar (a model tree species), Arabidopsis (a model plant for annual herbaceous dicots), grape (one model plant for perennial dicots), rice (a model plant for monocots) and Chinese pear (one of the economical fruit crops). In total, 58 GRF genes were identified, 12 genes in rice (Oryza sativa), 8 genes in grape (Vitis vinifera), 9 genes in Arabidopsis thaliana, 19 genes in poplar (Populus trichocarpa) and 10 genes in Chinese pear (Pyrus bretschneideri). The GRF genes were divided into five subfamilies based on the phylogenetic analysis, which was supported by their structural analysis. Furthermore, microsynteny analysis indicated that highly conserved regions of microsynteny were identified in all of the five species tested. And Ka/Ks analysis revealed that purifying selection plays an important role in the maintenance of GRF genes. Our results provide basic information on GRF genes in five plant species and lay the foundation for future research on the functions of these genes. PMID:27933074

  20. The effects of biochars from rice residue on the formation of iron plaque and the accumulation of Cd, Zn, Pb, As in rice (Oryza sativa L.) seedlings.

    PubMed

    Zheng, Rui-Lun; Cai, Chao; Liang, Jian-Hong; Huang, Qing; Chen, Zheng; Huang, Yi-Zong; Arp, Hans Peter H; Sun, Guo-Xin

    2012-10-01

    A historically multi-metal contaminated soil was amended with biochars produced from different parts of rice plants (straw, husk and bran) to investigate how biochar can influence the mobility of Cd, Zn, Pb and As in rice seedlings (Oryza sativa L.). Rice shoot concentrations of Cd, Zn and Pb decreased by up to 98%, 83% and 72%, respectively, due to biochar amendment, though that of As increased by up to 327%. Biochar amendments significantly decreased pore water concentrations (C(pw)) of Cd and Zn and increased that of As. For Pb it depended on the amendment. Porewater pH, dissolved organic carbon, dissolved phosphorus, silicon in pore water and iron plaque formation on root surfaces all increased significantly after the amendments. The proportions of Cd and Pb in iron plaque increased by factors 1.8-5.7 and 1.4-2.8, respectively; no increase was observed for As and Zn. Straw-char application significantly and noticeably decreased the plant transfer coefficients of Cd and Pb. This study, the first to investigate changes in metal mobility and iron plaque formation in rice plants due to amending a historically contaminated soil with biochar, indicates that biochar has a potential to decrease Cd, Zn and Pb accumulations in rice shoot but increase that of As. The main cause is likely biochar decreasing the C(pw) of Cd and Zn, increasing the C(pw) of As, and increasing the iron plaque blocking capacity for Cd and Pb.

  1. Examining Two Sets of Introgression Lines in Rice (Oryza sativa L.) Reveals Favorable Alleles that Improve Grain Zn and Fe Concentrations.

    PubMed

    Xu, Qin; Zheng, Tian-Qing; Hu, Xia; Cheng, Li-Rui; Xu, Jian-Long; Shi, Yu-Min; Li, Zhi-Kang

    2015-01-01

    In the modern world, the grain mineral concentration (GMC) in rice (Oryza sativa L.) not only includes important micronutrient elements such as iron (Fe) and zinc (Zn), but it also includes toxic heavy metal elements, especially cadmium (Cd) and lead (Pb). To date, the genetic mechanisms underlying the regulation of GMC, especially the genetic background and G × E effects of GMC, remain largely unknown. In this study, we adopted two sets of backcross introgression lines (BILs) derived from IR75862 (a Zn-dense rice variety) as the donor parent and two elite indica varieties, Ce258 and Zhongguangxiang1, as recurrent parents to detect QTL affecting GMC traits including Fe, Zn, Cd and Pb concentrations in two environments. We detected a total of 22 loci responsible for GMC traits, which are distributed on all 12 rice chromosomes except 5, 9 and 10. Six genetic overlap (GO) regions affecting multiple elements were found, in which most donor alleles had synergistic effects on GMC. Some toxic heavy metal-independent loci (such as qFe1, qFe2 and qZn12) and some regions that have opposite genetic effects on micronutrient (Fe and Zn) and heavy metal element (Pb) concentrations (such as GO-IV) may be useful for marker-assisted biofortification breeding in rice. We discuss three important points affecting biofortification breeding efforts in rice, including correlations between different GMC traits, the genetic background effect and the G × E effect.

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

    PubMed

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

    2015-01-01

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

  3. Genetic diversity and population structure of ‘Khao Kai Noi’, a Lao rice (Oryza sativa L.) landrace, revealed by microsatellite DNA markers

    PubMed Central

    Vilayheuang, Koukham; Machida-Hirano, Ryoko; Bounphanousay, Chay; Watanabe, Kazuo N.

    2016-01-01

    Rice (Oryza sativa L.) is the main food for people in Laos, where it has been grown and eaten since prehistory. Diverse landraces are grown in Laos. ‘Khao Kai Noi’, a landrace favored for its eating quality, is held in the nationwide collection of traditional landraces in the Lao national genebank. Genetic diversity is crucial for sustainable use of genetic resources and conservation. To investigate the genetic diversity of ‘Khao Kai Noi’ for conservation, we genotyped 70 accessions by using 23 polymorphic simple sequence repeat markers. The markers generated 2 to 17 alleles (132 in total), with an average of 5.7 per locus. The total expected heterozygosity over all ‘Khao Kai Noi’ accessions was 0.271. Genetic variation was largest among accessions and smallest within accessions. Khao Kai Noi accessions were classified into three different genetic backgrounds, but there was unclear association between the three inferred population and name subgroups and geographical distribution. Most of the accessions were clustered with temperate japonica and showed genetic relatedness to rice from neighboring provinces of Vietnam, suggesting a Vietnamese origin. The results of this study will contribute to the conservation, core collection and future breeding of the Khao Kai Noi population. PMID:27162492

  4. Enhanced Salt Tolerance under Nitrate Nutrition is Associated with Apoplast Na+ Content in Canola (Brassica. napus L.) and Rice (Oryza sativa L.) Plants.

    PubMed

    Gao, Limin; Liu, Mei; Wang, Min; Shen, Qirong; Guo, Shiwei

    2016-11-01

    To analyze the effect of nitrogen form on salt stress, we studied the response of two different plant species, canola (Brassica napus L.), a dicotyledon which prefers NO3(-) nutrition, and rice (Oryza sativa L.), a monocotyledon which prefers NH4(+) nutrition, to salt stress under NO3(-) (NN) and NH4(+) (AN) nutrition. Salt stress was simulated by the addition of 150 and 100 mM NaCl to NN (NNS) and AN (ANS) in canola and rice seedlings, respectively. Salt stress induced reductions of shoot and root biomass that were more drastic under ANS. A higher Na(+) content was obtained in NNS than in ANS. The impact of Na(+) on the reduction of biomass (Δbiomass/Na(+)) was 162, 181, 230 and 245% higher in canola root, canola shoot, rice root and rice shoot in ANS than in NNS, respectively. In both canola and rice seedlings, the ratio of leaf Na(+) content in apoplasts to symplasts ([Na(+)]apo/[Na(+)]sym) was higher in NNS than in ANS. Also, in canola seedlings, the ratio of apoplast Na(+) in the leaf edge to the leaf center ([Na(+)]LE/[Na(+)]LC) was 18 times higher in NNS than in ANS. Our results illustrate that the confinement of Na(+) in the canola leaf edge, as well as the restriction of Na(+) in leaf apoplasts of canola and rice seedlings, protect cells from suffering Na(+) stress and contribute to the higher tolerance of NO3(-)-fed plants.

  5. Novel roles of hydrogen peroxide (H₂O₂) in regulating pectin synthesis and demethylesterification in the cell wall of rice (Oryza sativa) root tips.

    PubMed

    Xiong, Jie; Yang, Yongjie; Fu, Guanfu; Tao, Longxing

    2015-04-01

    Hydrogen peroxide (H₂O₂) has been reported to increase lignin formation, enhance cell wall rigidification, restrict cell expansion and inhibit root elongation. However, our results showed that it not only inhibited rice (Oryza sativa) root elongation, but also increased root diameter. No study has reported how and why H₂O₂ increases cell expansion and root diameter. Exogenous H₂O₂ and its scavenger 4-hydroxy-Tempo were applied to confirm the roles of H₂O₂. Immunofluorescence, fluorescence probe, ruthenium red staining, histological section and spectrophotometry were used to monitor changes in the degree of pectin methylesterification, pectin content, pectin methylesterase (PME) activity and H₂O₂ content. Exogenous H₂O₂ inhibited root elongation, but increased cell expansion and root diameter significantly. H₂O₂ not only increased the region of pectin synthesis and pectin content in root tips, but also increased PME activity and pectin demethylesterification. The scavenger 4-hydroxy-Tempo reduced root H₂O₂ content and recovered H₂O₂-induced increases in cell expansion and root diameter by inhibiting pectin synthesis, PME activity and pectin demethylesterification. H₂O₂ plays a novel role in the regulation of pectin synthesis, PME activity and pectin demethylesterification. H₂O₂ increases cell expansion and root diameter by increasing pectin content and demethylesterification.

  6. Cd immobilization and reduced tissue Cd accumulation of rice (Oryza sativa wuyun-23) in the presence of heavy metal-resistant bacteria.

    PubMed

    Li, Ya; Pang, Hai-Dong; He, Lin-Yan; Wang, Qi; Sheng, Xia-Fang

    2017-04-01

    Two metal-resistant Bacillus megaterium H3 and Neorhizobium huautlense T1-17 were investigated for their immobilization of Cd in solution and tissue Cd accumulation of rice (Oryza sativa wuyun-23) in the Cd-contaminated soil. Strains H3 and T1-17 decreased 79-96% of water-soluble Cd in solution and increased grain biomass in the high Cd-contaminated soil. Inoculation with H3 and T1-17 significantly decreased the root (ranging from 25% to 58%), above-ground tissue (ranging from 13% to 34%), and polished rice (ranging from 45% to 72%) Cd contents as well as Cd bioconcentration factor of the rice compared to the controls. Furthermore, H3 and T1-17 significantly reduced the exchangeable Cd content of the rhizosphere soils compared with the controls. Notably, strain T1-17 had significantly higher ability to reduce Cd bioconcentration factor and polished rice Cd uptake than strain H3. The results demonstrated that H3 and T1-17 decreased the tissue (especially polished rice) Cd uptake by decreasing Cd availability in soil and Cd bioconcentration factor and the effect on the reduced polished rice Cd uptake was dependent on the strains. The results may provide an effective synergistic bioremediation of Cd-contaminated soils in the bacteria and rice plants and bacterial-assisted safe production of rice in Cd-contaminated soils.

  7. Overexpression of a glyoxalase gene, OsGly I, improves abiotic stress tolerance and grain yield in rice (Oryza sativa L.).

    PubMed

    Zeng, Zhengming; Xiong, Fangjie; Yu, Xiaohong; Gong, Xiaoping; Luo, Juntao; Jiang, Yudong; Kuang, Haochi; Gao, Bijun; Niu, Xiangli; Liu, Yongsheng

    2016-12-01

    Glyoxalase I (Gly I) is a component of the glyoxalase system which is involved in the detoxification of methylglyoxal, a byproduct of glycolysis. In the present study, a gene of rice (Oryza sativa L., cv. Nipponbare) encoding Gly I was cloned and characterized. The quantitative real-time PCR analysis indicated that rice Gly I (OsGly I) was ubiquitously expressed in root, stem, leaf, leaf sheath and spikelet with varying abundance. OsGly I was markedly upregulated in response to NaCl, ZnCl2 and mannitol in rice seedlings. For further functional investigation, OsGly I was overexpressed in rice using Agrobacterium-mediated transformation. Transgenic rice lines exhibited increased glyoxalase enzyme activity, decreased methylglyoxal level and improved tolerance to NaCl, ZnCl2 and mannitol compared to wild-type plants. Enhancement of stress tolerance in transgenic lines was associated with reduction of malondialdehyde content which was derived from cellular lipid peroxidation. In addition, the OsGly I-overexpression transgenic plants performed higher seed setting rate and yield. Collectively, these results indicate the potential of bioengineering the Gly I gene in crops.

  8. Abiotic stresses affect differently the intron splicing and expression of chloroplast genes in coffee plants (Coffea arabica) and rice (Oryza sativa).

    PubMed

    Nguyen Dinh, Sy; Sai, Than Zaw Tun; Nawaz, Ghazala; Lee, Kwanuk; Kang, Hunseung

    2016-08-20

    Despite the increasing understanding of the regulation of chloroplast gene expression in plants, the importance of intron splicing and processing of chloroplast RNA transcripts under stress conditions is largely unknown. Here, to understand how abiotic stresses affect the intron splicing and expression patterns of chloroplast genes in dicots and monocots, we carried out a comprehensive analysis of the intron splicing and expression patterns of chloroplast genes in the coffee plant (Coffea arabica) as a dicot and rice (Oryza sativa) as a monocot under abiotic stresses, including drought, cold, or combined drought and heat stresses. The photosynthetic activity of both coffee plants and rice seedlings was significantly reduced under all stress conditions tested. Analysis of the transcript levels of chloroplast genes revealed that the splicing of tRNAs and mRNAs in coffee plants and rice seedlings were significantly affected by abiotic stresses. Notably, abiotic stresses affected differently the splicing of chloroplast tRNAs and mRNAs in coffee plants and rice seedlings. The transcript levels of most chloroplast genes were markedly downregulated in both coffee plants and rice seedlings upon stress treatment. Taken together, these results suggest that coffee and rice plants respond to abiotic stresses via regulating the intron splicing and expression of different sets of chloroplast genes.

  9. Genomic Prediction of Biological Shape: Elliptic Fourier Analysis and Kernel Partial Least Squares (PLS) Regression Applied to Grain Shape Prediction in Rice (Oryza sativa L.)

    PubMed Central

    Iwata, Hiroyoshi; Ebana, Kaworu; Uga, Yusaku; Hayashi, Takeshi

    2015-01-01

    Shape is an important morphological characteristic both in animals and plants. In the present study, we examined a method for predicting biological contour shapes based on genome-wide marker polymorphisms. The method is expected to contribute to the acceleration of genetic improvement of biological shape via genomic selection. Grain shape variation observed in rice (Oryza sativa L.) germplasms was delineated using elliptic Fourier descriptors (EFDs), and was predicted based on genome-wide single nucleotide polymorphism (SNP) genotypes. We applied four methods including kernel PLS (KPLS) regression for building a prediction model of grain shape, and compared the accuracy of the methods via cross-validation. We analyzed multiple datasets that differed in marker density and sample size. Datasets with larger sample size and higher marker density showed higher accuracy. Among the four methods, KPLS showed the highest accuracy. Although KPLS and ridge regression (RR) had equivalent accuracy in a single dataset, the result suggested the potential of KPLS for the prediction of high-dimensional EFDs. Ordinary PLS, however, was less accurate than RR in all datasets, suggesting that the use of a non-linear kernel was necessary for accurate prediction using the PLS method. Rice grain shape can be predicted accurately based on genome-wide SNP genotypes. The proposed method is expected to be useful for genomic selection in biological shape. PMID:25825876

  10. Heat Stress Is More Damaging to Superior Spikelets than Inferiors of Rice (Oryza sativa L.) due to Their Different Organ Temperatures

    PubMed Central

    Fu, Guanfu; Feng, Baohua; Zhang, Caixia; Yang, Yongjie; Yang, Xueqin; Chen, Tingting; Zhao, Xia; Zhang, Xiufu; Jin, Qianyu; Tao, Longxing

    2016-01-01

    In general, the fertility and kernel weight of inferior spikelets of rice (Oryza Sativa L.) are obviously lower than those of superior spikelets, especially under abiotic stress. However, different responses to heat stress are seemed to show between the superior and inferior spikelet, and this response is scarcely documented that the intrinsic factors remain elusive. In order to reveal the mechanism underlying, two rice plants with different heat tolerance were subjected to heat stress of 40°C at anthesis. The results indicated that a greater decrease in fertility and kernel weight was observed in superior spikelets compared to inferior spikelets. This decrease was primarily ascribed to their different organ temperatures, in which the temperature of the superior spikelets was significantly higher than that of inferior spikelets. We inferred the differences in canopy temperature, light intensity and panicle types, were the primary reasons for the temperature difference between superior and inferior spikelets. Under heat stress, the fertility and kernel weight of superior and inferior spikelets decreased as the panicle numbers per plant were reduced, which was accompanied by significantly increasing the canopy temperatures. Thus, it was suggested that the rice plant with characteristic features of an upright growth habit and loose panicles might be more susceptible to heat stress resulting from their higher canopy and spikelets temperatures. PMID:27877180

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

    PubMed Central

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

    2016-01-01

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

  12. Screening of rice (Oryza sativa L.) OsPR1b-interacting factors and their roles in resisting bacterial blight.

    PubMed

    Luan, Z H; Zhou, D W

    2015-03-13

    PR genes, a type of genetic marker, are constitutively expressed at background levels, while being easily inducible by pathogenic bacteria. By using a yeast two-hybrid technique, four rice (Oryza sativa L.) OsPR1b-interacting factors were screened. Homozygous plants overexpressing OsPR1b were prepared by transgenic technology. We postulated that OsPR1b may participate in the resistance signaling pathway of rice. Of simultaneous treatments with hormones and pathogenic bacteria, exogenously applying JA and ET significantly increased the expression level of OsPR1b genes in seedlings. Compared with the control group that was inoculated with water, inoculation with a mixture of water and pathogenic bacteria hardly affected the expression level of OsPR1b gene, while cotreatment with SA and pathogenic bacteria slightly upregulated the expression level. However, cotreatment with JA or ET and pathogenic bacteria managed to significantly upregulate the expression level of the OsPR1b gene by 4.8 or 5.7 fold. PR genes, which are sensitive, are prone to many unknown factors during expression, and the detailed regulatory mechanisms in rice still require in-depth studies.

  13. Correlation and quantitative trait loci analyses of total chlorophyll content and photosynthetic rate of rice (Oryza sativa) under water stress and well-watered conditions.

    PubMed

    Hu, Song-Ping; Zhou, Ying; Zhang, Lin; Zhu, Xiu-Dong; Li, Lin; Luo, Li-Jun; Liu, Guo-Lan; Zhou, Qing-Ming

    2009-09-01

    In order to explore the relevant molecular genetic mechanisms of photosynthetic rate (PR) and chlorophyll content (CC) in rice (Oryza sativa L.), we conducted a series of related experiments using a population of recombinant inbred lines (Zhenshan97B x IRAT109). We found a significant correlation between CC and PR (R= 0.19**) in well-watered conditions, but no significant correlation during water stress (r= 0.08). We detected 13 main quantitative trait loci (QTLs) located on chromosomes 1, 2, 3, 4, 5, 6, and 10, which were associated with CC, including six QTLs located on chromosomes 1, 2, 3, 4, and 5 during water stress, and seven QTLs located on chromosomes 2, 3, 4, 6, and 10 in well-watered conditions. These QTLs explained 47.39% of phenotypic variation during water stress and 56.19% in well-watered conditions. We detected four main QTLs associated with PR; three of them (qPR2, qPR10, qPR11) were located on chromosomes 2, 10, and 11 during water stress, and one (qPR10) was located on chromosome 10 in well-watered conditions. These QTLs explained 34.37% and 18.41% of the phenotypic variation in water stress and well-watered conditions, respectively. In total, CC was largely controlled by main QTLs, and PR was mainly controlled by epistatic QTL pairs.

  14. Both overexpression and suppression of an Oryza sativa NB-LRR-like gene OsLSR result in autoactivation of immune response and thiamine accumulation

    PubMed Central

    Wang, Liangchao; Ye; Liu, Huachun; Liu, Xuejiao; Wei, Chuchu; Huang, Yuqing; Liu, Yujun; Tu, Jumin

    2016-01-01

    Tight and accurate regulation of immunity and thiamine biosynthesis is critical for proper defence mechanisms and several primary metabolic cycles in plants. Although thiamine is known to enhance plant defence by priming, the mechanism by which thiamine biosynthesis responds to immune signals remains poorly understood. Here we identified a novel rice (Oryza sativa L.) NB-LRR gene via an insertion mutation, this mutant confesses a low seed setting phenotype and the corresponding genetic locus was named OsLSR (Low seed setting related). Comparing with wildtype plant, both overexpression and suppression of OsLSR lead to the autoactivation of the rice immune system and accumulation of thiamine, which result in a great fitness cost and yield penalty. Moreover, when fused with eGFP at their C terminus, two fragments, OsLSR1-178 and OsLSR464-546, localized to chloroplasts where thiamine is produced. Our result suggests that OsLSR differs from traditional NB-LRR genes. Its expression is closely related to the immune status and thiamine level in plant cells and should be maintained within a narrow range for rice growth. PMID:27052628

  15. Optimizing tillage schedule for maintaining activity of the arbuscular mycorrhizal fungal population in a rainfed upland rice (Oryza sativa L.) agro-ecosystem.

    PubMed

    Maiti, D; Variar, M; Singh, R K

    2011-04-01

    Rainfed uplands in India are predominantly mono-cropped with rice (Oryza sativa L.) in the wet season (June/July to September/October) and grown under aerobic soil conditions. The remaining fallow period (winter followed by summer) of about 8-9 months leads to natural crash in the population of native arbuscular mycorrhizal fungi (AMF) in the soil. Attempts have been made to minimize this population crash by reducing soil disturbance-induced deleterious effects on native AMF activity of improperly scheduled off-season tillage, an agronomic recommendation for weed and disease (soil-borne) management, practiced by the upland farmers. On-farm (farmers' field) evaluation of effects of all suitable off-season tillage schedule combinations on rice during wet seasons of 2004, 2005, and 2006 revealed that a maximum of two off-season tillage schedules with a minimum gap of 13 weeks between them minimized the population crash of native AMF with a concomitant increase in phosphorus (P) uptake and grain yield of upland rice (variety "Vandana").

  16. Effect of atmospheric mercury deposition on selenium accumulation in rice (Oryza sativa L.) at a mercury mining region in southwestern China.

    PubMed

    Zhang, Chao; Qiu, Guangle; Anderson, Christopher W N; Zhang, Hua; Meng, Bo; Liang, Liang; Feng, Xinbin

    2015-03-17

    Selenium (Se) is an important trace element for human nutrition and has an interactive effect on mercury (Hg) uptake by plants and Hg toxicity in animals. Rice (Oryza sativa L.) is the dominant source of dietary Se in China, however the effect of soil Hg contamination on the Se concentration in rice is unknown. We collected 29 whole rice plant samples and corresponding soils from an active artisanal mercury mining area and an abandoned commercial mercury mining area. The soil Se concentration was similar across the two mining areas and greater than the background concentration for China. However, the Se concentration in rice grain was dramatically different (artisanal area 51±3 ng g(-1); abandoned area 235±99 ng g(-1)). The total gaseous mercury (TGM) concentration in ambient air at the artisanal mining site was significantly greater than at the abandoned area (231 and 34 ng m(-3), respectively) and we found a negative correlation between TGM and the Se concentration in grain for the artisanal area. Principal component analysis indicated that the source of Se in rice was the atmosphere for the artisanal area (no contribution from soil), and both the atmosphere and soil for the abandoned area. We propose that TGM falls to soil and reacts with Se, inhibiting the translocation of Se to rice grain. Our data suggest that Se intake by the artisanal mining community is insufficient to meet Se dietary requirements, predisposing this community to greater risk from Hg poisoning.

  17. Detection and verification of QTLs associated with heat-induced quality decline of rice (Oryza sativa L.) using recombinant inbred lines and near-isogenic lines

    PubMed Central

    Kobayashi, Asako; Sonoda, Junya; Sugimoto, Kazuhiko; Kondo, Motohiko; Iwasawa, Norio; Hayashi, Takeshi; Tomita, Katsura; Yano, Masahiro; Shimizu, Toyohiro

    2013-01-01

    Decline in the apparent quality of rice (Oryza sativa L.) grain due to high temperatures during ripening recently became a major concern in many areas in Japan. The occurrence of white-back kernels (WBK) is one of the main problems of heat-induced quality decline. We identified QTLs associated with the occurrence of WBK using recombinant inbred lines (RILs) and verified their effects using near-isogenic lines (NILs). The QTL analysis used F7 and F8 RILs derived from ‘Hana-echizen’ (HE), which is tolerant to high temperature, × ‘Niigata-wase’ (NW), which is sensitive to high temperature. Four QTLs were identified on chromosomes 3, 4, 6, and 9 (qWB3, qWB4, qWB6 and qWB9). To verify the effects of qWB6 and qWB9, we developed two NILs in which qWB6 or both were introduced from HE into the NW background. The HE allele at qWB6 significantly decreased WBK under multiple environments. The combination of qWB6 and qWB9 in an F2 population derived from a cross between a NIL and NW showed that the NW allele at qWB9 significantly decreased WBK if the qWB6 allele was HE. These results will be of value in marker-assisted selection for the breeding of rice with tolerance to heat-induced quality decline. PMID:24273430

  18. Thirty-three years of 2-acetyl-1-pyrroline, a principal basmati aroma compound in scented rice (Oryza sativa L.): a status review.

    PubMed

    Wakte, Kantilal; Zanan, Rahul; Hinge, Vidya; Khandagale, Kiran; Nadaf, Altafhusain; Henry, Robert

    2017-01-01

    Rice is the staple food of around 3 billion people, most of them in Asia which accounts for 90% of global rice consumption. Aromatic rices have been preferred over non-aromatic rice for hundreds of years. They have a premium value in national as well as international market owing to their unique aroma and quality. Many researchers were involved in identifying the compound responsible for the pleasant aroma in aromatic rice in the 20th century. However, due to its unstable nature, 2-acetyl-1-pyrroline (2AP) was discovered very late, in 1982. Buttery and co-workers found 2AP to be the principal compound imparting the pleasant aroma to basmati and other scented rice varieties. Since then, 2AP has been identified in all fragrant rice (Oryza sativa L.) varieties and a wide range of plants, animals, fungi, bacteria and various food products. The present article reviews in detail biochemical and genetic aspects of 2AP in living systems. The site of synthesis, site of storage and stability in plant systems in vivo is of interest. This compound requires more research on stability to facilitate use as a food additive. © 2016 Society of Chemical Industry.

  19. Genetic diversity and population structure of 'Khao Kai Noi', a Lao rice (Oryza sativa L.) landrace, revealed by microsatellite DNA markers.

    PubMed

    Vilayheuang, Koukham; Machida-Hirano, Ryoko; Bounphanousay, Chay; Watanabe, Kazuo N

    2016-03-01

    Rice (Oryza sativa L.) is the main food for people in Laos, where it has been grown and eaten since prehistory. Diverse landraces are grown in Laos. 'Khao Kai Noi', a landrace favored for its eating quality, is held in the nationwide collection of traditional landraces in the Lao national genebank. Genetic diversity is crucial for sustainable use of genetic resources and conservation. To investigate the genetic diversity of 'Khao Kai Noi' for conservation, we genotyped 70 accessions by using 23 polymorphic simple sequence repeat markers. The markers generated 2 to 17 alleles (132 in total), with an average of 5.7 per locus. The total expected heterozygosity over all 'Khao Kai Noi' accessions was 0.271. Genetic variation was largest among accessions and smallest within accessions. Khao Kai Noi accessions were classified into three different genetic backgrounds, but there was unclear association between the three inferred population and name subgroups and geographical distribution. Most of the accessions were clustered with temperate japonica and showed genetic relatedness to rice from neighboring provinces of Vietnam, suggesting a Vietnamese origin. The results of this study will contribute to the conservation, core collection and future breeding of the Khao Kai Noi population.

  20. A Ds-insertion mutant of OSH6 (Oryza sativa Homeobox 6) exhibits outgrowth of vestigial leaf-like structures, bracts, in rice.

    PubMed

    Park, Sung Han; Kim, Chul Min; Je, Byoung Il; Park, Su Hyun; Park, Soon Ju; Piao, Hai Long; Xuan, Yuan-Hu; Choe, Mi Sook; Satoh, Kouji; Kikuchi, Shoshi; Lee, Kon Ho; Cha, Young Soon; Ahn, Byung Ohg; Ji, Hyeon So; Yun, Doh Won; Lee, Myung Chul; Suh, Seok-Cheol; Eun, Moo Young; Han, Chang-Deok

    2007-12-01

    OSH6 (Oryza sativa Homeobox6) is an ortholog of lg3 (Liguleless3) in maize. We generated a novel allele, termed OSH6-Ds, by inserting a defective Ds element into the third exon of OSH6, which resulted in a truncated OSH6 mRNA. The truncated mRNA was expressed ectopically in leaf tissues and encoded the N-terminal region of OSH6, which includes the KNOX1 and partial KNOX2 subdomains. This recessive mutant showed outgrowth of bracts or produced leaves at the basal node of the panicle. These phenotypes distinguished it from the OSH6 transgene whose ectopic expression led to a "blade to sheath transformation" phenotype at the midrib region of leaves, similar to that seen in dominant Lg3 mutants. Expression of a similar truncated OSH6 cDNA from the 35S promoter (35S::DeltaOSH6) confirmed that the ectopic expression of this product was responsible for the aberrant bract development. These data suggest that OSH6-Ds interferes with a developmental mechanism involved in bract differentiation, especially at the basal nodes of panicles.

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

    NASA Astrophysics Data System (ADS)

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

    2013-07-01

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

  2. Molecular characterization of Oryza sativa arsenic-induced RING E3 ligase 1 (OsAIR1): Expression patterns, localization, functional interaction, and heterogeneous overexpression.

    PubMed

    Hwang, Sun-Goo; Park, Hyeon Mi; Han, A-Reum; Jang, Cheol Seong

    2016-02-01

    High levels of arsenic (As) in plants are a serious threat to human health, and arsenic accumulation affects plant metabolism and ultimately photosynthesis, growth, and development. We attempted to isolate As-responsive Really Interesting New Gene (RING) E3 ubiquitin ligase genes from rice, and we have designated one such gene Oryza sativa arsenic-induced RING E3 ligase 1 (OsAIR1). OsAIR1 expression was induced under abiotic stress conditions, including drought, salt, heat, and As exposure. Results from an in vitro ubiquitination assay showed that OsAIR1 possesses E3 ligase activity. Within the cell, the expression of this gene was found to be localized to the vacuole. In a network-based analysis, we found significantly enriched gene ontology (GO) functions, which included ribonucleoprotein complexes such as ribosomes, suggesting that the function of OsAIR1 are related to translation. Differences in the proportion of seedlings with expanded cotyledons and root lengths, and the lack of differences in germination rates between OsAIR1-overexpressing lines and control plants under AsV stress, suggest that OsAIR1 may positively regulate post-germination plant growth under stress conditions.

  3. Identification and expression analysis of microRNAs at the grain filling stage in rice(Oryza sativa L.)via deep sequencing.

    PubMed

    Yi, Rong; Zhu, Zhixuan; Hu, Jihong; Qian, Qian; Dai, Jincheng; Ding, Yi

    2013-01-01

    MicroRNAs (miRNAs) have been shown to play crucial roles in the regulation of plant development. In this study, high-throughput RNA-sequencing technology was used to identify novel miRNAs, and to reveal miRNAs expression patterns at different developmental stages during rice (Oryza sativa L.) grain filling. A total of 434 known miRNAs (380, 402, 390 and 392 at 5, 7, 12 and 17 days after fertilization, respectively.) were obtained from rice grain. The expression profiles of these identified miRNAs were analyzed and the results showed that 161 known miRNAs were differentially expressed during grain development, a high proportion of which were up-regulated from 5 to 7 days after fertilization. In addition, sixty novel miRNAs were identified, and five of these were further validated experimentally. Additional analysis showed that the predicted targets of the differentially expressed miRNAs may participate in signal transduction, carbohydrate and nitrogen metabolism, the response to stimuli and epigenetic regulation. In this study, differences were revealed in the composition and expression profiles of miRNAs among individual developmental stages during the rice grain filling process, and miRNA editing events were also observed, analyzed and validated during this process. The results provide novel insight into the dynamic profiles of miRNAs in developing rice grain and contribute to the understanding of the regulatory roles of miRNAs in grain filling.

  4. Gene body methylation shows distinct patterns associated with different gene origins and duplication modes and has a heterogeneous relationship with gene expression in Oryza sativa (rice).

    PubMed

    Wang, Yupeng; Wang, Xiyin; Lee, Tae-Ho; Mansoor, Shahid; Paterson, Andrew H

    2013-04-01

    Whole-genome duplication (WGD) has been recurring and single-gene duplication is also widespread in angiosperms. Recent whole-genome DNA methylation maps indicate that gene body methylation (i.e. of coding regions) has a functional role. However, whether gene body methylation is related to gene origins and duplication modes has yet to be reported. In rice (Oryza sativa), we computed a body methylation level (proportion of methylated CpG within coding regions) for each gene in five tissues. Body methylation levels follow a bimodal distribution, but show distinct patterns associated with transposable element-related genes; WGD, tandem, proximal and transposed duplicates; and singleton genes. For pairs of duplicated genes, divergence in body methylation levels increases with physical distance and synonymous (Ks) substitution rates, and WGDs show lower divergence than single-gene duplications of similar Ks levels. Intermediate body methylation tends to be associated with high levels of gene expression, whereas heavy body methylation is associated with lower levels of gene expression. The biological trends revealed here are consistent across five rice tissues, indicating that genes of different origins and duplication modes have distinct body methylation patterns, and body methylation has a heterogeneous relationship with gene expression and may be related to survivorship of duplicated genes.

  5. OsMOGS is required for N-glycan formation and auxin-mediated root development in rice (Oryza sativa L.).

    PubMed

    Wang, SuiKang; Xu, YanXia; Li, ZhiLan; Zhang, SaiNa; Lim, Jae-Min; Lee, Kyun Oh; Li, ChuanYou; Qian, Qian; Jiang, De An; Qi, YanHua

    2014-05-01

    N-glycosylation is a major modification of glycoproteins in eukaryotic cells. In Arabidopsis, great progress has been made in functional analysis of N-glycan production, however there are few studies in monocotyledons. Here, we characterized a rice (Oryza sativa L.) osmogs mutant with shortened roots and isolated a gene that coded a putative mannosyl-oligosaccharide glucosidase (OsMOGS), an ortholog of α-glucosidase I in Arabidopsis, which trims the terminal glucosyl residue of the oligosaccharide chain of nascent peptides in the endoplasmic reticulum (ER). OsMOGS is strongly expressed in rapidly cell-dividing tissues and OsMOGS protein is localized in the ER. Mutation of OsMOGS entirely blocked N-glycan maturation and inhibited high-mannose N-glycan formation. The osmogs mutant exhibited severe defects in root cell division and elongation, resulting in a short-root phenotype. In addition, osmogs plants had impaired root hair formation and elongation, and reduced root epidemic cell wall thickness due to decreased cellulose synthesis. Further analysis showed that auxin content and polar transport in osmogs roots were reduced due to incomplete N-glycosylation of the B subfamily of ATP-binding cassette transporter proteins (ABCBs). Our results demonstrate that involvement of OsMOGS in N-glycan formation is required for auxin-mediated root development in rice.

  6. N-glycan containing a core α1,3-fucose residue is required for basipetal auxin transport and gravitropic response in rice (Oryza sativa).

    PubMed

    Harmoko, Rikno; Yoo, Jae Yong; Ko, Ki Seong; Ramasamy, Nirmal Kumar; Hwang, Bo Young; Lee, Eun Ji; Kim, Ho Soo; Lee, Kyung Jin; Oh, Doo-Byoung; Kim, Dool-Yi; Lee, Sanghun; Li, Yang; Lee, Sang Yeol; Lee, Kyun Oh

    2016-10-01

    In plants, α1,3-fucosyltransferase (FucT) catalyzes the transfer of fucose from GDP-fucose to asparagine-linked GlcNAc of the N-glycan core in the medial Golgi. To explore the physiological significance of this processing, we isolated two Oryza sativa (rice) mutants (fuct-1 and fuct-2) with loss of FucT function. Biochemical analyses of the N-glycan structure confirmed that α1,3-fucose is missing from the N-glycans of allelic fuct-1 and fuct-2. Compared with the wild-type cv Kitaake, fuct-1 displayed a larger tiller angle, shorter internode and panicle lengths, and decreased grain filling as well as an increase in chalky grains with abnormal shape. The mutant allele fuct-2 gave rise to similar developmental abnormalities, although they were milder than those of fuct-1. Restoration of a normal tiller angle in fuct-1 by complementation demonstrated that the phenotype is caused by the loss of FucT function. Both fuct-1 and fuct-2 plants exhibited reduced gravitropic responses. Expression of the genes involved in tiller and leaf angle control was also affected in the mutants. We demonstrate that reduced basipetal auxin transport and low auxin accumulation at the base of the shoot in fuct-1 account for both the reduced gravitropic response and the increased tiller angle.

  7. Metabolome Analysis of Oryza sativa (Rice) Using Liquid Chromatography-Mass Spectrometry for Characterizing Organ Specificity of Flavonoids with Anti-inflammatory and Anti-oxidant Activity.

    PubMed

    Yang, Zhigang; Nakabayashi, Ryo; Mori, Tetsuya; Takamatsu, Satoshi; Kitanaka, Susumu; Saito, Kazuki

    2016-01-01

    Oryza sativa L. (rice) is an important staple crop across the world. In the previous study, we identified 36 specialized (secondary) metabolites including 28 flavonoids. In the present study, a metabolome analysis using liquid chromatography-mass spectrometry was conducted on the leaf, bran, and brown and polished rice grains to better understand the distribution of these metabolites. Principal component analysis using the metabolome data clearly characterized the accumulation patterns of the metabolites. Flavonoids, e.g., tricin, tricin 7-O-rutinoside, and tricin 7-O-β-D-glucopyranoside, were mainly present in the leaf and bran but not in the polished grain. In addition, anti-inflammatory and anti-oxidant activity of the metabolites were assayed in vitro. Tricin 4'-O-(erythro-β-guaiacylglyceryl)ether and isoscoparin 2″-O-(6‴-(E)-feruloyl)-glucopyranoside showed the strongest activity for inhibiting nitric oxide (NO) production and 1,1-diphenyl-2-picrylhydrazyl (DPPH) radical-scavenging, respectively.

  8. Toward better annotation in plant metabolomics: isolation and structure elucidation of 36 specialized metabolites from Oryza sativa (rice) by using MS/MS and NMR analyses.

    PubMed

    Yang, Zhigang; Nakabayashi, Ryo; Okazaki, Yozo; Mori, Tetsuya; Takamatsu, Satoshi; Kitanaka, Susumu; Kikuchi, Jun; Saito, Kazuki

    2014-01-01

    Metabolomics plays an important role in phytochemical genomics and crop breeding; however, metabolite annotation is a significant bottleneck in metabolomic studies. In particular, in liquid chromatography-mass spectrometry (MS)-based metabolomics, which has become a routine technology for the profiling of plant-specialized metabolites, a substantial number of metabolites detected as MS peaks are still not assigned properly to a single metabolite. Oryza sativa (rice) is one of the most important staple crops in the world. In the present study, we isolated and elucidated the structures of specialized metabolites from rice by using MS/MS and NMR. Thirty-six compounds, including five new flavonoids and eight rare flavonolignan isomers, were isolated from the rice leaves. The MS/MS spectral data of the isolated compounds, with a detailed interpretation of MS fragmentation data, will facilitate metabolite annotation of the related phytochemicals by enriching the public mass spectral data depositories, including the plant-specific MS/MS-based database, ReSpect.

  9. Effect of external iron and arsenic species on chelant-enhanced iron bioavailability and arsenic uptake in rice (Oryza sativa L.).

    PubMed

    Rahman, M Azizur; Rahman, M Mamunur; Kadohashi, K; Maki, T; Hasegawa, H

    2011-07-01

    This study was conducted to investigate the effect of external iron status and arsenic species on chelant-enhanced iron bioavailability and arsenic uptake. Rice seedlings (Oryza sativa L.) were used as model plant, and were grown in artificially contaminated sandy soils irrigated with Murashige and Skoog (MS) culture solution. Arsenate uptake in roots and shoots of rice seedlings were affected significantly (p>0.05) while dimethylarsinic acid (DMAA) was not by the additional iron and chelating ligand treatments. Regardless of iron concentrations in the soil solution, HIDS increased arsenic uptake for roots more than EDTA and EDDS. Chelating ligands and arsenic species also influenced iron uptake in rice roots. Irrespective of arsenic species, HIDS was found to be more effective in the increase of iron bioavailability and uptake in rice roots compared to other chelants. There was a significant positive correlation (r=0.78, p<0.05) between arsenate and iron concentrations in the roots of rice seedlings grown with or without additional iron indicating that arsenate inhibit iron uptake. In contrast, there was no correlation between iron and DMAA uptake in roots. Poor correlation between iron and arsenic in shoots indicated that iron uptake in shoots was neither affected by additional iron nor by arsenic species. Compared to the control, chelating ligands increased iron uptake in shoots of rice seedlings significantly (p<0.05). Regardless of additional iron and arsenic species, iron uptake in rice shoots did not differed among EDTA, EDDS, and HIDS treatments.

  10. Integration of crop rotation and arbuscular mycorrhiza (AM) inoculum application for enhancing AM activity to improve phosphorus nutrition and yield of upland rice (Oryza sativa L.).

    PubMed

    Maiti, Dipankar; Toppo, Neha Nancy; Variar, Mukund

    2011-11-01

    Upland rice (Oryza sativa L.) is a major crop of Eastern India grown during the wet season (June/July to September/October). Aerobic soils of the upland rice system, which are acidic and inherently phosphorus (P) limiting, support native arbuscular mycorrhizal (AM) activity. Attempts were made to improve P nutrition of upland rice by exploiting this natural situation through different crop rotations and application of AM fungal (AMF) inoculum. The effect of a 2-year crop rotation of maize (Zea mays L.) followed by horse gram (Dolichos biflorus L.) in the first year and upland rice in the second year on native AM activity was compared to three existing systems, with and without application of a soil-root-based inoculum. Integration of AM fungal inoculation with the maize-horse gram rotation had synergistic/additive effects in terms of AMF colonization (+22.7 to +42.7%), plant P acquisition (+11.2 to +23.7%), and grain yield of rice variety Vandana (+25.7 to +34.3%).

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

    PubMed

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

    2017-01-01

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

  12. Effects of different Fe supplies on mineral partitioning and remobilization during the reproductive development of rice (Oryza sativa L.)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Minimal information exists on whole-plant dynamics of mineral flow through rice plants or on the source tissues responsible for mineral export to developing seeds. Understanding these phenomena in a model plant could help in the development of nutritionally enhanced crop cultivars. A whole-plant acc...

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  14. Dietary supplementation of germinated pigmented rice (Oryza sativa L.) lowers dyslipidemia risk in ovariectomized Sprague–Dawley rats

    PubMed Central

    Lo, Lara Marie Pangan; Kang, Mi Young; Yi, Seong Joon; Chung, Soo Im

    2016-01-01

    Background In the recent years, cases of elderly women suffering from metabolic diseases such as dyslipidemias brought about by hormonal imbalance after menopause are continuously increasing. In this regard, a continuous and escalating demand to develop a more functional and highly nutritional food product as an adjunct supplement that can help alleviate these diseases is still being sought. Objective This study investigated the effects of germinated blackish-purple rice cultivars Keunnunjami, Superjami, and reddish-brown cultivar Superhongmi in the lipid metabolism of ovariectomized Sprague–Dawley rats. Method The animals were randomly divided into nine groups (n=5) and were supplemented with either non-germinated or germinated rice for 9 weeks. Then the plasma, liver, and fat samples were collected for the lipid metabolism effects analyses. Results Animals fed with germinated rice cultivars had improved lipid profile levels relative to the groups supplemented with non-germinated rice cultivars. The germinated rice groups, Keununjami and Superjami in particular, showed a low total cholesterol levels, high levels of high-density lipoproteins-cholesterol, high fecal lipid output, low hepatic lipid values, and low hepatic adipocyte accumulation. There was also an increase in the rate of lipolysis and decrease in lipogenesis based on the lipid-regulating enzyme activity profiles obtained for the groups that fed on germinated rice. Also, results revealed that pigmented rice cultivars had superior effects in improving the lipid metabolism relative to the non-pigmented normal brown rice variety. Conclusion Based on the results, this study suggests that germinated pigmented rice consumption can confer better lipid metabolism than ordinary white rice and constitutes as an effective functional food in alleviating the risk of having dyslipidemias like those suffering from menopausal co-morbidities. PMID:27032671

  15. Photosynthetic Diffusional Constraints Affect Yield in Drought Stressed Rice Cultivars during Flowering

    PubMed Central

    Lauteri, Marco; Haworth, Matthew; Serraj, Rachid; Monteverdi, Maria Cristina; Centritto, Mauro

    2014-01-01

    Global production of rice (Oryza sativa) grain is limited by water availability and the low ‘leaf-level’ photosynthetic capacity of many cultivars. Oryza sativa is extremely susceptible to water-deficits; therefore, predicted increases in the frequency and duration of drought events, combined with future rises in global temperatures and food demand, necessitate the development of more productive and drought tolerant cultivars. We investigated the underlying physiological, isotopic and morphological responses to water-deficit in seven common varieties of O. sativa, subjected to prolonged drought of varying intensities, for phenotyping purposes in open field conditions. Significant variation was observed in leaf-level photosynthesis rates (A) under both water treatments. Yield and A were influenced by the conductance of the mesophyll layer to CO2 (gm) and not by stomatal conductance (gs). Mesophyll conductance declined during drought to differing extents among the cultivars; those varieties that maintained gm during water-deficit sustained A and yield to a greater extent. However, the variety with the highest gm and yield under well-watered conditions (IR55419-04) was distinct from the most effective cultivar under drought (Vandana). Mesophyll conductance most effectively characterises the photosynthetic capacity and yield of O. sativa cultivars under both well-watered and water-deficit conditions; however, the desired attributes of high gm during optimal growth conditions and the capacity for gm to remain constant during water-deficit may be mutually exclusive. Nonetheless, future genetic and physiological studies aimed at enhancing O. sativa yield and drought stress tolerance should investigate the biochemistry and morphology of the interface between the sub-stomatal pore and mesophyll layer. PMID:25275452

  16. Photosynthetic diffusional constraints affect yield in drought stressed rice cultivars during flowering.

    PubMed

    Lauteri, Marco; Haworth, Matthew; Serraj, Rachid; Monteverdi, Maria Cristina; Centritto, Mauro

    2014-01-01

    Global production of rice (Oryza sativa) grain is limited by water availability and the low 'leaf-level' photosynthetic capacity of many cultivars. Oryza sativa is extremely susceptible to water-deficits; therefore, predicted increases in the frequency and duration of drought events, combined with future rises in global temperatures and food demand, necessitate the development of more productive and drought tolerant cultivars. We investigated the underlying physiological, isotopic and morphological responses to water-deficit in seven common varieties of O. sativa, subjected to prolonged drought of varying intensities, for phenotyping purposes in open field conditions. Significant variation was observed in leaf-level photosynthesis rates (A) under both water treatments. Yield and A were influenced by the conductance of the mesophyll layer to CO2 (g(m)) and not by stomatal conductance (g(s)). Mesophyll conductance declined during drought to differing extents among the cultivars; those varieties that maintained g(m) during water-deficit sustained A and yield to a greater extent. However, the variety with the highest g(m) and yield under well-watered conditions (IR55419-04) was distinct from the most effective cultivar under drought (Vandana). Mesophyll conductance most effectively characterises the photosynthetic capacity and yield of O. sativa cultivars under both well-watered and water-deficit conditions; however, the desired attributes of high g(m) during optimal growth conditions and the capacity for g(m) to remain constant during water-deficit may be mutually exclusive. Nonetheless, future genetic and physiological studies aimed at enhancing O. sativa yield and drought stress tolerance should investigate the biochemistry and morphology of the interface between the sub-stomatal pore and mesophyll layer.

  17. Development of casparian strip in rice cultivars

    PubMed Central

    Cai, Xia; Chen, Tong; Zhou, QingYuan; Xu, Lei; Qu, LeQing; Hua, XueJun

    2011-01-01

    The development of Casparian strips (CSs) on the endo- and exodermis and their chemical components in roots of three cultivars of rice (Oryza sativa) with different salt tolerance were compared using histochemistry and Fourier transform infrared (FTIR) spectroscopy. The development and deposition of suberin lamellae of CSs on the endo- and exodermis in the salt-tolerant cultivar Liaohan 109 was earlier than in the moderately tolerant cultivar Tianfeng 202 and the sensitive cultivar Nipponbare. The detection of chemical components indicated major contributions to the structure of the outer part from aliphatic suberin, lignin and cell wall proteins and carbohydrates to the rhizodermis, exodermis, sclerenchyma and one layer of cortical cells in series (OPR) and the endodermal Casparian strip. Moreover, the amounts of these major chemical components in the outer part of the Liaohan 109 root were higher than in Tianfeng 202 and Nipponbare, but there was no distinct difference in endodermal CSs among the three rice cultivars. The results suggest that the exodermis of the salt-tolerant cultivar Liaohan 109 functions as a barrier for resisting salt stress. PMID:21248477

  18. Root-induced changes to cadmium speciation in the rhizosphere of two rice (Oryza sativa L.) genotypes

    SciTech Connect

    Hu, Linfei; McBride, Murray B.; Cheng, Hao; Wu, Jianjun; Shi, Jiachun; Xu, Jianming; Wu, Laosheng

    2011-04-15

    Our aim was to investigate rhizosphere effects on the chemical behavior of Cd. This was done in a glasshouse experiment, where two rice cultivars (Zhenong54 and Sixizhan) were grown in soil spiked with cadmium (Cd) at two levels, 3.9{+-}0.5 and 8.3{+-}0.5 mg kg{sup -1} soil, placed in a rhizobox until ripening stage. Chemical forms of cadmium near the root surface were then assessed using a sequential extraction procedure (SEP). There were significant differences in Cd species, especially exchangeable Cd (EXC-Cd) between the two rice cultivars as affected by rice roots. The lowest EXC-Cd with Zhenong54 appeared in the near-rhizosphere area with little difference between tillering stage and ripening stage while Sixizhan had its lowest EXC-Cd concentration in the root compartment. Both cultivars had slight changes in the Fe/Mn oxide-bound fraction of Cd (FMO-Cd) at the grain ripening stage while the control treatments without plants had a significant increase in FMO-Cd at the same time, indicating a transformation from a less bioavailable form (FMO-Cd) to more bioavailable forms (EXC-Cd). Soil microbial biomass in the vicinity of the root surface had opposite trends to some extent with EXC-Cd, partly because of the root-induced changes to bioavailable Cd. Unlike Zhenong54, Sixizhan had a higher Cd concentration in the root, but only a small proportion of Cd translocated from the root to grain. - Research highlights: {yields}We investigated genotypic effects on Cd speciation in the rhizosphere of rice. {yields}Zhenong54 (ZN) and Sixizhan (SX) were grown in rhizobox to show root-induced changes. {yields}Lowest exchangeable-Cd of ZN was in near-rhizosphere while SX in root compartment. {yields}Soil microbial biomass had opposite trends with exchangeable-Cd in both cultivars. {yields}Unlike ZN, SX had higher Cd content in roots, but lower Cd content in shoots.

  19. Genetic Diversity and Elite Allele Mining for Grain Traits in Rice (Oryza sativa L.) by Association Mapping.

    PubMed

    Edzesi, Wisdom M; Dang, Xiaojing; Liang, Lijun; Liu, Erbao; Zaid, Imdad U; Hong, Delin

    2016-01-01

    Mining elite alleles for grain size and weight is of importance for the improvement of cultivated rice and selection for market demand. In this study, association mapping for grain traits was performed on a selected sample of 628 rice cultivars using 262 SSRs. Grain traits were evaluated by grain length (GL), grain width (GW), grain thickness (GT), grain length to width ratio (GL/GW), and 1000-grain weight (TGW) in 2013 and 2014. Our result showed abundant phenotypic and genetic diversities found in the studied population. In total, 2953 alleles were detected with an average of 11.3 alleles per locus. The population was divided into seven subpopulations and the levels of linkage disequilibrium (LD) ranged from 34 to 84 cM. Genome-wide association mapping detected 10 marker trait association (MTAs) loci for GL, 1MTAs locus for GW, 7 MTAs loci for GT, 3 MTAs loci for GL/GW, and 1 MTAs locus for TGW. Twenty-nine, 2, 10, 5, and 3 elite alleles were found for the GL, GW, GT, GL/GW, and TGW, respectively. Optimal cross designs were predicted for improving the target traits. The accessions containing elite alleles for grain traits mined in this study could be used for breeding rice cultivars and cloning the candidate genes.

  20. Molecular Breeding to Improve Salt Tolerance of Rice (Oryza sativa L.) in the Red River Delta of Vietnam.

    PubMed

    Linh, Le Hung; Linh, Ta Hong; Xuan, Tran Dang; Ham, Le Huy; Ismail, Abdelbagi M; Khanh, Tran Dang

    2012-01-01

    Rice is a stable food in Vietnam and plays a key role in the economy of the country. However, the production and the cultivating areas are adversely affected from the threats of devastation caused by the rise of sea level. Using marker-assisted backcrossing (MABC) to develop a new salt tolerance rice cultivar is one of the feasible methods to cope with these devastating changes. To improve rice salt tolerance in BT7 cultivar, FL478 was used as a donor parent to introgress the Saltol QTL conferring salt tolerance into BT7. Three backcrosses were conducted and successfully transferred positive alleles of Saltol from FL478 into BT7. The plants numbers IL-30 and IL-32 in BC(3)F(1) population expected recurrent genome recovery of up to 99.2% and 100%, respectively. These selected lines that carried the Saltol alleles were screened in field for their agronomic traits. All improved lines had Saltol allele similar to the donor parent FL478, whereas their agronomic performances were the same as the original BT7. We show here the success of improving rice salt tolerance by MABC and the high efficiency of selection in early generations. In the present study, MABC has accelerated the development of superior qualities in the genetic background of BT7.

  1. Genetic Diversity and Elite Allele Mining for Grain Traits in Rice (Oryza sativa L.) by Association Mapping

    PubMed Central

    Edzesi, Wisdom M.; Dang, Xiaojing; Liang, Lijun; Liu, Erbao; Zaid, Imdad U.; Hong, Delin

    2016-01-01

    Mining elite alleles for grain size and weight is of importance for the improvement of cultivated rice and selection for market demand. In this study, association mapping for grain traits was performed on a selected sample of 628 rice cultivars using 262 SSRs. Grain traits were evaluated by grain length (GL), grain width (GW), grain thickness (GT), grain length to width ratio (GL/GW), and 1000-grain weight (TGW) in 2013 and 2014. Our result showed abundant phenotypic and genetic diversities found in the studied population. In total, 2953 alleles were detected with an average of 11.3 alleles per locus. The population was divided into seven subpopulations and the levels of linkage disequilibrium (LD) ranged from 34 to 84 cM. Genome-wide association mapping detected 10 marker trait association (MTAs) loci for GL, 1MTAs locus for GW, 7 MTAs loci for GT, 3 MTAs loci for GL/GW, and 1 MTAs locus for TGW. Twenty-nine, 2, 10, 5, and 3 elite alleles were found for the GL, GW, GT, GL/GW, and TGW, respectively. Optimal cross designs were predicted for improving the target traits. The accessions containing elite alleles for grain traits mined in this study could be used for breeding rice cultivars and cloning the candidate genes. PMID:27375646

  2. Development of pyramidal lines with two major QTLs conferring resistance to sheath blight in rice (Oryza sativa L.)

    NASA Astrophysics Data System (ADS)

    Hossain, Md Kamal; Jena, Kshirod; Bhuiyan, Md Atiqur Rahman; Ratnam, Wickneswari

    2014-09-01

    Sheath blight is an emerging threat in rice cultivation. It is animportant disease caused by the soil-borne necrotrophic pathogenic fungus, Rhizoctonia solani Kühn. However, to date neither known major genes for quantitative resistance, nor any rice lines immune to this disease has been identified. The disease resistance is quantitative in nature. Numerous genes are involved in this resistance process. There are few quantitative trait loci (QTLs) detected conferring improved resistance against the disease. Teqing and Tetepshowimproved resistance having QTLs, qSB-9 and qSBR11-1, respectively. Since, these QTLs demonstrates additive effects, pyramiding of these QTLs might be an option to increase the sheath blight resistance in rice. Nine rice cultivars were screened at greenhouse conditions. Results showed that Tetep and Teqing had the lowest disease ratings. UKMRC2a new high yielding cultivar was as recipient parent. Crosses between UKMRC2 and Teqing, and UKMRC2 and Tetep were made and confirmed. Subsequently 4-way crosses between the two F1s were performed to develop pyramidal lines.

  3. Temporal variability in trace metal solubility in a paddy soil not reflected in uptake by rice (Oryza sativa L.).

    PubMed

    Pan, Yunyu; Koopmans, Gerwin F; Bonten, Luc T C; Song, Jing; Luo, Yongming; Temminghoff, Erwin J M; Comans, Rob N J

    2016-12-01

    Alternating flooding and drainage conditions have a strong influence on redox chemistry and the solubility of trace metals in paddy soils. However, current knowledge of how the effects of water management on trace metal solubility are linked to trace metal uptake by rice plants over time is still limited. Here, a field-contaminated paddy soil was subjected to two flooding and drainage cycles in a pot experiment with two rice plant cultivars, exhibiting either high or low Cd accumulation characteristics. Flooding led to a strong vertical gradient in the redox potential (Eh). The pH and Mn, Fe, and dissolved organic carbon concentrations increased with decreasing Eh and vice versa. During flooding, trace metal solubility decreased markedly, probably due to sulfide mineral precipitation. Despite its low solubility, the Cd content in rice grains exceeded the food quality standards for both cultivars. Trace metal contents in different rice plant tissues (roots, stem, and leaves) increased at a constant rate during the first flooding and drainage cycle but decreased after reaching a maximum during the second cycle. As such, the high temporal variability in trace metal solubility was not reflected in trace metal uptake by rice plants over time. This might be due to the presence of aerobic conditions and a consequent higher trace metal solubility near the root surface, even during flooding. Trace metal solubility in the rhizosphere should be considered when linking water management to trace metal uptake by rice over time.

  4. Zn uptake, translocation and grain Zn loading in rice (Oryza sativa L.) genotypes selected for Zn deficiency tolerance and high grain Zn.

    PubMed

    Impa, Somayanda M; Morete, Mark J; Ismail, Abdelbagi M; Schulin, Rainer; Johnson-Beebout, Sarah E

    2013-07-01

    Zn deficiency is a widespread problem in rice (Oryza sativa L.) grown under flooded conditions, limiting growth and grain Zn accumulation. Genotypes with Zn deficiency tolerance or high grain Zn have been identified in breeding programmes, but little is known about the physiological mechanisms conferring these traits. A protocol was developed for growing rice to maturity in agar nutrient solution (ANS), with optimum Zn-sufficient growth achieved at 1.5 μM ZnSO4.7H2O. The redox potential in ANS showed a decrease from +350 mV to -200 mV, mimicking the reduced conditions of flooded paddy soils. In subsequent experiments, rice genotypes contrasting for Zn deficiency tolerance and grain Zn were grown in ANS with sufficient and deficient Zn to assess differences in root uptake of Zn, root-to-shoot Zn translocation, and in the predominant sources of Zn accumulation in the grain. Zn efficiency of a genotype was highly influenced by root-to-shoot translocation of Zn and total Zn uptake. Translocation of Zn from root to shoot was more limiting at later growth stages than at the vegetative stage. Under Zn-sufficient conditions, continued root uptake during the grain-filling stage was the predominant source of grain Zn loading in rice, whereas, under Zn-deficient conditions, some genotypes demonstrated remobilization of Zn from shoot and root to grain in addition to root uptake. Understanding the mechanisms of grain Zn loading in rice is crucial in selecting high grain Zn donors for target-specific breeding and also to establish fertilizer and water management strategies for achieving high grain Zn.

  5. Effect of land preparation methods on growth, seed yields of Jasmine 105 paddy rice (Oryza sativa L.) and growth of weeds, grown in Northeast Thailand.

    PubMed

    Srisa-Ard, K

    2008-01-01

    This experiment was carried out on a grower's paddy field, Ban Som Hoeng Village, Kantarawichai, Mahasarakham Province, Northeast Thailand with the use of Roi-Et soil series (Oxic Paleustults) in the rainy season of the 2006 (May to November) to investigate effect of land preparation methods on rice plant heights, amounts of weeds and seed yields of Jasmine 105 aromatic paddy rice (Oryza sativa L.). The experiment was laid in a Randomized Complete Block Design (RCBD) with four replications. The results showed that plant height due to treatments was significantly highest for T3 but T3 was similar to T2, whilst T1 (control) was the least. Mean values of dry weight of narrow leaf type of weeds, in most cases, were significantly lowest with T3 followed by T2 and T3, particularly at the final two sampling periods. Broad leaf type of weeds was significantly highest with T2 throughout the experimental period, whilst T1 and T3, in most cases, were similar. Unfilled seeds were significantly highest with T3 but similar to T1 but T2 was the lowest, whilst filled seeds were significantly highest with T3, both T1 and T2 gave a similar weight. Numbers of panicles m(-2) were significantly highest with T3 but T3 was similar to T2, whilst T1 was the least. Seed size or 1000-seed weight was significantly highest with T3, whilst T2 and T1 were similar. Seed yield was highest and highly significant with T3 (1,136.25 kg ha(-1)) but T3 was similar to T2 (1,083.31 kg ha(-1)), whilst T1 was the lowest (487.50 kg ha(-1)). Land preparation method of T3 treatment may be recommended as the first choice, whilst T2 may be used as an alternative choice.

  6. OsSUV3 dual helicase functions in salinity stress tolerance by maintaining photosynthesis and antioxidant machinery in rice (Oryza sativa L. cv. IR64).

    PubMed

    Tuteja, Narendra; Sahoo, Ranjan Kumar; Garg, Bharti; Tuteja, Renu

    2013-10-01

    To overcome the salinity-induced loss of crop yield, a salinity-tolerant trait is required. The SUV3 helicase is involved in the regulation of RNA surveillance and turnover in mitochondria, but the helicase activity of plant SUV3 and its role in abiotic stress tolerance have not been reported so far. Here we report that the Oryza sativa (rice) SUV3 protein exhibits DNA and RNA helicase, and ATPase activities. Furthermore, we report that SUV3 is induced in rice seedlings in response to high levels of salt. Its expression, driven by a constitutive cauliflower mosaic virus 35S promoter in IR64 transgenic rice plants, confers salinity tolerance. The T1 and T2 sense transgenic lines showed tolerance to high salinity and fully matured without any loss in yields. The T2 transgenic lines also showed tolerance to drought stress. These results suggest that the introduced trait is functional and stable in transgenic rice plants. The rice SUV3 sense transgenic lines showed lesser lipid peroxidation, electrolyte leakage and H2 O2 production, along with higher activities of antioxidant enzymes under salinity stress, as compared with wild type, vector control and antisense transgenic lines. These results suggest the existence of an efficient antioxidant defence system to cope with salinity-induced oxidative damage. Overall, this study reports that plant SUV3 exhibits DNA and RNA helicase and ATPase activities, and provides direct evidence of its function in imparting salinity stress tolerance without yield loss. The possible mechanism could be that OsSUV3 helicase functions in salinity stress tolerance by improving photosynthesis and antioxidant machinery in transgenic rice.

  7. Improved plant growth and Zn accumulation in grains of rice (Oryza sativa L.) by inoculation of endophytic microbes isolated from a Zn Hyperaccumulator, Sedum alfredii H.

    PubMed

    Wang, Yuyan; Yang, Xiaoe; Zhang, Xincheng; Dong, Lanxue; Zhang, Jie; Wei, Yanyan; Feng, Ying; Lu, Lingli

    2014-02-26

    This study is to investigate the possibility of zinc (Zn) biofortification in the grains of rice (Oryza sativa L.) by inoculation of endophytic strains isolated from a Zn hyperaccumulator, Sedum alfredii Hance. Five endophytic strains, Burkholderia sp. SaZR4, Burkholderia sp. SaMR10, Sphingomonas sp. SaMR12, Variovorax sp. SaNR1, and Enterobacter sp. SaCS20, isolated from S. alfredii, were inoculated in the roots of Japonica rice Nipponbare under hydroponic condition. Fluorescence images showed that endophytic strains successfully colonized rice roots after 72 h. Improved root morphology and plant growth of rice was observed after inoculation with endophytic strains especially SaMR12 and SaCS20. Under hydroponic conditions, endophytic inoculation with SaMR12 and SaCS20 increased Zn concentration by 44.4% and 51.1% in shoots, and by 73.6% and 83.4% in roots, respectively. Under soil conditions, endophytic inoculation with SaMR12 and SaCS20 resulted in an increase of grain yields and elevated Zn concentrations by 20.3% and 21.9% in brown rice and by 13.7% and 11.2% in polished rice, respectively. After inoculation of SaMR12 and SaCS20, rhizosphere soils of rice plants contained higher concentration of DTPA-Zn by 10.4% and 20.6%, respectively. In situ micro-X-ray fluorescence mapping of Zn confirmed the elevated Zn content in the rhizosphere zone of rice treated with SaMR12 as compared with the control. The above results suggested that endophytic microbes isolated from S. alfredii could successfully colonize rice roots, resulting in improved root morphology and plant growth, increased Zn bioavailability in rhizosphere soils, and elevated grain yields and Zn densities in grains.

  8. Role of blue green algae biofertilizer in ameliorating the nitrogen demand and fly-ash stress to the growth and yield of rice (Oryza sativa L.) plants.

    PubMed

    Tripathi, R D; Dwivedi, S; Shukla, M K; Mishra, S; Srivastava, S; Singh, R; Rai, U N; Gupta, D K

    2008-02-01

    Rice is a major food crop throughout the world; however, accumulation of toxic metals and metalloids in grains in contaminated environments is a matter of growing concern. Field experiments were conducted to analyze the growth performance, elemental composition (Fe, Si, Zn, Mn, Cu, Ni, Cd and As) and yield of the rice plants (Oryza sativa L. cv. Saryu-52) grown under different doses of fly-ash (FA; applied @ 10 and 100 tha(-1) denoted as FA(10) and FA(100), respectively) mixed with garden soil (GS) in combination with nitrogen fertilizer (NF; applied @ 90 and 120 kg ha(-1) denoted as NF(90) and NF(120), respectively) and blue green algae biofertilizer (BGA; applied @ 12.5 kg ha(-1) denoted as BGA(12.5)). Significant enhancement of growth was observed in the plants growing on amended soils as compared to GS and best response was obtained in amendment of FA(10)+NF(90)+BGA(12.5). Accumulation of Si, Fe, Zn and Mn was higher than Cu, Cd, Ni and As. Arsenic accumulation was detected only in FA(100) and its amendments. Inoculation of BGA(12.5) caused slight reduction in Cd, Ni and As content of plants as compared to NF(120) amendment. The high levels of stress inducible non-protein thiols (NP-SH) and cysteine in FA(100) were decreased by application of NF and BGA indicating stress amelioration. Study suggests integrated use of FA, BGA and NF for improved growth, yield and mineral composition of the rice plants besides reducing the high demand of nitrogen fertilizers.

  9. Potential Application of the Oryza sativa Monodehydroascorbate Reductase Gene (OsMDHAR) to Improve the Stress Tolerance and Fermentative Capacity of Saccharomyces cerevisiae

    PubMed Central

    Kim, Yul-Ho; Park, Ae-Kyung; Kim, Han-Woo; Lee, Jun-Hyuk; Yoon, Ho-Sung

    2016-01-01

    Monodehydroascorbate reductase (MDHAR; EC 1.6.5.4) is an important enzyme for ascorbate recycling. To examine whether heterologous expression of MDHAR from Oryza sativa (OsMDHAR) can prevent the deleterious effects of unfavorable growth conditions, we constructed a transgenic yeast strain harboring a recombinant plasmid carrying OsMDHAR (p426GPD::OsMDHAR). OsMDHAR-expressing yeast cells displayed enhanced tolerance to hydrogen peroxide by maintaining redox homoeostasis, proteostasis, and the ascorbate (AsA)-like pool following the accumulation of antioxidant enzymes and molecules, metabolic enzymes, and molecular chaperones and their cofactors, compared to wild-type (WT) cells carrying vector alone. The addition of exogenous AsA or its analogue isoascorbic acid increased the viability of WT and ara2Δ cells under oxidative stress. Furthermore, the survival of OsMDHAR-expressing cells was greater than that of WT cells when cells at mid-log growth phase were exposed to high concentrations of ethanol. High OsMDHAR expression also improved the fermentative capacity of the yeast during glucose-based batch fermentation at a standard cultivation temperature (30°C). The alcohol yield of OsMDHAR-expressing transgenic yeast during fermentation was approximately 25% (0.18 g·g-1) higher than that of WT yeast. Accordingly, OsMDHAR-expressing transgenic yeast showed prolonged survival during the environmental stresses produced during fermentation. These results suggest that heterologous OsMDHAR expression increases tolerance to reactive oxygen species-induced oxidative stress by improving cellular redox homeostasis and improves survival during fermentation, which enhances fermentative capacity. PMID:27392090

  10. 2'-Deoxymugineic acid promotes growth of rice (Oryza sativa L.) by orchestrating iron and nitrate uptake processes under high pH conditions.

    PubMed

    Araki, Ryoichi; Kousaka, Kayoko; Namba, Kosuke; Murata, Yoshiko; Murata, Jun

    2015-01-01

    Poaceae plants release 2'-deoxymugineic acid (DMA) and related phytosiderophores to chelate iron (Fe), which often exists as insoluble Fe(III) in the rhizosphere, especially under high pH conditions. Although the molecular mechanisms behind the biosynthesis and secretion of DMA have been studied extensively, little information is known about whether DMA has biological roles other than chelating Fe in vivo. Here, we demonstrate that hydroponic cultures of rice (Oryza sativa) seedlings show almost complete restoration in shoot height and soil-plant analysis development (SPAD) values after treatment with 3-30 μm DMA at high pH (pH 8.0), compared with untreated control seedlings at normal pH (pH 5.8). These changes were accompanied by selective accumulation of Fe over other metals. While this enhanced growth was evident under high pH conditions, DMA application also enhanced seedling growth under normal pH conditions in which Fe was fairly accessible. Microarray and qRT-PCR analyses revealed that exogenous DMA application attenuated the increased expression levels of various genes related to Fe transport and accumulation. Surprisingly, despite the preferential utilization of ammonium over nitrate as a nitrogen source by rice, DMA application also increased nitrate reductase activity and the expression of genes encoding high-affinity nitrate transporters and nitrate reductases, all of which were otherwise considerably lower under high pH conditions. These data suggest that exogenous DMA not only plays an important role in facilitating the uptake of environmental Fe, but also orchestrates Fe and nitrate assimilation for optimal growth under high pH conditions.

  11. A novel epistatic interaction at two loci causing hybrid male sterility in an inter-subspecific cross of rice (Oryza sativa L.).

    PubMed

    Kubo, Takahiko; Yamagata, Yoshiyuki; Eguchi, Maki; Yoshimura, Atsushi

    2008-12-01

    Postzygotic reproductive isolation (RI) often arises in inter-subspecific crosses as well as inter-specific crosses of rice (Oryza sativa L.). To further understand the genetic architecture of the postzygotic RI, we analyzed genes causing hybrid sterility and hybrid breakdown in a rice inter-subspecific cross. Here we report hybrid male sterility caused by epistatic interaction between two novel genes, S24 and S35, which were identified on rice chromosomes 5 and 1, respectively. Genetic analysis using near-isogenic lines (NILs) carrying IR24 (ssp. indica) segments with Asominori (ssp. japonica) genetic background revealed a complicated aspect of the epistasis. Allelic interaction at the S24 locus in the heterozygous plants caused abortion of male gametes carrying the Asominori allele (S24-as) independent of the S35 genotype. On the other hand, male gametes carrying the Asominori allele at the S35 locus (S35-as) showed abortion only when the IR24 allele at the S24 locus (S24-ir) was concurrently introgressed into the S35 heterozygous plants, indicating that the sterility phenotype due to S35 was dependent on the S24 genotype through negative epistasis between S24-ir and S35-as alleles. Due to the interaction between S24 and S35, self-pollination of the double heterozygous plants produced pollen-sterile progeny carrying the S24-ir/S24-ir S35-as/S35-ir genotype in addition to the S24 heterozygous plants. This result suggests that the S35 gene might function as a modifier of S24. This study presents strong evidence for the importance of epistatic interaction as a part of the genetic architecture of hybrid sterility in rice. In addition, it suggests that diverse systems have been developed as postzygotic RI mechanisms within the rice.

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

    PubMed

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

    2014-09-01

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

  13. Emerging Importance of Helicases in Plant Stress Tolerance: Characterization of Oryza sativa Repair Helicase XPB2 Promoter and Its Functional Validation in Tobacco under Multiple Stresses

    PubMed Central

    Raikwar, Shailendra; Srivastava, Vineet K.; Gill, Sarvajeet S.; Tuteja, Renu; Tuteja, Narendra

    2015-01-01

    Genetic material always remains at the risk of spontaneous or induced damage which challenges the normal functioning of DNA molecule, thus, DNA repair is vital to protect the organisms against genetic damage. Helicases, the unique molecular motors, are emerged as prospective molecules to engineer stress tolerance in plants and are involved in nucleic acid metabolism including DNA repair. The repair helicase, XPB is an evolutionary conserved protein present in different organisms, including plants. Availability of few efficient promoters for gene expression in plants provoked us to study the promoter of XPB for better understanding of gene regulation under stress conditions. Here, we report the in silico analysis of novel stress inducible promoter of Oryza sativa XPB2 (OsXPB2). The in vivo validation of functionality/activity of OsXPB2 promoter under abiotic and hormonal stress conditions was performed by Agrobacterium-mediated transient assay in tobacco leaves using OsXPB2::GUS chimeric construct. The present research revealed that OsXPB2 promoter contains cis-elements accounting for various abiotic stresses (salt, dehydration, or cold) and hormone (Auxin, ABA, or MeJA) induced GUS expression/activity in the promoter-reporter assay. The promoter region of OsXPB2 contains CACG, GTAACG, CACGTG, CGTCA CCGCCGCGCT cis acting-elements which are reported to be salt, dehydration, cold, MeJA, or ABA responsive, respectively. Functional analysis was done by Agrobacterium-mediated transient assay using agroinfiltration in tobacco leaves, followed by GUS staining and fluorescence quantitative analyses. The results revealed high induction of GUS activity under multiple abiotic stresses as compared to mock treated control. The present findings suggest that OsXPB2 promoter is a multi-stress inducible promoter and has potential applications in sustainable crop production under abiotic stresses by regulating desirable pattern of gene expression. PMID:26734018

  14. Physiological basis of genetic variation in leaf photosynthesis among rice (Oryza sativa L.) introgression lines under drought and well-watered conditions.

    PubMed

    Gu, Junfei; Yin, Xinyou; Stomph, Tjeerd-Jan; Wang, Huaqi; Struik, Paul C

    2012-09-01

    To understand the physiological basis of genetic variation and resulting quantitative trait loci (QTLs) for photosynthesis in a rice (Oryza sativa L.) introgression line population, 13 lines were studied under drought and well-watered conditions, at flowering and grain filling. Simultaneous gas exchange and chlorophyll fluorescence measurements were conducted at various levels of incident irradiance and ambient CO(2) to estimate parameters of a model that dissects photosynthesis into stomatal conductance (g(s)), mesophyll conductance (g(m)), electron transport capacity (J(max)), and Rubisco carboxylation capacity (V(cmax)). Significant genetic variation in these parameters was found, although drought and leaf age accounted for larger proportions of the total variation. Genetic variation in light-saturated photosynthesis and transpiration efficiency (TE) were mainly associated with variation in g(s) and g(m). One previously mapped major QTL of photosynthesis was associated with variation in g(s) and g(m), but also in J(max) and V(cmax) at flowering. Thus, g(s) and g(m), which were demonstrated in the literature to be responsible for environmental variation in photosynthesis, were found also to be associated with genetic variation in photosynthesis. Furthermore, relationships between these parameters and leaf nitrogen or dry matter per unit area, which were previously found across environmental treatments, were shown to be valid for variation across genotypes. Finally, the extent to which photosynthesis rate and TE can be improved was evaluated. Virtual ideotypes were estimated to have 17.0% higher photosynthesis and 25.1% higher TE compared with the best genotype investigated. This analysis using introgression lines highlights possibilities of improving both photosynthesis and TE within the same genetic background.

  15. OsWOX3A is involved in negative feedback regulation of the gibberellic acid biosynthetic pathway in rice (Oryza sativa).

    PubMed

    Cho, Sung-Hwan; Kang, Kiyoon; Lee, Sang-Hwa; Lee, In-Jung; Paek, Nam-Chon

    2016-03-01

    The plant-specific WUSCHEL-related homeobox (WOX) nuclear proteins have important roles in the transcriptional regulation of many developmental processes. Among the rice (Oryza sativa) WOX proteins, a loss of OsWOX3A function in narrow leaf2 (nal2) nal3 double mutants (termed nal2/3) causes pleiotropic effects, such as narrow and curly leaves, opened spikelets, narrow grains, more tillers, and fewer lateral roots, but almost normal plant height. To examine OsWOX3A function in more detail, transgenic rice overexpressing OsWOX3A (OsWOX3A-OX) were generated; unexpectedly, all of them consistently exhibited severe dwarfism with very short and wide leaves, a phenotype that resembles that of gibberellic acid (GA)-deficient or GA-insensitive mutants. Exogenous GA3 treatment fully rescued the developmental defects of OsWOX3A-OX plants, suggesting that constitutive overexpression of OsWOX3A downregulates GA biosynthesis. Quantitative analysis of GA intermediates revealed significantly reduced levels of GA20 and bioactive GA1 in OsWOX3A-OX, possibly due to downregulation of the expression of KAO, which encodes ent-kaurenoic acid oxidase, a GA biosynthetic enzyme. Yeast one-hybrid and electrophoretic mobility shift assays revealed that OsWOX3A directly interacts with the KAO promoter. OsWOX3A expression is drastically and temporarily upregulated by GA3 and downregulated by paclobutrazol, a blocker of GA biosynthesis. These data indicate that OsWOX3A is a GA-responsive gene and functions in the negative feedback regulation of the GA biosynthetic pathway for GA homeostasis to maintain the threshold levels of endogenous GA intermediates throughout development.

  16. OsWOX3A is involved in negative feedback regulation of the gibberellic acid biosynthetic pathway in rice (Oryza sativa)

    PubMed Central

    Cho, Sung-Hwan; Kang, Kiyoon; Lee, Sang-Hwa; Lee, In-Jung; Paek, Nam-Chon

    2016-01-01

    The plant-specific WUSCHEL-related homeobox (WOX) nuclear proteins have important roles in the transcriptional regulation of many developmental processes. Among the rice (Oryza sativa) WOX proteins, a loss of OsWOX3A function in narrow leaf2 (nal2) nal3 double mutants (termed nal2/3) causes pleiotropic effects, such as narrow and curly leaves, opened spikelets, narrow grains, more tillers, and fewer lateral roots, but almost normal plant height. To examine OsWOX3A function in more detail, transgenic rice overexpressing OsWOX3A (OsWOX3A-OX) were generated; unexpectedly, all of them consistently exhibited severe dwarfism with very short and wide leaves, a phenotype that resembles that of gibberellic acid (GA)-deficient or GA-insensitive mutants. Exogenous GA3 treatment fully rescued the developmental defects of OsWOX3A-OX plants, suggesting that constitutive overexpression of OsWOX3A downregulates GA biosynthesis. Quantitative analysis of GA intermediates revealed significantly reduced levels of GA20 and bioactive GA1 in OsWOX3A-OX, possibly due to downregulation of the expression of KAO, which encodes ent-kaurenoic acid oxidase, a GA biosynthetic enzyme. Yeast one-hybrid and electrophoretic mobility shift assays revealed that OsWOX3A directly interacts with the KAO promoter. OsWOX3A expression is drastically and temporarily upregulated by GA3 and downregulated by paclobutrazol, a blocker of GA biosynthesis. These data indicate that OsWOX3A is a GA-responsive gene and functions in the negative feedback regulation of the GA biosynthetic pathway for GA homeostasis to maintain the threshold levels of endogenous GA intermediates throughout development. PMID:26767749

  17. Characterization of pullulanase (PUL)-deficient mutants of rice (Oryza sativa L.) and the function of PUL on starch biosynthesis in the developing rice endosperm

    PubMed Central

    Fujita, Naoko; Toyosawa, Yoshiko; Utsumi, Yoshinori; Higuchi, Toshiyuki; Hanashiro, Isao; Ikegami, Akira; Akuzawa, Sayuri; Yoshida, Mayumi; Mori, Akiko; Inomata, Kotaro; Itoh, Rumiko; Miyao, Akio; Hirochika, Hirohiko; Satoh, Hikaru; Nakamura, Yasunori

    2009-01-01

    Rice (Oryza sativa) allelic sugary1 (sug1) mutants defective in isoamylase 1 (ISA1) accumulate varying levels of starch and phytoglycogen in their endosperm, and the activity of a pullulanase-type of a debranching enzyme (PUL) was found to correlate closely with the severity of the sug1 phenotype. Thus, three PUL-deficient mutants were generated to investigate the function of PUL in starch biosynthesis. The reduction of PUL activity had no pleiotropic effects on the other enzymes involved in starch biosynthesis. The short chains (DP ≤13) of amylopectin in PUL mutants were increased compared with that of the wild type, but the extent of the changes was much smaller than that of sug1 mutants. The α-glucan composition [amylose, amylopectin, water-soluble polysaccharide (WSP)] and the structure of the starch components (amylose and amylopectin) of the PUL mutants were essentially the same, although the average chain length of the B2-3 chains of amylopectin in the PUL mutant was ∼3 residues longer than that of the wild type. The double mutants between the PUL-null and mild sug1 mutants still retained starch in the outer layer of endosperm tissue, while the amounts of WSP and short chains (DP ≤7) of amylopectin were higher than those of the sug1 mutant; this indicates that the PUL function partially overlaps with that of ISA1 and its deficiency has a much smaller effect on the synthesis of amylopectin than ISA1 deficiency and the variation of the sug1 phenotype is not significantly dependent on the PUL activities. PMID:19190097

  18. Time-series RNA-seq analysis package (TRAP) and its application to the analysis of rice, Oryza sativa L. ssp. Japonica, upon drought stress.

    PubMed

    Jo, Kyuri; Kwon, Hawk-Bin; Kim, Sun

    2014-06-01

    Measuring expression levels of genes at the whole genome level can be useful for many purposes, especially for revealing biological pathways underlying specific phenotype conditions. When gene expression is measured over a time period, we have opportunities to understand how organisms react to stress conditions over time. Thus many biologists routinely measure whole genome level gene expressions at multiple time points. However, there are several technical difficulties for analyzing such whole genome expression data. In addition, these days gene expression data is often measured by using RNA-sequencing rather than microarray technologies and then analysis of expression data is much more complicated since the analysis process should start with mapping short reads and produce differentially activated pathways and also possibly interactions among pathways. In addition, many useful tools for analyzing microarray gene expression data are not applicable for the RNA-seq data. Thus a comprehensive package for analyzing time series transcriptome data is much needed. In this article, we present a comprehensive package, Time-series RNA-seq Analysis Package (TRAP), integrating all necessary tasks such as mapping short reads, measuring gene expression levels, finding differentially expressed genes (DEGs), clustering and pathway analysis for time-series data in a single environment. In addition to implementing useful algorithms that are not available for RNA-seq data, we extended existing pathway analysis methods, ORA and SPIA, for time series analysis and estimates statistical values for combined dataset by an advanced metric. TRAP also produces visual summary of pathway interactions. Gene expression change labeling, a practical clustering method used in TRAP, enables more accurate interpretation of the data when combined with pathway analysis. We applied our methods on a real dataset for the analysis of rice (Oryza sativa L. Japonica nipponbare) upon drought stress. The result

  19. The Effect of Silicon on Photosynthesis and Expression of Its Relevant Genes in Rice (Oryza sativa L.) under High-Zinc Stress

    PubMed Central

    Song, Alin; Li, Ping; Fan, Fenliang; Li, Zhaojun; Liang, Yongchao

    2014-01-01

    The main objectives of this study were to elucidate the roles of silicon (Si) in alleviating the effects of 2 mM zinc (high Zn) stress on photosynthesis and its related gene expression levels in leaves of rice (Oryza sativa L.) grown hydroponically with high-Zn stress. The results showed that photosynthetic parameters, including net photosynthetic rate, transpiration rate, stomatal conductance, intercellular CO2 concentration, chlorophyll concentration and the chlorophyll fluorescence, were decreased in rice exposed to high-Zn treatment. The leaf chloroplast structure was disordered under high-Zn stress, including uneven swelling, disintegrated and missing thylakoid membranes, and decreased starch granule size and number, which, however, were all counteracted by the addition of 1.5 mM Si. Furthermore, the expression levels of Os08g02630 (PsbY), Os05g48630 (PsaH), Os07g37030 (PetC), Os03g57120 (PetH), Os09g26810 and Os04g38410 decreased in Si-deprived plants under high-Zn stress. Nevertheless, the addition of 1.5 mM Si increased the expression levels of these genes in plants under high-Zn stress at 72 h, and the expression levels were higher in Si-treated plants than in Si-deprived plants. Therefore, we conclude that Si alleviates the Zn-induced damage to photosynthesis in rice. The decline of photosynthesis in Zn-stressed rice was attributed to stomatal limitation, and Si activated and regulated some photosynthesis-related genes in response to high-Zn stress, consequently increasing photosynthesis. PMID:25426937

  20. Bio-protective microbial agents from rhizosphere eco-systems trigger plant defense responses provide protection against sheath blight disease in rice (Oryza sativa L.).

    PubMed

    Singh, Udai B; Malviya, Deepti; Wasiullah; Singh, Shailendra; Pradhan, Jatindra K; Singh, Bhanu P; Roy, Manish; Imram, Mohd; Pathak, Neelam; Baisyal, B M; Rai, Jai P; Sarma, B K; Singh, Rajiv K; Sharma, P K; Kaur, Saman Deep; Manna, M C; Sharma, Sushil K; Sharma, Arun K

    2016-11-01

    Sheath blight of rice (Oryza sativa L.) caused by Rhizoctonia solani is a major disease and attempts are being made to develop microbe based technologies for biocontrol of this pathogen. However, the mechanisms of biocontrol are not fully understood and still require indepth study in the backdrop of emerging concepts in biological systems. The present investigation was aimed at deciphering the mechanisms of biocontrol of sheath blight of rice employing Pseudomonas fluorescens and Trichoderma harzianum as model agents for biocontrol. Initially 25, 5 and 5 strains of P. fluorescens, T. viride and T. harzianum, respectively, were screened for their biocontrol potential. Out of which, six strains with higher value of percent inhibition of fungal mycelium in dual plate assay were selected. The role of P. fluorescens, T. viride and T. harzianum were investigated in induction and bioaccumulation of natural antioxidants, defence-related biomolecules and other changes in plant which lead not only to growth promotion but also protection from pathogenic stress conditions in rice. The two most promising strains, P. fluorescens PF-08 and T. harzianum UBSTH-501 selected on the basis of in planta evaluation, when applied individually or in combination, significantly enhanced the accumulation of defence-related biomolecules, enzymes and exhibited biocontrol potential against R. solani. A modified/newly developed delivery system was applied for the first time in the experiments involving inoculation of plants with both bioagents, viz. P. fluorescens PF-08 and T. harzianum UBSTH-501. Results suggested that application of P. fluorescens PF-08 and T. harzianum UBSTH-501 alone or in combination, not only helps in control of the disease but also increases plant growth along with reduction in application of toxic chemical pesticides.

  1. Screening of candidate genes and fine mapping of drought tolerance quantitative trait loci on chromosome 4 in rice (Oryza sativa L.) under drought stress.

    PubMed

    Nie, Yuan-Yuan; Zhang, Lin; Wu, Yun-Hua; Liu, Hao-Jie; Mao, Wei-Wei; Du, Juan; Xiu, Hai-Lin; Wu, Xiao-Yu; Li, Xia; Yan, Yu-Wei; Liu, Guo-Lan; Liu, Hong-Yan; Hu, Song-Ping

    2015-11-01

    Due to severe water resource shortage, genetics of and breeding for DT (drought tolerance) in rice (Oryza sativa L.) have become one of the hot research topics. Identification of grain yield QTLs (quantitative trait loci) directly related to the DT trait of rice can provide useful information for breeding new drought-resistant and water-saving rice varieties via marker-assisted selection. A population of 105 advanced BILs (backcross introgression lines) derived from a cross between Zhenshan97B and IRAT109 in Zhenshan97B background were grown under drought stress in a field experiment and phenotypic traits were investigated. The results showed that in the target interval of RM273-RM255 on chromosome 4, three main-effect QTLs related to panicle length, panicle number, and spikelet number per panicle were identified (LOD [logarithm of the odds] > 2.0). The panicle length-related QTL had two loci located in the neighboring intervals of RM17308-RM17305 and RM17349-RM17190, which explained 18.80% and 20.42%, respectively, of the phenotypic variation, while the panicle number-related QTL was identified in the interval of RM1354-RM17308, explaining 11.47% of the phenotypic variation. As far as the spikelet number per panicle-related QTL was concerned, it was found to be located in the interval of RM17308-RM17305, which explained 28.08% of the phenotypic variation. Using the online Plant-GE query system, a total of 13 matched ESTs (expressed sequence tags) were found in the target region, and of the 13 ESTs, 12 had corresponding predicted genes. For instance, the two ESTs CB096766 and CA765747 were corresponded to the same predicted gene LOC_Os04g46370, while the other four ESTs, CA754286, CB000011, CX056247, and CX056240, were corresponded to the same predicted gene LOC_Os04g46390.

  2. [Responses of rice (Oryza sativa) growth and its C, N and P composition to FACE (free-air carbon dioxide enrichment) and N, P fertilization].

    PubMed

    Xie, Zubin; Zhu, Jianguo; Zhang, Yali; Ma, Hongliang; Liu, Gang; Han, Yong; Zeng, Qing; Cai, Zucong

    2002-10-01

    FACE (Free-air Carbon Dioxide Enrichment) was used to study the effects of elevated CO2 on rice (Oryza sativa) growth, tissue C/N, N and P concentration and uptake at different development stages under two N and two P levels. Results showed that elevated CO2 increased dry matter accumulation in rice stem, ear and root. Leaf dry matter was increased at tillering stage and no significant effect was found at jointing, heading and ripening stages. N concentration of stem and leaf was decreased. Ear N concentration at heading stage was increased but was decreased at ripening stage. No significant effect was found on root N concentration at tillering stage but root N concentration at jointing, heading and ripening was decreased. Leaf P concentration at jointing, heading and ripening was increased but no significant effect was found on P concentration in stem, ear and root. C content in various tissues changed unremarkably and the ratio of C over N (C/N) was increased. Elevated CO2 significantly increased P uptake in aboveground tissues; and increased N uptake, but the difference was not statistically significant. N and P fertilization had no significant effect on various tissue dry biomass. Tissue N content at higher N fertilization was higher than at lower N fertilization but no such effect of P fertilization on tissue P content was found. At higher N fertilization, elevated CO2 increased the ratio of below-ground biomass over above-ground biomass at ripening stage. Possible reasons are discussed for the differences of tissue N and P content and the ratio of below-ground biomass over above-ground biomass between elevated and ambient atmospheric CO2 concentrations.

  3. Transcriptomes of isolated Oryza sativa gametes characterized by deep sequencing: evidence for distinct sex-dependent chromatin and epigenetic states before fertilization.

    PubMed

    Anderson, Sarah N; Johnson, Cameron S; Jones, Daniel S; Conrad, Liza J; Gou, Xiaoping; Russell, Scott D; Sundaresan, Venkatesan

    2013-12-01

    The formation of a zygote by the fusion of egg and sperm involves the two gametic transcriptomes. In flowering plants, the embryo sac embedded within the ovule contains the egg cell, whereas the pollen grain contains two sperm cells inside a supporting vegetative cell. The difficulties of collecting isolated gametes and consequent low recovery of RNA have restricted in-depth analysis of gametic transcriptomes in flowering plants. We isolated living egg cells, sperm cells and pollen vegetative cells from Oryza sativa (rice), and identified transcripts for approximately 36 000 genes by deep sequencing. The three transcriptomes are highly divergent, with about three-quarters of those genes differentially expressed in the different cell types. Distinctive expression profiles were observed for genes involved in chromatin conformation, including an unexpected expression in the sperm cell of genes associated with active chromatin. Furthermore, both the sperm cell and the pollen vegetative cell were deficient in expression of key RNAi components. Differences in gene expression were also observed for genes for hormonal signaling and cell cycle regulation. The egg cell and sperm cell transcriptomes reveal major differences in gene expression to be resolved in the zygote, including pathways affecting chromatin configuration, hormones and cell cycle. The sex-specific differences in the expression of RNAi components suggest that epigenetic silencing in the zygote might act predominantly through female-dependent pathways. More generally, this study provides a detailed gene expression landscape for flowering plant gametes, enabling the identification of specific gametic functions, and their contributions to zygote and seed development.

  4. The effects of free-air CO2 enrichment (FACE) on carbon and nitrogen accumulation in grains of rice (Oryza sativa L.)

    PubMed Central

    Zhu, Chunwu; Hasegawa, Toshihiro

    2013-01-01

    Rising atmospheric CO2 concentrations will probably increase rice (Oryza sativa L.) yield but decrease grain nitrogen (GN) concentration. Grains attached to different positions in the panicles differ greatly in weight and quality, but their responses to elevated CO2 (e[CO2]) are poorly understood, which limits our understanding of the mechanisms of yield enhancement and quality degradation. Thus a free-air CO2 enrichment experiment was conducted to examine the effects of e[CO2] on grain mass (GM), grain carbon (GC), and GN accumulation in the spikelets attached to the upper primary rachis branch (superior spikelets; SS) and those attached to the lower secondary rachis (inferior spikelets; IS). e[CO2] stimulated the rice yield by 13% but decreased the N concentration in the panicle by 7% when averaged over two levels of N fertilizations (P < 0.01). The responses of SS and IS to e[CO2] were different particularly under higher N supply. For SS, e[CO2] decreased GN by 24% (P < 0.01) but did not affect GM. For IS, e[CO2] increased GM by 13% (P < 0.05) but GN was not affected. The reduction of GN due to e[CO2] started to appear at the beginning of grain filling. These results suggest that future [CO2] levels probably stimulate the grain growth of IS, most of which are not marketable due to limited size, at the expense of GN reduction in SS. Translocation of N from SS to IS may be a possible mechanism for reduction in GN of SS. This may degrade the grain quality of marketable rice under e[CO2]. PMID:23918962

  5. 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.

  6. The effect of Silicon on photosynthesis and expression of its relevant genes in rice (Oryza sativa L.) under high-zinc stress.

    PubMed

    Song, Alin; Li, Ping; Fan, Fenliang; Li, Zhaojun; Liang, Yongchao

    2014-01-01

    The main objectives of this study were to elucidate the roles of silicon (Si) in alleviating the effects of 2 mM zinc (high Zn) stress on photosynthesis and its related gene expression levels in leaves of rice (Oryza sativa L.) grown hydroponically with high-Zn stress. The results showed that photosynthetic parameters, including net photosynthetic rate, transpiration rate, stomatal conductance, intercellular CO2 concentration, chlorophyll concentration and the chlorophyll fluorescence, were decreased in rice exposed to high-Zn treatment. The leaf chloroplast structure was disordered under high-Zn stress, including uneven swelling, disintegrated and missing thylakoid membranes, and decreased starch granule size and number, which, however, were all counteracted by the addition of 1.5 mM Si. Furthermore, the expression levels of Os08g02630 (PsbY), Os05g48630 (PsaH), Os07g37030 (PetC), Os03g57120 (PetH), Os09g26810 and Os04g38410 decreased in Si-deprived plants under high-Zn stress. Nevertheless, the addition of 1.5 mM Si increased the expression levels of these genes in plants under high-Zn stress at 72 h, and the expression levels were higher in Si-treated plants than in Si-deprived plants. Therefore, we conclude that Si alleviates the Zn-induced damage to photosynthesis in rice. The decline of photosynthesis in Zn-stressed rice was attributed to stomatal limitation, and Si activated and regulated some photosynthesis-related genes in response to high-Zn stress, consequently increasing photosynthesis.

  7. Photosynthesis mediated decrease in cadmium translocation protect shoot growth of Oryza sativa seedlings up on ammonium phosphate-sulfur fertilization.

    PubMed

    Sebastian, Abin; Prasad, M N V

    2014-01-01

    Cadmium (Cd) stress responses in seedlings of two Indian rice cultivars, MTU 7029 and MO 16 were investigated under ammonium-based fertilizer amendment. Cd translocation was reduced by fertilizer treatment. An increase in the production of organic acids as well as nitrogenous compounds and maintenance of nutrient status were implicated for decrease in Cd translocation which in turn promoted shoot growth. Fertilizer treatment increased photosynthetic pigments and activity of antioxidant enzymes that ensured steady photosynthetic rate during Cd stress. MO 16 showed Cd exclusion characteristics when compared with MTU 7029. Photosynthesis performance of MO 16 was not affected by Cd treatments. These findings suggest that photosynthesis influenced decrease in Cd translocation enhanced shoot growth of seedlings during ammonium phosphate-sulfur fertilizer supplementation.

  8. Genetic Diversity and Population Structure in Aromatic and Quality Rice (Oryza sativa L.) Landraces from North-Eastern India.

    PubMed

    Roy, Somnath; Banerjee, Amrita; Mawkhlieng, Bandapkuper; Misra, A K; Pattanayak, A; Harish, G D; Singh, S K; Ngachan, S V; Bansal, K C

    2015-01-01

    The North-eastern (NE) India, comprising of Arunachal Pradesh, Assam, Manipur, Meghalaya, Mizoram, Nagaland, Sikkim and Tripura, possess diverse array of locally adapted non-Basmati aromatic germplasm. The germplasm collections from this region could serve as valuable resources in breeding for abiotic stress tolerance, grain yield and cooking/eating quality. To utilize such collections, however, breeders need information about the extent and distribution of genetic diversity present within collections. In this study, we report the result of population genetic analysis of 107 aromatic and quality rice accessions collected from different parts of NE India, as well as classified these accessions in the context of a set of structured global rice cultivars. A total of 322 alleles were amplified by 40 simple sequence repeat (SSR) markers with an average of 8.03 alleles per locus. Average gene diversity was 0.67. Population structure analysis revealed that NE Indian aromatic rice can be subdivided into three genetically distinct population clusters: P1, joha rice accessions from Assam, tai rices from Mizoram and those from Sikkim; P2, aromatic rice accessions from Nagaland; and P3, chakhao rice germplasm from Manipur [corrected]. Pair-wise FST between three groups varied from 0.223 (P1 vs P2) to 0.453 (P2 vs P3). With reference to the global classification of rice cultivars, two major groups (Indica and Japonica) were identified in NE Indian germplasm. The aromatic accessions from Assam, Manipur and Sikkim were assigned to the Indica group, while the accessions from Nagaland exhibited close association with Japonica. The tai accessions of Mizoram along with few chakhao accessions collected from the hill districts of Manipur were identified as admixed. The results highlight the importance of regional genetic studies for understanding diversification of aromatic rice in India. The data also suggest that there is scope for exploiting the genetic diversity of aromatic and

  9. Different isoforms of starch-synthesizing enzymes controlling amylose and amylopectin content in rice (Oryza sativa L.).

    PubMed

    Pandey, Manish K; Rani, N Shobha; Madhav, M Sheshu; Sundaram, R M; Varaprasad, G S; Sivaranjani, A K P; Bohra, Abhishek; Kumar, G Ram; Kumar, Anirudh

    2012-01-01

    Starch, composed of amylose and amylopectin, greatly influences rice cooking and textural quality, which in turn is controlled by various isoforms of several enzymes. Activity of one or more isoforms of starch-synthesizing enzymes results in various forms of starch structure based on the amylopectin chain length and average external, internal and core chain length distribution and hence results in varying physicochemical and cooking quality. Since the synthesis of starch is highly complex, it is crucial but essential to understand its biosynthetic pathway, starch structure and effects on the physicochemical properties that control eating and cooking quality, and alongside conduct research on gene/QTL mapping for use in marker-assisted selection (MAS) with a view to improve and select cultivars with most desirable range and class of rice starch properties. This article presents the updates on current understanding of the coordination among various enzymes/isoforms towards rice starch synthesis in endosperm and their effect on rice grain physicochemical, cooking and eating qualities. The efforts in identifying regions responsible for these enzymes by mapping the gene/QTLs have provided a glimpse on their association with physicochemical and cooking properties of rice and, hence, improvement is possible by modifying the allelic pattern, resulting in down or nil regulation of a particular enzyme. The clear understanding of the tissue specific coordination between enzyme isoforms and their subsequent effect in controlling eating and cooking properties will enhance the chances to manipulate them for getting desired range of amylose content (AC) and gelatinization temperature (GT) in improved cultivars through combining desired alleles through MAS.

  10. Enzymic feruloylation of arabinoxylan-trisaccharide by feruloyl-CoA:arabinoxylan-trisaccharide O-hydroxycinnamoyl transferase from Oryza sativa.

    PubMed

    Yoshida-Shimokawa, T; Yoshida, S; Kakegawa, K; Ishii, T

    2001-02-01

    Feruloyl-CoA:arabinoxylan-trisaccharide O-hydroxycinnamoyl transferase, which catalyzes the transfer of ferulic acid from Fer-CoA to arabinoxylan-trisaccharide in the formation of feruloyl arabinoxylan-trisaccharide (Fer-AXX), has been found in an ionically bound fraction and a cytosol fraction of suspension-cultured rice (Oriza sativa L. cv. Nipponbare) cells. Analysis of reaction products by high-performance liquid chromatography showed the formation of product A, which is one of the transfer products having the same retention time as authentic Fer-AXX. Product A was purified by reverse-phase chromatographies to characterize its structure. The isolated product A showed the same ultraviolet spectrum and molecular weight on fast atom bombardment mass spectrometric analysis as those of authentic Fer-AXX. Alakaline saponification of product A released ferulic acid and oligosaccharide. The released oligosaccharide consisted of arabinose and xylose in a molar ratio of 1:2. These results support the identity of product A as feruloylated arabinoxylan-trisaccharide and show the existence of a feruloyltransferase catalyzing the feruloylation of a hemicellulosic fragment.

  11. Molecular dissection of developmental behavior of tiller number and plant height and their relationship in rice (Oryza sativa L.).

    PubMed

    Yang, Guohua; Xing, Yongzhong; Li, Shaoqing; Ding, Jingzhen; Yue, Bing; Deng, Kai; Li, Yangsheng; Zhu, Yingguo

    2006-12-01

    Plant height and tiller number are two important characters related to yield in rice (Oriza sativa L.). Zhenshan97 x Minghui63 recombinant inbred lines were employed to dissect the genetic basis of development of plant height and tiller number using conditional and unconditional composite interval mapping approaches. The traits were normally distributed with transgressive segregation in both directions. Increasingly negative correlations were observed between tiller number and plant height at five consecutive growth stages. A total of 23 and 24 QTL were identified for tiller number and plant height, respectively. More QTL were detected by conditional mapping than by conventional mapping. Different QTL/genes apparently controlled the traits at different developmental stages. Three genomic regions were identified as putative co-located QTL, which showed opposite additive effects on tiller number and plant height. Furthermore, in the period reaching maximum tiller number, the expression of QTL for tiller number was active, whereas that of QTL for plant height was inactive. These facts provided a possible genetic explanation for the negative correlations between the traits. The research demonstrates conditional mapping to be superior to conventional mapping for this type of research. Implications of the results for hybrid rice improvement are discussed.

  12. Protein evaluation of four oat (Avena sativa L.) cultivars adapted for cultivation in the south of Brazil.

    PubMed

    Pedó, I; Sgarbieri, V C; Gutkoski, L C

    1999-01-01

    Four oat cultivars adapted for soil and climate conditions in the southern region of Brazil were evaluated for protein nutritive value. Evaluations were done both in vitro and in vivo. In vitro evaluation was done by essential amino acid profile, available lysine, amino acid scoring, and protein digestibility corrected amino acid-scoring (PDCAAS). Nitrogen balance indices and PER were determined in vivo with rats. In all four cultivars (UFP-15, UFP-16, CTC-03, UFRGS-14), lysine was the most limiting amino acid. Available lysine, amino acid score and PDCAAS were highest for cultivar UFRGS-14 and lowest for CTC-03. When compared to casein, only nitrogen retention for UFRGS-14 did not differ statistically (p>0.05); all other indices of protein quality were inferior to casein for the oat cultivars. The oat cultivars tended to be identical among themselves, except for apparent protein digestibility which was significantly higher in the UFRGS-14 and CTC-03 cultivars. On average, the PER values of the oat cultivars were 82% of casein; the net protein utilization was 88% of casein as determined in vivo and 49% by the estimation in vitro (PDCAAS).

  13. Effects of hydrothermal processes on antioxidants in brown, purple and red bran whole grain rice (Oryza sativa L.).

    PubMed

    Min, Byungrok; McClung, Anna; Chen, Ming-Hsuan

    2014-09-15

    The impacts of parboiling and wet-cooking, alone and in combination, on the concentrations of lipophilic antioxidants (vitamin E and γ-oryzanol), soluble (including proanthocyanidins and anthocyanins) and cell wall-bound phenolics, and antioxidant capacities in whole grain rice from six cultivars having different bran colours were investigated. Parboiling rough and brown rice increased the concentrations of lipophilic antioxidants in whole grain rice but decreased the concentrations of total phenolics and antioxidant capacities found in the soluble fraction. After hydrothermal processing of purple bran rice, the retention of extractable anthocyanins was low, but was high for simple phenolics. For proanthocyanidins found in red bran rice, the extractable oligomers with a degree of polymerization (DP) less than 4, increased up to 6-fold; while for oligomers with DP⩾4 and polymers, there was a significant decrease that was positively correlated with the DP and the temperature of the processing methods. The presence of hulls helped to retain water-soluble antioxidants during parboiling.

  14. Influence of leaf vein density and thickness on hydraulic conductance and photosynthesis in rice (Oryza sativa L.) during water stress

    PubMed Central

    Tabassum, Muhammad Adnan; Zhu, Guanglong; Hafeez, Abdul; Wahid, Muhammad Atif; Shaban, Muhammad; Li, Yong

    2016-01-01

    The leaf venation architecture is an ideal, highly structured and efficient irrigation system in plant leaves. Leaf vein density (LVD) and vein thickness are the two major properties of this system. Leaf laminae carry out photosynthesis to harvest the maximum biological yield. It is still unknown whether the LVD and/or leaf vein thickness determines the plant hydraulic conductance (Kplant) and leaf photosynthetic rate (A). To investigate this topic, the current study was conducted with two varieties under three PEG-induced water deficit stress (PEG-IWDS) levels. The results showed that PEG-IWDS significantly decreased A, stomatal conductance (gs), and Kplant in both cultivars, though the IR-64 strain showed more severe decreases than the Hanyou-3 strain. PEG-IWDS significantly decreased the major vein thickness, while it had no significant effect on LVD. A, gs and Kplant were positively correlated with each other, and they were negatively correlated with LVD. A, gs and Kplant were positively correlated with the inter-vein distance and major vein thickness. Therefore, the decreased photosynthesis and hydraulic conductance in rice plants under water deficit conditions are related to the decrease in the major vein thickness. PMID:27848980

  15. Identification of quantitative trait loci for four morphologic traits under water stress in rice (Oryza sativa L.).

    PubMed

    Yue, Bing; Xue, Weiya; Luo, Lijun; Xing, Yongzhong

    2008-09-01

    Late season drought coinciding with the rice booting to heading stage affects the development of plant height, panicle exsertion, and flag leaf size, and causes significant yield loss. In this study, a recombinant inbred line population derived from a cross between paddy and upland cultivars was used for data collection of the morphologic traits under well water and drought stress conditions. Drought stress was applied at the stage of panicle initiation in the field in 2002 and at the booting stage in PVC pipes in 2003. The data from stress conditions and their ratios (trait measured under stress condition/trait measured under well water condition) or differences (trait measured under stress condition minus trait measured under well water condition) were used for QTL analysis. Totally, 17 and 36 QTLs for these traits were identified in 2002 and 2003, respectively, which explained a range of 2.58%-29.82% of the phenotypic variation. Among them, six QTLs were commonly identified in the two years, suggesting that the drought stress in the two years was different. The genetic basis of these traits will provide useful information for improving rice late season drought resistance, and their application as indirect indices in rice late season drought resistance screening was also discussed.

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

    PubMed

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

    2015-02-01

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

  17. Comparative proteomic analysis of seed embryo proteins associated with seed storability in rice (Oryza sativa L) during natural aging.

    PubMed

    Gao, Jiadong; Fu, Hua; Zhou, Xinqiao; Chen, Zhongjian; Luo, Yi; Cui, Baiyuan; Chen, Guanghui; Liu, Jun

    2016-06-01

    Seed storability is considered an important trait in rice breeding; however, the underlying regulating mechanisms remain largely unknown. Here, we carried out a physiological and proteomic study to identify proteins possibly related to seed storability under natural conditions. Two hybrid cultivars, IIYou998 (IIY998) and BoYou998 (BY998), were analyzed in parallel because they share the same restorer line but have significant differences in seed storability. After a 2-year storage period, the germination percentage of IIY998 was significantly lower than that of BY998, whereas the level of malondialdehyde was reversed, indicating that IIY998 seeds may suffer from more severe damage than BY998 during storage. However, we did not find correlation between activities of antioxidant enzymes of superoxide dismutase, peroxidase, and catalase and seed storability. We identified 78 embryo proteins in embryo whose abundance varied more than 3-fold different during storage or between IIY998 and BY998. More proteins changed in abundance in IIY998 embryo (67 proteins) during storage than in BY998 (10 proteins). Several redox regulation proteins, mainly glutathione-related proteins, exhibited different degree of change during storage between BY998 and IIY998 and might play an important role protecting embryo proteins from oxidation. In addition, some disease/defense proteins, including DNA-damage-repair/toleration proteins, and a putative late embryogenesis abundant protein were significantly downregulated in IIY998, whereas their levels did not change in BY998, indicating that they might be correlated with seed storability. Further studies on these candidate seed storage proteins might help improve our understanding of seed aging.

  18. [Pyramiding of senescence-inhibition IPT gene and Xa23 for resistance to bacterial blight in rice (Oryza sativa L.)].

    PubMed

    He, Guang-Ming; Sun, Chuan-Qing; Fu, Yong-Cai; Fu, Qiang; Zhao, Kai-Jun; Wang, Chun-Lian; Zhang, Qi; Ling, Zhong-Zhuan; Wang, Xiang-Kun

    2004-08-01

    Transgenic lines (GC-1) carrying a senescence-inhibition cheimeric gene, IPT (isopentenyl transferase) gene, CBB23, a isogenic lines carrying Xa23 gene for resistance to bacterial blight, and Hexi15, a commercial cultivar showing high resistance to blast disease, were used as donors to pyramid IPT gene and Xa23 by marker-assisted selection (MAS). Seventeen BC1F1 plants pyramiding Xa23 gene and IPT genes were obtained from three multi-cross combinations. Then, the plants carrying Xa23 and IPT genes were crossed with parental lines of two-line hybrid rice, such as 9311, E32, Pei' ai 64S and W9834S. The progenies were backcrossed the acceptor parents. A total of 17 plants carrying Xa23 and IPT genes were detected by PCR, disease resistance identification and analysis of CTK contents of in the four combinations of "(9311///Hexi15/CBB23// GC-1) x 9311", "(E32///Hexi15/CBB23//GC-1) x E32", "(Pei'ai 64S///Hexi15/CBB23//GC-1) x Pei' ai 64S" and "(GC-1/CBB23//W9834S/Hexi15) x W9834S". These plants showed resistance to blast disease by inoculating test using 21 the lines of Pyricularia grisea from Northern China. Six plants of BC2F1 pyramiding Xa23 and IPT genes were further obtained in the combinations of "[(9311///Hexi15/CBB23//GC-1) x 9311] x 9311", "[(E32///Hexi15/CBB23//GC-1) x E32] x E32". After backcrossed and self-crossed 1 approximately 2nd, the plants pyramiding Xa23 and IPT genes can be used in the program of hybrid rice breeding.

  19. Salt-responsive mechanisms in chromosome segment substitution lines of rice (Oryza sativa L. cv. KDML105).

    PubMed

    Nounjan, Noppawan; Siangliw, Jonaliza L; Toojinda, Theerayut; Chadchawan, Supachitra; Theerakulpisut, Piyada

    2016-06-01

    Two chromosome segment substitution lines of Khao Dawk Mali 105 (KDML105) rice that carry quantitative trait loci for drought tolerance located on chromosome 8 (DT-QTL8) designated CSSL8-94 and CSSL8-116 were investigated for co-expression network and physiological responses to salinity compared to their parents (KDML105; drought and salt sensitive recurrent parent, and DH103; drought tolerant QTL donor). These CSSL lines show different salt-response traits under salt stress (CSSL8-94 shows higher tolerance than CSSL8-116) and possess different segments of DT-QTL8. To identify specific biological process(es) associated with salt-stress response, co-expression network analysis was constructed from each DT-QTL segment. To evaluate differential physiological mechanisms responding to salt stress, all rice lines/cultivar were grown for 21 d in soils submerged in nutrient solutions, then subjected to 150 mM NaCl for 7 d. Physiological parameters related to co-expression network analysis (photosynthetic parameters) and salt responsive parameters (Na(+)/K(+) ratio, proline content, malondialdehyde and ascorbate peroxidase activity; EC1.11.1.1) were investigated along with the expression analysis of related genes. Physiological responses under salt stress particularly photosynthesis-related parameters of CSSL8-94 were similar to DH103, whereas those of CSSL8-116 were similar to KDML105. Moreover, expression levels of photosynthesis-related genes selected from the co-expression networks (Os08g41460, Os08g44680, Os06g01850, Os03g07300 and Os02g42570) were slightly decreased or stable in CSSL8-94 and DH103 but were dramatically down-regulated in CSSL8-116 and KDML105. These differential responses may contribute to the photosynthesis systems of CSSL8-94 being less damaged under salt stress in comparison to those of CSSL8-116. It can be concluded that the presence of the specific DT-QTL8 segment in CSSL8-94 not only confers drought tolerant traits but also enhances its salt

  20. Three genetic systems controlling growth, development and productivity of rice (Oryza sativa L.): a reevaluation of the 'Green Revolution'.

    PubMed

    Zhang, Fan; Jiang, Yun-Zhu; Yu, Si-Bin; Ali, J; Paterson, A H; Khush, G S; Xu, Jian-Long; Gao, Yong-Ming; Fu, Bin-Ying; Lafitte, R; Li, Zhi-Kang

    2013-04-01

    The Green Revolution (GR-I) included worldwide adoption of semi-dwarf rice cultivars (SRCs) with mutant alleles at GA20ox2 or SD1 encoding gibberellin 20-oxidase. Two series of experiments were conducted to characterize the pleiotropic effects of SD1 and its relationships with large numbers of QTLs affecting rice growth, development and productivity. The pleiotropic effects of SD1 in the IR64 genetic background for increased height, root length/mass and grain weight, and for reduced spikelet fertility and delayed heading were first demonstrated using large populations derived from near isogenic IR64 lines of SD1. In the second set of experiments, QTLs controlling nine growth and yield traits were characterized using a new molecular quantitative genetics model and the phenotypic data of the well-known IR64/Azucena DH population evaluated across 11 environments, which revealed three genetic systems: the SD1-mediated, SD1-repressed and SD1-independent pathways that control rice growth, development and productivity. The SD1-mediated system comprised 43 functional genetic units (FGUs) controlled by GA. The SD1-repressed system was the alternative one comprising 38 FGUs that were only expressed in the mutant sd1 backgrounds. The SD1-independent one comprised 64 FGUs that were independent of SD1. GR-I resulted from the overall differences between the former two systems in the three aspects: (1) trait/environment-specific contributions; (2) distribution of favorable alleles for increased productivity in the parents; and (3) different responses to (fertilizer) inputs. Our results suggest that at 71.4 % of the detected loci, a QTL resulted from the difference between a functional allele and a loss-of-function mutant, whereas at the remaining 28.6 % of loci, from two functional alleles with differentiated effects. Our results suggest two general strategies to achieve GR-II (1) by further exploiting the genetic potential of the SD1-repressed and SD1-independent pathways and (2

  1. Modest amendment of sewage sludge biochar to reduce the accumulation of cadmium into rice(Oryza sativa L.): A field study.

    PubMed

    Zhang, Youchi; Chen, Tingting; Liao, Yongkai; Reid, Brian J; Chi, Haifeng; Hou, Yanwei; Cai, Chao

    2016-09-01

    Much research has considered the influence of biochars on the availability and phytoaccumulation of potentially toxic elements (PTEs) from soil. However, the vast majority of these studies use, what are arguably, unrealistic and unpractical amounts of biochar (10, 50 and even up to 100 t/ha). To offer a more realistic insight into the influence of biochar on PTE partitioning and phytoaccumulation, a field study, using modest rates of biochar application (1.5, 3.0 t/ha), was undertaken. Specifically, the research investigated the influence of sewage sludge biochar (SSBC) on the accumulation of Cd into rice (Oryza sativa L.) grown in Cd contaminated (0.82 ± 0.07 mg/kg) paddy soil. Results indicated, Cd concentrations in rice grains to significantly (p < 0.05) decrease from 1.35 ± 0.09 mg/kg in the control to 0.82 ± 0.07 mg/kg and 0.80 ± 0.21 mg/kg in the 1.5 t/ha and 3.0 t/ha treatments, respectively. Accordingly, the hazardous quotient (HQ) indices for Cd, associated with rice grain consumption, were also reduced by ∼40%. SSBC amendment significantly (p < 0.05) increased grain yields from 1.90 ± 0.08 g/plant in the control to 2.17 ± 0.30 g/plant and 3.40 ± 0.27 g/plant in the 1.5 t/ha and 3.0 t/ha treatments, respectively. Thus, the amendment of SSBC to contaminated paddy soils, even at low application rates, could be an effective approach to mitigate Cd accumulation into rice plants, to improve rice grain yields, and to thereby improve food security and protect public health.

  2. A DESD-box helicase functions in salinity stress tolerance by improving photosynthesis and antioxidant machinery in rice (Oryza sativa L. cv. PB1).

    PubMed

    Gill, Sarvajeet Singh; Tajrishi, Marjan; Madan, Meenu; Tuteja, Narendra

    2013-05-01

    The exact mechanism of helicase-mediated salinity tolerance is not yet understood. We have isolated a DESD-box containing cDNA from Pisum sativum (Pea) and named it as PDH45. It is a unique member of DEAD-box helicase family; containing DESD instead of DEAD/H. PDH45 overexpression driven by constitutive cauliflower mosaic virus-35S promoter in rice transgenic [Oryza sativa L. cv. Pusa Basmati 1 (PB1)] plants confers salinity tolerance by improving the photosynthesis and antioxidant machinery. The Na(+) ion concentration and oxidative stress parameters in leaves of the NaCl (0, 100 or 200 mM) treated PDH45 overexpressing T1 transgenic lines were lower as compared to wild type (WT) rice plants under similar conditions. The 200 mM NaCl significantly reduced the leaf area, plant dry mass, net photosynthetic rate (PN), stomatal conductance (gs), intercellular CO2 (Ci), chlorophyll (Chl) content in WT plants as compared to the transgenics. The T1 transgenics exhibited higher glutathione (GSH) and ascorbate (AsA) contents under salinity stress. The activities of antioxidant enzymes viz. superoxide dismutase (SOD), ascorbate peroxidase (APX), guaiacol peroxidase (GPX) and glutathione reductase (GR) were significantly higher in transgenics; suggesting the existence of an efficient antioxidant defence system to cope with salinity induced-oxidative damage. Yeast two-hybrid assay indicated that the PDH45 protein interacts with Cu/Zn SOD, adenosine-5'-phosphosulfate-kinase, cysteine proteinase and eIF(4G), thus confirming the involvement of ROS scavenging machinery in the transgenic plants to provide salt tolerance. Furthermore, the T2 transgenics were also able to grow, flower, and set viable seeds under continuous salinity stress of 200 mM NaCl. This study provides insights into the mechanism of PDH45 mediated salinity stress tolerance by controlling the generation of stress induced reactive oxygen species (ROS) and also by protecting the photosynthetic machinery through a

  3. Determination of supplier-to-supplier and lot-to-lot variability in glycation of recombinant human serum albumin expressed in Oryza sativa.

    PubMed

    Frahm, Grant E; Smith, Daryl G S; Kane, Anita; Lorbetskie, Barry; Cyr, Terry D; Girard, Michel; Johnston, Michael J W

    2014-01-01

    The use of different expression systems to produce the same recombinant human protein can result in expression-dependent chemical modifications (CMs) leading to variability of structure, stability and immunogenicity. Of particular interest are recombinant human proteins expressed in plant-based systems, which have shown particularly high CM variability. In studies presented here, recombinant human serum albumins (rHSA) produced in Oryza sativa (Asian rice) (OsrHSA) from a number of suppliers have been extensively characterized and compared to plasma-derived HSA (pHSA) and rHSA expressed in yeast (Pichia pastoris and Saccharomyces cerevisiae). The heterogeneity of each sample was evaluated using size exclusion chromatography (SEC), reversed-phase high-performance liquid chromatography (RP-HPLC) and capillary electrophoresis (CE). Modifications of the samples were identified by liquid chromatography-mass spectrometry (LC-MS). The secondary and tertiary structure of the albumin samples were assessed with far U/V circular dichroism spectropolarimetry (far U/V CD) and fluorescence spectroscopy, respectively. Far U/V CD and fluorescence analyses were also used to assess thermal stability and drug binding. High molecular weight aggregates in OsrHSA samples were detected with SEC and supplier-to-supplier variability and, more critically, lot-to-lot variability in one manufactures supplied products were identified. LC-MS analysis identified a greater number of hexose-glycated arginine and lysine residues on OsrHSA compared to pHSA or rHSA expressed in yeast. This analysis also showed supplier-to-supplier and lot-to-lot variability in the degree of glycation at specific lysine and arginine residues for OsrHSA. Both the number of glycated residues and the degree of glycation correlated positively with the quantity of non-monomeric species and the chromatographic profiles of the samples. Tertiary structural changes were observed for most OsrHSA samples which correlated well

  4. Efficacy of Oryza sativa husk and Quercus phillyraeoides extracts for the in vitro and in vivo control of fungal rot disease of white yam (Dioscorea rotundata Poir).

    PubMed

    Dania, Victor Ohileobo; Fadina, Olubunmi Omowunmi; Ayodele, Maria; Kumar, P Lava

    2014-01-01

    Tuber rot disease is a major constraint to white yam (Dioscorea rotundata) production, accounting for 50-60% of annual yield losses in Nigeria. The main method of control using synthetic fungicides is being discouraged due to human and environmental health hazards. The potential of Oryza sativa husk (OSH) and Quercus phillyraeoides (QP) extracts for the in vitro and in vivo control of six virulent rot-causing fungal pathogens, Lasiodiplodia theobromae, Aspergillus niger, Rhizoctonia solani, Penicillium oxalicum, Sclerotium rolfsii, and Fusarium oxysporum was evaluated, using five different extract concentrations of 0.5%, 1.0%, 1.5%, 2.5%, and 3.5% w/v. These fungi were isolated from rotted tubers of D. rotundata, across three agroecological zones in Nigeria-the Humid rainforest, Derived savanna, and southern Guinea savanna. All treatments were subjected to three methods of inoculation 48 hours before the application of both extracts and stored at 28 ± 2°C for 6 months. Radial mycelial growth of the test pathogens was effectively inhibited at concentrations ≤ 3.5% w/v in vitro for both OSH and QP extracts. Rotting was significantly reduced (P ≤ 0.05) to between 0 to 18.8% and 0% to 20.9% for OSH and QP extracts respectively. The extracts significantly (P ≤ 0.05) inhibited percent rot of the test pathogens at 3.5% concentration w/v in vivo. Rot incidence was, however, lower in replicate tubers that were inoculated, treated with extracts and exposed than treatments that were covered. Phytochemical analysis of OSH and QP extracts revealed the presence of secondary metabolites such as alkaloids, flavonoids, saponins, tannins, ferulic acid, phlobatanins, Terpenoids, phenols, anthraquinone and pyroligneous acid. The efficacy of both extracts in reducing rot in this study recommends their development as prospective biopesticide formulation and use in the management of post-harvest rot of yam tubers.

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

    PubMed Central

    2012-01-01

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

  6. Expression of salt-induced 2-Cys peroxiredoxin from Oryza sativa increases stress tolerance and fermentation capacity in genetically engineered yeast Saccharomyces cerevisiae.

    PubMed

    Kim, Il-Sup; Kim, Young-Saeng; Yoon, Ho-Sung

    2013-04-01

    Peroxiredoxins (Prxs), also termed thioredoxin peroxidases (TPXs), are a family of thiol-specific antioxidant enzymes that are critically involved in cell defense and protect cells from oxidative damage. In this study, a putative chloroplastic 2-Cys thioredoxin peroxidase (OsTPX) was identified by proteome analysis from leaf tissue samples of rice (Oryza sativa) seedlings exposed to 0.1 M NaCl for 3 days. To investigate the relationship between the OsTPX gene and the stress response, OsTPX was cloned into the yeast expression vector p426GPD under the control of the glyceraldehyde-3-phosphate dehydrogenase (GPD1) promoter, and the construct was transformed into Saccharomyces cerevisiae cells. OsTPX expression was confirmed by semi-quantitative reverse transcription-polymerase chain reaction and western blot analyses. OsTPX contained two highly conserved cysteine residues (Cys114 and Cys236) and an active site region (FTFVCPT), and it is structurally very similar to human 2-Cys Prx. Heterologous OsTPX expression increased the ability of the transgenic yeast cells to adapt and recover from reactive oxygen species (ROS)-induced oxidative stresses, such as a reduction of cellular hydroperoxide levels in the presence of hydrogen peroxide and menadione, by improving redox homeostasis. OsTPX expression also conferred enhanced tolerance to tert-butylhydroperoxide, heat shock, and high ethanol concentrations. Furthermore, high OsTPX expression improved the fermentation capacity of the yeast during glucose-based batch fermentation at a high temperature (40 °C) and at the general cultivation temperature (30 °C). The alcohol yield in OsTPX-expressing transgenic yeast increased by approximately 29 % (0.14 g g(-1)) and 21 % (0.12 g g(-1)) during fermentation at 40 and 30 °C, respectively, compared to the wild-type yeast. Accordingly, OsTPX-expressing transgenic yeast showed prolonged cell survival during the environmental stresses produced during fermentation. These

  7. Sugars profiles of different chestnut (Castanea sativa Mill.) and almond (Prunus dulcis) cultivars by HPLC-RI.

    PubMed

    Barreira, João C M; Pereira, José Alberto; Oliveira, M Beatriz P P; Ferreira, Isabel C F R

    2010-03-01

    Sugar profiles of different almond and chestnut cultivars were obtained by high-performance liquid chromatography (HPLC), by means of a refractive index (RI) detector. A solid-liquid extraction procedure was used in defatted and dried samples. The chromatographic separation was achieved using a Eurospher 100-5 NH(2) column using an isocratic elution with acetonitrile/water (70:30, v/v) at a flow rate of 1.0 ml/min. All the compounds were separated in 16 min. The method was optimized and proved to be reproducible and accurate. Generally, more than 95% of sugars were identified for both matrixes. Sugars profiles were quite homogeneous for almond cultivars; sucrose was the main sugar (11.46 +/- 0.14 in Marcona to 22.23 +/- 0.59 in Ferragnes g/100 g of dried weight), followed by raffinose (0.71 +/- 0.05 in Ferraduel to 2.11 +/- 0.29 in Duro Italiano), glucose (0.42 +/- 0.12 in Pegarinhos two seeded to 1.47 +/- 0.19 in Ferragnes) and fructose (0.11 +/- 0.02 in Pegarinhos two seeded to 0.59 +/- 0.05 in Gloriette). Commercial cultivars proved to have higher sucrose contents, except in the case of Marcona. Nevertheless, chestnut cultivars revealed a high heterogeneity. Sucrose was the main sugar in Aveleira (22.05 +/- 1.48), Judia (23.30 +/- 0.83) and Longal (9.56 +/- 0.91), while glucose was slightly prevalent in Boa Ventura (6.63 +/- 0.49). The observed variance could serve for inter-cultivar discrimination.

  8. Potential oil yield, fatty acid composition, and oxidation stability of the hempseed oil from four Cannabis sativa L. cultivars.

    PubMed

    Da Porto, Carla; Decorti, Deborah; Natolino, Andrea

    2015-03-01

    The cultivation of four industrial hemp cultivars (Felina 32, Chamaeleon, Uso31, and Finola) was investigated for oil production in the north-east of Italy along two years. The oils of all cultivars resulted in rich amount of linoleic acid (ω-6) and α-linolenic acid (ω-3). Felina 32 and Chamaeleon oils exhibited the highest amount of linoleic acid (59%) and α-linolenic acid (18%). Finola and Uso31 oils resulted in the richest of γ-linolenic acid (5-6%). All hempseed oils presented high oxidation stability and an acceptable initial quality. It is suggested that these oils can be used to produce EFA dietary supplements high in ω-6 and ω-3 of vegetal origin.

  9. Open-pit coal-mining effects on rice paddy soil composition and metal bioavailability to Oryza sativa L. plants in Cam Pha, northeastern Vietnam.

    PubMed

    Martinez, Raul E; Marquez, J Eduardo; Hòa, Hoàng Thị Bích; Gieré, Reto

    2013-11-01

    This study quantified Cd, Pb, and Cu content, and the soil-plant transfer factors of these elements in rice paddies within Cam Pha, Quang Ninh province, northeastern Vietnam. The rice paddies are located at a distance of 2 km from the large Coc Sau open-pit coal mine. Electron microprobe analysis combined with backscattered electron imaging and energy-dispersive spectroscopy revealed a relatively high proportion of carbon particles rimmed by an iron sulfide mineral (probably pyrite) in the quartz-clay matrix of rice paddy soils at 20-30 cm depth. Bulk chemical analysis of these soils revealed the presence of Cd, Cu, and Pb at concentrations of 0.146±0.004, 23.3±0.1, and 23.5±0.1 mg/kg which exceeded calculated background concentrations of 0.006±0.004, 1.9±0.5, and 2.4±1.5 mg/kg respectively at one of the sites. Metals and metalloids in Cam Pha rice paddy soils, including As, Cd, Cr, Cu, Hg, Mn, Ni, Pb, and Zn, were found in concentrations ranging from 0.2±0.1 to 140±3 mg/kg, which were in close agreement with toxic metal contents in mine tailings and Coc Sau coal samples, suggesting mining operations as a major cause of paddy soil contamination. Native and model Oryza sativa L. rice plants were grown in the laboratory in a growth medium to which up to 1.5 mg/kg of paddy soil from Cam Pha was added to investigate the effects on plant growth. A decrease in growth by up to 60% with respect to a control sample was found for model plants, whereas a decrease of only 10% was observed for native (Nep cai hoa vang variety) rice plants. This result suggests an adaptation of native Cam Pha rice plants to toxic metals in the agricultural lands. The Cd, Cu, and Pb contents of the native rice plants from Cam Pha paddies exceeded permitted levels in foods. Cadmium and Pb were highest in the rice plant roots with concentrations of 0.84±0.02 and 7.7±0.3 mg/kg, suggesting an intake of these metals into the rice plant as shown, for example, by Cd and Pb concentrations of 0

  10. Analyses of Ca2+ dynamics using a ubiquitin-10 promoter-driven Yellow Cameleon 3.6 indicator reveal reliable transgene expression and differences in cytoplasmic Ca2+ responses in Arabidopsis and rice (Oryza sativa) roots.

    PubMed

    Behera, Smrutisanjita; Wang, Nili; Zhang, Chunxia; Schmitz-Thom, Ina; Strohkamp, Sarah; Schültke, Stefanie; Hashimoto, Kenji; Xiong, Lizhong; Kudla, Jörg

    2015-04-01

    Ca(2+) signatures are central to developmental processes and adaptive responses in plants. However, high-resolution studies of Ca(2+) dynamics using genetically encoded Ca(2+) indicators (GECIs) such as Yellow Cameleon (YC) proteins have so far not been conducted in important model crops such as rice (Oryza sativa). We conducted a comparative study of 35S and ubiquitin-10 (UBQ10) promoter functionality in Arabidopsis thaliana and O. sativa plants expressing the Ca(2+) indicator Yellow Cameleon 3.6 (YC3.6) under control of the UBQ10 or 35S promoter. Ca(2+) signatures in roots of both species were analyzed during exposure to hyperpolarization/depolarization cycles or in response to application of the amino acid glutamate. We found a superior performance of the UBQ10 promoter with regard to expression pattern, levels and expression stabilities in both species. We observed remarkable differences between the two species in the spatiotemporal parameters of the observed Ca(2+) signatures. Rice appeared in general to respond with a lower maximal signal amplitude but greatly increased signal duration when compared with Arabidopsis. Our results identify important advantages to using the UBQ10 promoter in Arabidopsis and rice and in T-DNA mutant backgrounds. Moreover, the observed differences in Ca(2+) signaling in the two species underscore the need for comparative studies to achieve a comprehensive understanding of Ca(2+) signaling in plants.

  11. 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

  12. Effect of supplemental ultraviolet radiation on the concentration of phytonutrients in green and red leaf lettuce (Lactuca sativa) cultivars

    NASA Astrophysics Data System (ADS)

    Britz, Steven; Caldwell, Charles; Mirecki, Roman; Slusser, James; Gao, Wei

    2005-08-01

    Eight cultivars each of red and green leaf lettuce were raised in a greenhouse with supplemental UV radiation, either UV-A (wavelengths greater than ca. 315 nm) or UV-A+UV-B (wavelengths greater than ca. 290 nm; 6.4 kJ m-2 daily biologically effective UV-B), or no supplemental UV (controls). Several phytonutrients were analyzed in leaf flours to identify lines with large differences in composition and response to UV-B. Red leaf lettuce had higher levels of phenolic acid esters, flavonols and anthocyanins than green lines. Both green and red lines exposed to UV-B for 9 days showed 2-3-fold increases in flavonoids compared to controls, but only 45% increases in phenolic acid esters, suggesting these compounds may be regulated by different mechanisms. There were large differences between cultivars in levels of phenolic compounds under control conditions and also large differences in UV-B effects. Among red varieties, cv. Galactic was notable for high levels of phenolics and a large response to UV-B. Among green varieties, cvs. Black-Seeded Simpson and Simpson Elite had large increases in phenolics with UV-B exposure. Photosynthetic pigments were also analyzed. Green leaf lettuce had high levels of pheophytin, a chlorophyll degradation product. Total chlorophylls (including pheophytin) were much lower in green compared to red varieties. Lutein, a carotenoid, was similar for green and red lines. Total chlorophylls and lutein increased 2-fold under supplemental UV-B in green lines but decreased slightly under UV-B in red lines. Lettuce appears to be a valuable crop to use to study phytochemical-environment interactions.

  13. Dye characteristics of Zingiber officinale var rubrum, Cinnamomum zaylanicum, Curcuma longa L., Oryza sativa L. Indica in dye sensitized solar cell (DSSC)

    NASA Astrophysics Data System (ADS)

    Cari; Mahfudli Fadli, U.; Bayu Prasada, A.; Supriyanto, A.

    2017-01-01

    The aims of the research to were know performance of DSSC using the dye of Zingiber, Cinnamomum, Curcuma, and Oryza as a photosensitizer with a variation of dye deposition area with spin coating techniques. The structure of the samples as a sandwich consisting of the working electrode (TiO2), dye, electrodes of platinum (Pt) and the electrolyte sandwiched between two electrodes. Test absorbance dye using UV-Visible Spectrophotometer Lambda 25, using a two-point conductivity test probes El Kahfi 100 and characterization test IV using a Keithley 2602A. For Zingiber results showed that absorbance at 243 nm and 279 nm, photoconductivity of 0.29 Ω-1m-1 and the efficiency is 0.015% on 0.5 cm2. Cinnamomum results showed that absorbance at 253 nm and 403 nm, photoconductivity of 0.11 Ω-1m-1 and the efficiency is 0.002% on 3 cm2. Curcuma results showed that absorbance at 243 nm and 422 nm, photoconductivity of 0.177 Ω-1m-1 and the efficiency is 0.072% on 3 cm2. Oryza results showed that absorbance at 240 nm and 423 nm, photoconductivity of 0.21 Ω-1m-1 and the efficiency is 0.04% on 2.25 cm2. Best absorbance value was obtained from Oryza dye; the highest photoconductivity was obtained from Zingiber dye, and the highest efficiency was obtained from Curcuma dye.

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

    PubMed

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

    2011-07-01

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

  15. Genetic interactions between diverged alleles of Early heading date 1 (Ehd1) and Heading date 3a (Hd3a)/ RICE FLOWERING LOCUS T1 (RFT1) control differential heading and contribute to regional adaptation in rice (Oryza sativa).

    PubMed

    Zhao, Jing; Chen, Hongyi; Ren, Ding; Tang, Huiwu; Qiu, Rong; Feng, Jinglei; Long, Yunming; Niu, Baixiao; Chen, Danping; Zhong, Tianyu; Liu, Yao-Guang; Guo, Jingxin

    2015-11-01

    Initiation of flowering, also called heading, in rice (Oryza sativa) is determined by the florigens encoded by Heading date 3a (Hd3a) and RICE FLOWERING LOCUS T1 (RFT1). Early heading date 1 (Ehd1) regulates Hd3a and RFT1. However, different rice varieties have diverged alleles of Ehd1 and Hd3a/RFT1 and their genetic interactions remain largely unclear. Here we generated three segregating populations for different combinations of diverged Ehd1 and Hd3a/RFT1 alleles, and analyzed their genetic interactions between these alleles. We demonstrated that, in an ehd1 mutant background, Hd3a was silenced, but RFT1 was expressed (although at lower levels than in plants with a functional Ehd1) under short-day (SD) and long-day (LD) conditions. We identified a nonfunctional RFT1 allele (rft1); the lines carrying homozygous ehd1 and Hd3a/rft1 failed to induce the floral transition under SD and LD conditions. Like Hd3a, RFT1 also interacted with 14-3-3 proteins, the florigen receptors, but a nonfunctional RFT1 with a crucial E105K mutation failed to interact with 14-3-3 proteins. Furthermore, analyses of sequence variation and geographic distribution suggested that functional RFT1 alleles were selected during rice adaptation to high-latitude regions. Our results demonstrate the important roles of RFT1 in rice flowering and regional adaptation.

  16. Characterization of a pollen-preferential gene OSIAGP from rice (Oryza sativa L. subspecies indica) coding for an arabinogalactan protein homologue, and analysis of its promoter activity during pollen development and pollen tube growth.

    PubMed

    Anand, Saurabh; Tyagi, Akhilesh K

    2010-06-01

    During differential screening of inflorescence-specific cDNA libraries from Oryza sativa indica, an arabinogalactan protein (OSIAGP) cDNA (586 bp) expressing preferentially in the inflorescence has been isolated. It encodes an arabinogalactan protein of 59 amino acids (6.4 kDa) with a transmembrane domain and a secretory domain at the N terminus. The protein shows homology with AGP23 from Arabidopsis, and its homologue in japonica rice is located on chromosome 6. OSIAGP transcripts also accumulate in shoots and roots of rice seedling grown in the dark, but light represses expression of the gene. Analysis of a genomic clone of OSIAGP revealed that its promoter contains several pollen-specificity and light-regulatory elements. The promoter confers pollen-preferential activity on gus, starting from the release of microspores to anther dehiscence in transgenic tobacco, and is also active during pollen tube growth. Analysis of pollen preferential activity of the promoter in the transgenic rice system revealed that even the approximately 300 bp fragment has activity in pollen and the anther wall and further deletion down to approximately 100 bp completely abolishes this activity, which is consistent with in-silico analysis of the promoter. Arabinogalactan proteins have been shown to be involved in the cell elongation process. The homology of OSIAGP with AGP23 and the fact that seedling growth in the dark and pollen tube growth are events based on cell elongation strengthen the possibility of OSIAGP performing a similar function.

  17. Expression of Arabidopsis glycine-rich RNA-binding protein AtGRP2 or AtGRP7 improves grain yield of rice (Oryza sativa) under drought stress conditions.

    PubMed

    Yang, Deok Hee; Kwak, Kyung Jin; Kim, Min Kyung; Park, Su Jung; Yang, Kwang-Yeol; Kang, Hunseung

    2014-01-01

    Although posttranscriptional regulation of RNA metabolism is increasingly recognized as a key regulatory process in plant response to environmental stresses, reports demonstrating the importance of RNA metabolism control in crop improvement under adverse environmental stresses are severely limited. To investigate the potential use of RNA-binding proteins (RBPs) in developing stress-tolerant transgenic crops, we generated transgenic rice plants (Oryza sativa) that express Arabidopsis thaliana glycine-rich RBP (AtGRP) 2 or 7, which have been determined to harbor RNA chaperone activity and confer stress tolerance in Arabidopsis, and analyzed the response of the transgenic rice plants to abiotic stresses. AtGRP2- or AtGRP7-expressing transgenic rice plants displayed similar phenotypes comparable with the wild-type plants under high salt or cold stress conditions. By contrast, AtGRP2- or AtGRP7-expressing transgenic rice plants showed much higher recovery rates and grain yields compared with the wild-type plants under drought stress conditions. The higher grain yield of the transgenic rice plants was due to the increases in filled grain numbers per panicle. Collectively, the present results show the importance of posttranscriptional regulation of RNA metabolism in plant response to environmental stress and suggest that GRPs can be utilized to improve the yield potential of crops under stress conditions.

  18. 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.

  19. Arsenic tolerances in rice (Oryza sativa) have a predominant role in transcriptional regulation of a set of genes including sulphur assimilation pathway and antioxidant system.

    PubMed

    Rai, Arti; Tripathi, Preeti; Dwivedi, Sanjay; Dubey, Sonali; Shri, Manju; Kumar, Smita; Tripathi, Pankaj Kumar; Dave, Richa; Kumar, Amit; Singh, Ragini; Adhikari, Bijan; Bag, Manas; Tripathi, Rudra Deo; Trivedi, Prabodh K; Chakrabarty, Debasis; Tuli, Rakesh

    2011-02-01

    World wide arsenic (As) contamination of rice has raised much concern as it is the staple crop for millions. Four most commonly cultivated rice cultivars, Triguna, IR-36, PNR-519 and IET-4786, of the West Bengal region were taken for a hydroponic study to examine the effect of arsenate (As(V)) and arsenite (As(III)) on growth response, expression of genes and antioxidants vis-à-vis As accumulation. The rice genotypes responded differentially under As(V) and As(III) stress in terms of gene expression and antioxidant defences. Some of the transporters were up-regulated in all rice cultivars at lower doses of As species, except IET-4786. Phytochelatin synthase, GST and γ-ECS showed considerable variation in their expression pattern in all genotypes, however in IET-4786 they were generally down-regulated in higher As(III) stress. Similarly, most of antioxidants such as superoxide dismutase (SOD), ascorbate peroxidase (APX), guaiacol peroxidase (GPX), catalase (CAT), monodehydroascorbate reductase (MDHAR) and dehydroascorbate reductase (DHAR) increased significantly in Triguna, IR-36 and PNR-519 and decreased in IET-4786. Our study suggests that Triguna, IR-36 and PNR-519 are tolerant rice cultivars accumulating higher arsenic; however IET-4786 is susceptible to As-stress and accumulates less arsenic than other cultivars.

  20. Collection and comparative analysis of 1888 full-length cDNAs from wild rice Oryza rufipogon Griff. W1943.

    PubMed

    Lu, Tingting; Yu, Shuliang; Fan, Danlin; Mu, Jie; Shangguan, Yingying; Wang, Zixuan; Minobe, Yuzo; Lin, Zhixin; Han, Bin

    2008-10-01

    A huge amount of cDNA and EST resources have been developed for cultivated rice species Oryza sativa; however, only few cDNA resources are available for wild rice species. In this study, we isolated and completely sequenced 1888 putative full-length cDNA (FLcDNA) clones from wild rice Oryza rufipogon Griff. W1943 for comparative analysis between wild and cultivated rice species. Two cDNA libraries were constructed from 3-week-old leaf samples under either normal or cold-treated conditions. Homology searching of these cDNA sequences revealed that >96.8% of the wild rice cDNAs were matched to the cultivated rice O. sativa ssp. japonica cv. Nipponbare genome sequence. However, <22% of them were fully matched to the cv. Nipponbare genome sequence. The comparative analysis showed that O. rufipogon W1943 had greater similarity to O. sativa ssp. japonica than to ssp. indica cultivars. In addition, 17 novel rice cDNAs were identified, and 41 putative tissue-specific expression genes were defined through searching the rice massively parallel signature-sequencing database. In conclusion, these FLcDNA clones are a resource for further function verification and could be broadly utilized in rice biological studies.

  1. Evaluation of antioxidant, lipid, and protein fractions of accessions of Oryza Species.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The genus Oryza has given rise to rice (Oryza sativa L.), a major source of food for much of the human population. The Oryza genus is small, including only 23 species, but it is remarkably diverse in terms of its ecological adaptation. This diversity may not only be restricted to ecological characte...

  2. Cuticular Defects in Oryza sativa ATP-binding Cassette Transporter G31 Mutant Plants Cause Dwarfism, Elevated Defense Responses and Pathogen Resistance.

    PubMed

    Garroum, Imène; Bidzinski, Przemyslaw; Daraspe, Jean; Mucciolo, Antonio; Humbel, Bruno M; Morel, Jean-Benoit; Nawrath, Christiane

    2016-06-01

    The cuticle covers the surface of the polysaccharide cell wall of leaf epidermal cells and forms an essential diffusion barrier between plant and environment. Homologs of the ATP-binding cassette (ABC) transporter AtABCG32/HvABCG31 clade are necessary for the formation of a functional cuticle in both monocots and dicots. Here we characterize the osabcg31 knockout mutant and hairpin RNA interference (RNAi)-down-regulated OsABCG31 plant lines having reduced plant growth and a permeable cuticle. The reduced content of cutin in leaves and structural alterations in the cuticle and at the cuticle-cell wall interface in plants compromised in OsABCG31 expression explain the cuticle permeability. Effects of modifications of the cuticle on plant-microbe interactions were evaluated. The cuticular alterations in OsABCG31-compromised plants did not cause deficiencies in germination of the spores or the formation of appressoria of Magnaporthe oryzae on the leaf surface, but a strong reduction of infection structures inside the plant. Genes involved in pathogen resistance were constitutively up-regulated in OsABCG31-compromised plants, thus being a possible cause of the resistance to M. oryzae and the dwarf growth phenotype. The findings show that in rice an abnormal cuticle formation may affect the signaling of plant growth and defense.

  3. Fine mapping of a gene causing hybrid pollen sterility between Yunnan weedy rice and cultivated rice (Oryza sativa L.) and phylogenetic analysis of Yunnan weedy rice.

    PubMed

    Wang, Yong; Zhong, Zheng Zheng; Zhao, Zhi Gang; Jiang, Ling; Bian, Xiao Feng; Zhang, Wen Wei; Liu, Ling Long; Ikehashi, H; Wan, Jian Min

    2010-02-01

    Weedy rice represents an important resource for rice improvement. The F(1) hybrid between the japonica wide compatibility rice cultivar 02428 and a weedy rice accession from Yunnan province (SW China) suffered from pollen sterility. Pollen abortion in the hybrid occurred at the early bicellular pollen stage, as a result of mitotic failure in the microspore, although the tapetum developed normally. Genetic mapping in a BC(1)F(1) population (02428//Yunnan weedy rice (YWR)/02428) showed that a major QTL for hybrid pollen sterility (qPS-1) was present on chromosome 1. qPS-1 was fine-mapped to a 110 kb region known to contain the hybrid pollen sterility gene Sa, making it likely that qPS-1 is either identical to, or allelic with Sa. Interestingly, F(1) hybrid indicated that Dular and IR36 were assumed to carry the sterility-neutral allele, Sa ( n ). Re-sequencing SaM and SaF, the two component genes present at Sa, suggested that variation for IR36 and Dular may be responsible for the loss of male sterility, and the qPS-1 sequence might be derived from wild rice or indica cultivars. A phylogenetic analysis based on microsatellite genotyping suggested that the YWR accession is more closely related to wild rice and indica type cultivars than to japonica types. Thus it is probable that the YWR accession evolved from a spontaneous hybrid between wild rice and an ancient cultivated strain of domesticated rice.

  4. Effects of manganese oxide-modified biochar composites on arsenic speciation and accumulation in an indica rice (Oryza sativa L.) cultivar.

    PubMed

    Yu, Zhihong; Qiu, Weiwen; Wang, Fei; Lei, Ming; Wang, Di; Song, Zhengguo

    2017-02-01

    A pot experiment was used to investigate arsenic (As) speciation and accumulation in rice, as well as its concentration in both heavily contaminated and moderately contaminated soils amended with manganese oxide-modified biochar composites (MBC) and biochar alone (BC). In heavily As-contaminated soil, application of BC and MBC improved the weight of above-ground part and rice root, whereas in moderately As-contaminated soil, the application of MBC and low rate BC amendment increased rice root, grain weight and the biomass of the plant. Arsenic reduction in different parts of rice grown in MBC-amended soils was greater than that in plants cultivated in BC-amended soils. Such reduction can be attributed to the oxidation of arsenite, As(III), to arsenate, As(V), by Mn-oxides, which also had a strong adsorptive capacity for As(V). MBC amended to As-contaminated soil had a positive effect on amino acids. The Fe and Mn levels in the iron-manganese plaque that formed on the rice root surface differed among the treatments. MBC addition significantly increased Mn content (p < 0.05); the application of 2.0% MBC increased Mn content 36- and 10-fold compared to the control in heavily and moderately As-contaminated soils, respectively. The results indicate that application of Mn oxide-modified biochar to As-contaminated paddy soil could effectively remediate contaminated soil and reduce As accumulation in edible parts of rice.

  5. Efficient in vitro plant regeneration through leaf base derived callus cultures of abiotic stress sensitive popular Asian Indica rice cultivar IR 64 (Oryza sativa L.).

    PubMed

    Mohana Priya, A; Karutha Pandian, S; Ramesh, M

    2011-12-01

    A simple and efficient protocol has been developed for high frequency plant regeneration through callus cultures derived from leaf bases of abiotic stress sensitive Asian indica rice variety IR 64. Leaf base segments (4-5 mm diameter) were obtained from 6-day-old dark grown seedlings germinated on halfstrength Murashige and Skoog medium and cultured on MS medium supplemented with different concentrations of 2,4-Dichlorophenoxyacetic acid (2.2-18 μM) and Kinetin (0.2-1.7 μM). Among the various combinations, 13.5 μM 2,4-D and 1.3 μM Kn resulted in high callus induction frequency (87.5%) with a maximum fresh weight of 0.22 g per segment. The regeneration frequency was 75.5% with multiple shoots within 3 weeks of transfer on MS medium supplemented with 13.3 μM 6-benzylamino purine and 8 μM Naphthaleneacetic acid. The shoots readily rooted on half-strength MS medium without any hormonal supplements. In vitro regenerated plantlets with multiple shoots and roots were transferred to sterile soil and vermiculite mix and maintained in shade house for 30 days. Complete plantlets were then transferred to nursery and acclimatized to the external environment until seed set. RAPD profile reveals monomorphism and thus confirming the genetic stability of the regenerated plants. This method has the potential for both direct as well as indirect method of transformation for the production of genetically modified plants.

  6. Molecular characterization and functional analysis by heterologous expression in E. coli under diverse abiotic stresses for OsLEA5, the atypical hydrophobic LEA protein from Oryza sativa L.

    PubMed

    He, Shuai; Tan, Lili; Hu, Zongli; Chen, Guoping; Wang, Guixue; Hu, Tingzhang

    2012-01-01

    In this study, we report the molecular characterization and functional analysis of OsLEA5 gene, which belongs to the atypical late embryogenesis abundant (LEA) group 5C from Oryza sativa L. The cDNA of OsLEA5 contains a 456 bp ORF encoding a polypeptide of 151 amino acids with a calculated molecular mass of 16.5 kDa and a theoretical pI of 5.07. The OsLEA5 polypeptide is rich in Leu (10%), Ser (8.6%), and Asp (8.6%), while Cys, Trp, and Gln residue contents are very low, which are 2, 1.3, and 1.3%, respectively. Bioinformatic analysis revealed that group 5C LEA protein subfamily contains a Pfam:LEA_2 domain architecture and is highly hydrophobic, intrinsically ordered with largely β-sheet and specific amino acid composition and distribution. Real-time PCR analysis showed that OsLEA5 was expressed in different tissue organs during different development stages of rice. The expression levels of OsLEA5 in the roots and panicles of full ripe stage were dramatically increased. The results of stress tolerance and cell viability assay demonstrated that recombinant E. coli cells producing OsLEA5 fusion protein exhibited improved resistance against diverse abiotic stresses: high salinity, osmotic, freezing, heat, and UV radiation. The OsLEA5 protein confers stabilization of the LDH under different abiotic stresses, such as heating, freeze-thawing, and drying in vitro. The combined results indicated that OsLEA5 protein was a hydrophobic atypical LEA and closely associated with resistance to multiple abiotic stresses. This research offered the valuable information for the development of crops with enhanced resistance to diverse stresses.

  7. Short-chain chlorinated paraffins in soil, paddy seeds (Oryza sativa) and snails (Ampullariidae) in an e-waste dismantling area in China: Homologue group pattern, spatial distribution and risk assessment.

    PubMed

    Yuan, Bo; Fu, Jianjie; Wang, Yawei; Jiang, Guibin

    2017-01-01

    Short-chain chlorinated paraffins (SCCPs) in multi-environmental matrices are studied in Taizhou, Zhejiang Province, China, which is a notorious e-waste dismantling area. The investigated matrices consist of paddy field soil, paddy seeds (Oryza sativa, separated into hulls and rice unpolished) and apple snails (Ampullariidae, inhabiting the paddy fields). The sampling area covered a 65-km radius around the contamination center. C10 and C11 are the two predominant homologue groups in the area, accounting for about 35.7% and 33.0% of total SCCPs, respectively. SCCPs in snails and hulls are generally higher than in soil samples (30.4-530 ng/g dw), and SCCPs in hulls are approximate five times higher than in corresponding rice samples (4.90-55.1 ng/g dw). Homologue pattern analysis indicates that paddy seeds (both hull and rice) tend to accumulate relatively high volatile SCCP homologues, especially the ones with shorter carbon chain length, while snails tend to accumulate relatively high lipophilic homologues, especially the ones with more substituted chlorines. SCCPs in both paddy seeds and snails are linearly related to those in the soil. The e-waste dismantling area, which covers a radius of approximate 20 km, shows higher pollution levels for SCCPs according to their spatial distribution in four matrices. The preliminary assessment indicates that SCCP levels in local soils pose no significant ecological risk for soil dwelling organisms, but higher risks from dietary exposure of SCCPs are suspected for people living in e-waste dismantling area.

  8. Overexpression of a partial fragment of the salt-responsive gene OsNUC1 enhances salt adaptation in transgenic Arabidopsis thaliana and rice (Oryza sativa L.) during salt stress.

    PubMed

    Sripinyowanich, Siriporn; Chamnanmanoontham, Nontalee; Udomchalothorn, Thanikarn; Maneeprasopsuk, Somporn; Santawee, Panudda; Buaboocha, Teerapong; Qu, Li-Jia; Gu, Hongya; Chadchawan, Supachitra

    2013-12-01

    The rice (Oryza sativa L.) nucleolin gene, OsNUC1, transcripts were expressed in rice leaves, flowers, seeds and roots but differentially expressed within and between two pairs of salt-sensitive and salt-resistant rice lines when subjected to salt stress. Salt-resistant lines exhibited higher OsNUC1 transcript expression levels than salt-sensitive lines during 0.5% (w/v) NaCl salt stress for 6d. Two sizes of OsNUC1 full-length cDNA were found in the rice genome database and northern blot analysis confirmed their existence in rice tissues. The longer transcript (OsNUC1-L) putatively encodes for a protein with a serine rich N-terminal, RNA recognition motifs in the central domain and a glycine- and arginine-rich repeat in the C-terminal domain, while the shorter one (OsNUC1-S) putatively encodes for the similar protein without the N-terminus. Without salt stress, OsNUC1-L expressing Arabidopsis thaliana Atnuc1-L1 plants displayed a substantial but incomplete revertant phenotype, whereas OsNUC1-S expression only induced a weak effect. However, under 0.5% (w/v) NaCl salt stress they displayed a higher relative growth rate, longer root length and a lower H2O2 level than the wild type plants, suggesting a higher salt resistance. Moreover, they displayed elevated AtSOS1 and AtP5CS1 transcript levels. We propose that OsNUC1-S plays an important role in salt resistance during salt stress, a new role for nucleolin in plants.

  9. CaPUB1, a Hot Pepper U-box E3 Ubiquitin Ligase, Confers Enhanced Cold Stress Tolerance and Decreased Drought Stress Tolerance in Transgenic Rice (Oryza sativa L.).

    PubMed

    Min, Hye Jo; Jung, Ye Jin; Kang, Bin Goo; Kim, Woo Taek

    2016-03-01

    Abiotic stresses such as drought and low temperature critically restrict plant growth, reproduction, and productivity. Higher plants have developed various defense strategies against these unfavorable conditions. CaPUB1 (Capsicum annuum Putative U-box protein 1) is a hot pepper U-box E3 Ub ligase. Transgenic Arabidopsis plants that constitutively expressed CaPUB1 exhibited drought-sensitive phenotypes, suggesting that it functions as a negative regulator of the drought stress response. In this study, CaPUB1 was over-expressed in rice (Oryza sativa L.), and the phenotypic properties of transgenic rice plants were examined in terms of their drought and cold stress tolerance. Ubi:CaPUB1 T3 transgenic rice plants displayed phenotypes hypersensitive to dehydration, suggesting that its role in the negative regulation of drought stress response is conserved in dicot Arabidopsis and monocot rice plants. In contrast, Ubi:CaPUB1 progeny exhibited phenotypes markedly tolerant to prolonged low temperature (4°C) treatment, compared to those of wild-type plants, as determined by survival rates, electrolyte leakage, and total chlorophyll content. Cold stress-induced marker genes, including DREB1A, DREB1B, DREB1C, and Cytochrome P450, were more up-regulated by cold treatment in Ubi:CaPUB1 plants than in wild-type plants. These results suggest that CaPUB1 serves as both a negative regulator of the drought stress response and a positive regulator of the cold stress response in transgenic rice plants. This raises the possibility that CaPUB1 participates in the cross-talk between drought and low-temperature signaling pathways.

  10. Distinctive expression patterns and roles of the miRNA393/TIR1 homolog module in regulating flag leaf inclination and primary and crown root growth in rice (Oryza sativa).

    PubMed

    Bian, Hongwu; Xie, Yakun; Guo, Fu; Han, Ning; Ma, Shengyun; Zeng, Zhanghui; Wang, Junhui; Yang, Yinong; Zhu, Muyuan

    2012-10-01

    • MicroRNA (miRNA)-mediated regulation of auxin signaling components plays a critical role in plant development. miRNA expression and functional diversity contribute to the complexity of regulatory networks of miRNA/target modules. • This study functionally characterizes two members of the rice (Oryza sativa) miR393 family and their target genes, OsTIR1 and OsAFB2 (AUXIN SIGNALING F-BOX), the two closest homologs of Arabidopsis TRANSPORT INHIBITOR RESPONSE 1 (TIR1). • We found that the miR393 family members possess distinctive expression patterns, with miR393a expressed mainly in the crown and lateral root primordia, as well as the coleoptile tip, and miR393b expressed in the shoot apical meristem. Transgenic plants overexpressing miR393a/b displayed a severe phenotype with hallmarks of altered auxin signaling, mainly including enlarged flag leaf inclination and altered primary and crown root growth. Furthermore, OsAFB2- and OsTIR1-suppressed lines exhibited increased inclination of flag leaves at the booting stage, resembling miR393-overexpressing plants. Moreover, yeast two-hybrid and bimolecular fluorescence complementation assays showed that OsTIR1 and OsAFB2 interact with OsIAA1. • Expression diversification of miRNA393 implies the potential role of miRNA regulation during species evolution. The conserved mechanisms of the miR393/target module indicate the fundamental importance of the miR393-mediated regulation of auxin signal transduction in rice.

  11. RNAi-directed downregulation of betaine aldehyde dehydrogenase 1 (OsBADH1) results in decreased stress tolerance and increased oxidative markers without affecting glycine betaine biosynthesis in rice (Oryza sativa).

    PubMed

    Tang, Wei; Sun, Jiaqi; Liu, Jia; Liu, Fangfang; Yan, Jun; Gou, Xiaojun; Lu, Bao-Rong; Liu, Yongsheng

    2014-11-01

    As an important osmoprotectant, glycine betaine (GB) plays an essential role in resistance to abiotic stress in a variety of organisms, including rice (Oryza sativa L.). However, GB content is too low to be detectable in rice, although rice genome possesses several orthologs coding for betaine aldehyde dehydrogenase (BADH) involved in plant GB biosynthesis. Rice BADH1 (OsBADH1) has been shown to be targeted to peroxisome and its overexpression resulted in increased GB biosynthesis and tolerance to abiotic stress. In this study, we demonstrated a pivotal role of OsBADH1 in stress tolerance without altering GB biosynthesis capacity, using the RNA interference (RNAi) technique. OsBADH1 was ubiquitously expressed in different organs, including roots, stems, leaves and flowers. Transgenic rice lines downregulating OsBADH1 exhibited remarkably reduced tolerance to NaCl, drought and cold stresses. The decrease of stress tolerance occurring in the OsBADH1-RNAi repression lines was associated with an elevated level of malondialdehyde content and hydrogen peroxidation. No GB accumulation was detected in transgene-positive and transgene-negative lines derived from heterozygous transgenic T0 plants. Moreover, transgenic OsBADH1-RNAi repression lines showed significantly reduced seed set and yield. In conclusion, the downregulation of OsBADH1, even though not causing any change of GB content, was accounted for the reduction of ability to dehydrogenate the accumulating metabolism-derived aldehydes and subsequently resulted in decreased stress tolerance and crop productivity. These results suggest that OsBADH1 possesses an enzyme activity to catalyze other aldehydes in addition to betaine aldehyde (the precursor of GB) and thus alleviate their toxic effects under abiotic stresses.

  12. A High Temperature-Dependent Mitochondrial Lipase EXTRA GLUME1 Promotes Floral Phenotypic Robustness against Temperature Fluctuation in Rice (Oryza sativa L.)

    PubMed Central

    Zhang, Yu’e; Xu, Ting; Guo, Feifei; Tang, Huashan; Li, Xiang; Wang, Pengfei; Qian, Wenfeng; Xue, Yongbiao

    2016-01-01

    The sessile plants have evolved diverse intrinsic mechanisms to control their proper development under variable environments. In contrast to plastic vegetative development, reproductive traits like floral identity often show phenotypic robustness against environmental variations. However, it remains obscure about the molecular basis of this phenotypic robustness. In this study, we found that eg1 (extra glume1) mutants of rice (Oryza savita L.) showed floral phenotypic variations in different growth locations resulting in a breakdown of floral identity robustness. Physiological and biochemical analyses showed that EG1 encodes a predominantly mitochondria-localized functional lipase and functions in a high temperature-dependent manner. Furthermore, we found that numerous environmentally responsive genes including many floral identity genes are transcriptionally repressed in eg1 mutants and OsMADS1, OsMADS6 and OsG1 genetically act downstream of EG1 to maintain floral robustness. Collectively, our results demonstrate that EG1 promotes floral robustness against temperature fluctuation by safeguarding the expression of floral identify genes through a high temperature-dependent mitochondrial lipid pathway and uncovers a novel mechanistic insight into floral developmental control. PMID:27367609

  13. Mapping QTLs for Fertility Restoration of Different Cytoplasmic Male Sterility Types in Rice Using Two Oryza sativa ×O. rufipogon Backcross Inbred Line Populations.

    PubMed

    Hu, Biao-Lin; Xie, Jian-Kun; Wan, Yong; Zhang, Jin-Wei; Zhang, Fan-Tao; Li, Xia

    2016-01-01

    Hybrid rice breeding using cytoplasmic male sterility/fertility restoration (CMS/Rf) systems plays an important role in ensuring global food security. Two backcross inbred line (BIL) populations derived from either Xieqingzao B (XB)//XB/Dongxiang wild rice (DWR) (XXD) or XB//DWR/XB (XDX) were used to detect quantitative trait loci (QTLs) for fertility restoration of Dwarf wild abortive- (DA-), Indonesia Paddy- (ID-), and DWR-type CMS in rice. Lines with ID- and DA-type CMS were testcrossed with both the XXD- and XDX-BILs, while the line with DWR-type CMS was testcrossed with the XDX-BILs only. A total of 16 QTLs for fertility restoration of CMS systems were identified, including three for DWR-type CMS, six for DA-type CMS, and seven for ID-type CMS. All of the additive alleles in the QTLs were derived from Oryza rufipogon. Eleven QTLs were clustered in five chromosomal regions, indicating that common Rf loci restored different CMS systems, and the favorable O. rufipogon alleles could be used to develop restorer lines for various CMS types by marker-assisted selection.

  14. Mapping QTLs for Fertility Restoration of Different Cytoplasmic Male Sterility Types in Rice Using Two Oryza sativa ×O. rufipogon Backcross Inbred Line Populations

    PubMed Central

    Hu, Biao-lin; Wan, Yong; Zhang, Jin-wei; Zhang, Fan-tao; Li, Xia

    2016-01-01

    Hybrid rice breeding using cytoplasmic male sterility/fertility restoration (CMS/Rf) systems plays an important role in ensuring global food security. Two backcross inbred line (BIL) populations derived from either Xieqingzao B (XB)//XB/Dongxiang wild rice (DWR) (XXD) or XB//DWR/XB (XDX) were used to detect quantitative trait loci (QTLs) for fertility restoration of Dwarf wild abortive- (DA-), Indonesia Paddy- (ID-), and DWR-type CMS in rice. Lines with ID- and DA-type CMS were testcrossed with both the XXD- and XDX-BILs, while the line with DWR-type CMS was testcrossed with the XDX-BILs only. A total of 16 QTLs for fertility restoration of CMS systems were identified, including three for DWR-type CMS, six for DA-type CMS, and seven for ID-type CMS. All of the additive alleles in the QTLs were derived from Oryza rufipogon. Eleven QTLs were clustered in five chromosomal regions, indicating that common Rf loci restored different CMS systems, and the favorable O. rufipogon alleles could be used to develop restorer lines for various CMS types by marker-assisted selection. PMID:27872859

  15. Development of chromosome segment substitution lines harboring Oryza nivara genomic segments in Koshihikari and evaluation of yield-related traits

    PubMed Central

    Furuta, Tomoyuki; Uehara, Kanako; Angeles-Shim, Rosalyn B.; Shim, Junghyun; Nagai, Keisuke; Ashikari, Motoyuki; Takashi, Tomonori

    2016-01-01

    Chromosome segment substitution lines (CSSLs) are rich genetic resources that can be mined for novel, agriculturally useful loci or that can be used directly as materials for breeding. To date, a number of rice CSSLs have been developed by crossing rice cultivars with its wild relatives as a means to tap into the potential of wild alleles in rice improvement. Oryza nivara is a wild relative of rice that is thought to be a progenitor of O. sativa spp. indica. In the present study, 26 CSSLs that covers the entire genome of O. nivara as contiguous, overlapping segments in the genomic background of a japonica cultivar, O. sativa cv. Koshihikari were developed. Evaluation of the CSSLs for several agriculturally important traits identified candidate chromosome segments that harbors QTLs associated with yield and yield-related traits. The results of the study revealed the potential of O. nivara as a source of novel alleles that can be used to improve the existing japonica cultivar. PMID:28163601

  16. Quantitative trait loci identification, fine mapping and gene expression profiling for ovicidal response to whitebacked planthopper (Sogatella furcifera Horvath) in rice (Oryza sativa L.)

    PubMed Central

    2014-01-01

    Background The whitebacked planthopper (WBPH), Sogatella furcifera Horváth, is a serious rice pest in Asia. Ovicidal resistance is a natural rice defense mechanism against WBPH and is characterized by the formation of watery lesions (WLs) and increased egg mortality (EM) at the WBPH oviposition sites. Results This study aimed to understand the genetic and molecular basis of rice ovicidal resistance to WBPH by combining genetic and genomic analyses. First, the ovicidal trait in doubled haploid rice lines derived from a WBPH-resistant cultivar (CJ06) and a WBPH-susceptible cultivar (TN1) were phenotyped based on the necrotic symptoms of the leaf sheaths and EM. Using a constructed molecular linkage map, 19 quantitative trait loci (QTLs) associated with WLs and EM were identified on eight chromosomes. Of them, qWL6 was determined to be a major QTL for WL. Based on chromosome segment substitution lines and a residual heterozygous population, a high-resolution linkage analysis further defined the qWL6 locus to a 122-kb region on chromosome 6, which was annotated to encode 20 candidate genes. We then conducted an Affymetrix microarray analysis to determine the transcript abundance in the CJ06 and TN1 plants. Upon WBPH infestation, 432 genes in CJ06 and 257 genes in TN1 were significantly up-regulated, while 802 genes in CJ06 and 398 genes in TN1 were significantly down-regulated. This suggests that remarkable global changes in gene expression contribute to the ovicidal resistance of rice. Notably, four genes in the 122-kb region of the qWL6 locus were differentially regulated between CJ06 and TN1 in response to the WBPH infestation, suggesting they may be candidate resistance genes. Conclusions The information obtained from the fine mapping of qWL6 and the microarray analyses will facilitate the isolation of this important resistance gene and its use in breeding WBPH-resistant rice. PMID:24886295

  17. Marker Aided Incorporation of Saltol, a Major QTL Associated with Seedling Stage Salt Tolerance, into Oryza sativa ‘Pusa Basmati 1121’

    PubMed Central

    Babu, N. Naresh; Krishnan, S. Gopala; Vinod, K. K.; Krishnamurthy, S. L.; Singh, Vivek K.; Singh, Madan P.; Singh, Renu; Ellur, Ranjith K.; Rai, Vandna; Bollinedi, Haritha; Bhowmick, Prolay K.; Yadav, Ashutosh K.; Nagarajan, Mariappan; Singh, Nagendra K.; Prabhu, Kumble V.; Singh, Ashok K.

    2017-01-01

    Pusa Basmati 1121 (PB1121), an elite Basmati rice cultivar is vulnerable to salinity at seedling stage. A study was undertaken to impart seedling-stage salt tolerance into PB1121 by transferring a quantitative trait locus (QTL), Saltol, using FL478 as donor, through marker assisted backcrossing. Sequence tagged microsatellite site (STMS) marker RM 3412, tightly linked to Saltol was used for foreground selection. Background recovery was estimated using 90 genome-wide STMS markers. Systematic phenotypic selection helped in accelerated recovery of recurrent parent phenome (RPP). A set of 51 BC3F2 lines homozygous for Saltol were advanced to develop four improved near isogenic lines (NILs) of PB1121 with seedling stage salt tolerance. The background genome recovery in the NILs ranged from 93.3 to 99.4%. The improved NILs were either similar or better than the recurrent parent PB1121 for yield, grain and cooking quality and duration. Biochemical analyses revealed significant variation in shoot and root Na+ and K+ concentrations. Correlation between shoot and root Na+ concentration was stronger than that between root and shoot K+ concentration. The effect of QTL integration into the NILs was studied through expression profiling of OsHKT1;5, one of the genes present in the Saltol region. The NILs had significantly higher OsHKT1;5 expression than the recurrent parent PB1121, but lower than FL478 on salt exposure validating the successful introgression of Saltol in the NILs. This was also confirmed under agronomic evaluation, wherein the NILs showed greater salt tolerance at seedling stage. One of the NILs, Pusa1734-8-3-3 (NIL3) showed comparable yield and cooking quality to the recurrent parent PB1121, with high field level seedling stage salinity tolerance and shorter duration. This is the first report of successful introgression of Saltol into a Basmati rice cultivar. PMID:28184228

  18. 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.

  19. A putative gene sbe3-rs for resistant starch mutated from SBE3 for starch branching enzyme in rice (Oryza sativa L.).

    PubMed

    Yang, Ruifang; Sun, Chunlong; Bai, Jianjiang; Luo, Zhixiang; Shi, Biao; Zhang, Jianming; Yan, Wengui; Piao, Zhongze

    2012-01-01

    Foods high in resistant starch (RS) are beneficial to prevent various diseases including diabetes, colon cancers, diarrhea and chronic renal or hepatic diseases. Elevated RS in rice is important for public health since rice is a staple food for half of the world population. A japonica mutant 'Jiangtangdao 1' (RS = 11.67%) was crossed with an indica cultivar 'Miyang 23' (RS = 0.41%). The mutant sbe3-rs that explained 60.4% of RS variation was mapped between RM6611 and RM13366 on chromosome 2 (LOD = 36) using 178 F(2) plants genotyped with 106 genome-wide polymorphic SSR markers. Using 656 plants from four F(3:4) families, sbe3-rs was fine mapped to a 573.3 Kb region between InDel 2 and InDel 6 using one STS, five SSRs and seven InDel markers. SBE3 which codes for starch branching enzyme was identified as a candidate gene within the putative region. Nine pairs of primers covering 22 exons were designed to sequence genomic DNA of the wild type for SBE3 and the mutant for sbe3-rs comparatively. Sequence analysis identified a missense mutation site where Leu-599 of the wild was changed to Pro-599 of the mutant in the SBE3 coding region. Because the point mutation resulted in the loss of a restriction enzyme site, sbe3-rs was not digested by a CAPS marker for SpeI site while SBE3 was. Co-segregation of the digestion pattern with RS content among 178 F(2) plants further supported sbe3-rs responsible for RS in rice. As a result, the CAPS marker could be used in marker-assisted breeding to develop rice cultivars with elevated RS which is otherwise difficult to accurately assess in crops. Transgenic technology should be employed for a definitive conclusion of the sbe3-rs.

  20. Root transcriptome of two contrasting indica rice cultivars uncovers regulators of root development and physiological responses

    PubMed Central

    Singh, Alka; Kumar, Pramod; Gautam, Vibhav; Rengasamy, Balakrishnan; Adhikari, Bijan; Udayakumar, Makarla; Sarkar, Ananda K.

    2016-01-01

    The huge variation in root system architecture (RSA) among different rice (Oryza sativa) cultivars is conferred by their genetic makeup and different growth or climatic conditions. Unlike model plant Arabidopsis, the molecular basis of such variation in RSA is very poorly understood in rice. Cultivars with stable variation are valuable resources for identification of genes involved in RSA and related physiological traits. We have screened for RSA and identified two such indica rice cultivars, IR-64 (OsAS83) and IET-16348 (OsAS84), with stable contrasting RSA. OsAS84 produces robust RSA with more crown roots, lateral roots and root hairs than OsAS83. Using comparative root transcriptome analysis of these cultivars, we identified genes related to root development and different physiological responses like abiotic stress responses, hormone signaling, and nutrient acquisition or transport. The two cultivars differ in their response to salinity/dehydration stresses, phosphate/nitrogen deficiency, and different phytohormones. Differential expression of genes involved in salinity or dehydration response, nitrogen (N) transport, phosphate (Pi) starvation signaling, hormone signaling and root development underlies more resistance of OsAS84 towards abiotic stresses, Pi or N deficiency and its robust RSA. Thus our study uncovers gene-network involved in root development and abiotic stress responses in rice. PMID:28000793

  1. Oviposition behavior of Diatraea saccharalis (Lepidoptera: Crambidae) on different rice cultivars in Louisiana.

    PubMed

    Hamm, Jason C; Sidhu, Jaspreet K; Stout, Michael J; Hummel, Natalie A; Reagan, Thomas E

    2012-06-01

    The sugarcane borer, Diatraea saccharalis (F.), is a pest of a variety of graminaceous crops in the southern United States, including sugarcane, maize, and rice in Louisiana. This study examined several aspects of D. saccharalis oviposition behavior on rice (Oryza sativa). The vertical distribution of egg masses on four phenological stages of rice in the field showed that D. saccharalis prefers to oviposit on the uppermost portions of rice plants, regardless of plant stage. In greenhouse choice experiments, females strongly preferred plants at the boot and panicle differentiation stages over plants at the tillering stage for oviposition. Greenhouse studies were also conducted to quantify the oviposition preference of D. saccharalis for different cultivars of. When plants were at the tillering stage, cultivars Cocodrie, Priscilla, Bengal, Cheniere, and CL161 were more preferred than cultivars Jupiter, XL723, and XP744. When plants reached the panicle initiation stage, cultivars Cocodrie, CL161, and Priscilla were more preferred than Bengal, Cheniere, Jupiter, XL723, and XP744. Females also oviposited significantly more egg masses on the adaxial surfaces of rice leaves than on the abaxial surfaces. These results will facilitate scouting and management of sugarcane borer and can be used as a foundation for the development of sugarcane borer resistant cultivars.

  2. Effects on growth and oxidative stress status of rice plants (Oryza sativa) exposed to two extracts of toxin-producing cyanobacteria (Aphanizomenon ovalisporum and Microcystis aeruginosa).

    PubMed

    Prieto, Ana; Campos, Alexandre; Cameán, Ana; Vasconcelos, Vitor

    2011-10-01

    Toxic cyanobacteria are considered emerging world threats, being responsible for the degradation of the aquatic ecosystems. Aphanizomenon ovalisporum produces the toxin Cylindrospermopsin (CYN) being a concern in fresh water habitats. This work aims to increase our knowledge on the effects of this toxic cyanobacterium in plants by studying the alterations in growth parameters and oxidative stress status of rice (Oriza sativa) exposed to the cyanobacteria cell extracts containing CYN. Significant increases in glutathione S-transferase (GST) and glutathione peroxidase (GPx) activities were detected in the different experiments performed. The roots showed to be more sensitive than leaves regarding the enzyme activities. A reduction in the leaf tissue fresh weight was observed after 9 days of plant treatment suggesting a major physiological stress. The exposure of rice plants to a mixture of A. ovalisporum and Microcystis aeruginosa cell extracts containing CYN and microcystins including microcystin-LR, resulted in a significant increase in the GST and GPx activities, suggesting a synergistic effect of both extracts. Together these results point out the negative effects of cyanotoxins on plant growth and oxidative status, induced by A. ovalisporum cell extracts, raising also concerns in the accumulation of CYN.

  3. CPPU elevates photosynthetic abilities, growth performances and yield traits in salt stressed rice (Oryza sativa L. spp. indica) via free proline and sugar accumulation.

    PubMed

    Gashaw, Arega; Theerawitaya, Cattarin; Samphumphuang, Thapanee; Cha-um, Suriyan; Supaibulwatana, Kanyaratt

    2014-01-01

    Application of N-2-(chloro-4-pyridyl)-N-phenyl urea (CPPU) to salt susceptible cultivar of indica rice (cv. PTT1) effected on free proline and soluble sugar accumulation and regulated the physio-morphological responses when subjected to salt stress condition was firstly demonstrated in this study. Soluble sugars, including sucrose, glucose and fructose, in leaf blade and leaf sheath were enriched in 0.1 mM CPPU pretreated plants subsequently exposed to 16.6 dS m(-1) NaCl for 10 days. In the long period (15 days) salt stress, free proline content in the leaf blade and leaf sheath were evidently peaked to act as osmotic adjustment in the salt-stressed plants. In addition, the photosynthetic pigments, including chlorophyll a, chlorophyll b, total chlorophyll and total carotenoids, were maintained by the functional regulation of soluble sugar and free proline in the cellular levels, thereby leading to higher net photosynthetic rate. Further, the stomatal closure and transpiration rate in CPPU pretreated plants were retained under salt stress, thereby resulting in alleviation of growth performance and yield traits. This study suggested that exogenous application of CPPU may alternatively play effective role to improve the salt tolerant abilities of salt susceptible rice crop.

  4. Identification of neutral genes at pollen sterility loci Sd and Se of cultivated rice (Oryza sativa) with wild rice (O. rufipogon) origin.

    PubMed

    Liu, B; Li, J Q; Liu, X D; Shahid, M Q; Shi, L G; Lu, Y G

    2011-10-31

    Pollen sterility is one of the main hindrances against the utilization of strong intersubspecific (indica-japonica) heterosis in rice. We looked for neutral alleles at known pollen sterility loci Sd and Se that could overcome this pollen sterility characteristic. Taichung 65, a typical japonica cultivar, and its near isogenic lines E7 and E8 for pollen sterility loci Sd and Se were employed as tester lines for crossing with 13 accessions of wild rice (O. rufipogon). Pollen fertility and genotypic segregations of the molecular markers tightly linked with Sd and Se loci were analyzed in the paired F(1)s and F(2) populations. One accession of wild rice (GZW054) had high pollen fertility in the paired F(1)s between Taichung 65 and E7 or E8. Genotypic segregations of the molecular markers tightly linked with Sd and Se loci fit the expected Mendelian ratio (1:2:1), and non-significances were shown among the mean pollen fertilities with the maternal, parental, and heterozygous genotypes of each molecular markers tightly linked with Sd and Se loci. Evidentially, it indicated that the alleles of Sd and Se loci for GZW054 did not interact with those of Taichung 65 and its near isogenic lines, and, thus were identified as neutral alleles Sd(n) and Se(n). These neutral genes could become important germplasm resources for overcoming pollen sterility in indica-japonica hybrids, making utilization of strong heterosis in such hybrids viable.

  5. Variation of the light stable isotopes in the superior and inferior grains of rice (Oryza sativa L.) with different geographical origins.

    PubMed

    Chen, Tianjin; Zhao, Yan; Zhang, Weixing; Yang, Shuming; Ye, Zhihua; Zhang, Guoyou

    2016-10-15

    Trying to explore a new research angle to increase the resolution and accessibility of isotopic based traceability technique, light stable isotopes (δ(13)C, δ(15)N, δD and δ(18)O) in the superior (SS) and inferior (IS) grains of a rice cultivar Daohuaxiang were analyzed with relatively limited sample numbers and adjacent sites in Fujin and Wuchang, Heilongjiang Province, PR China. Distribution of δ(13)C, δ(15)N and δ(18)O in the SS and IS grains were found to be different. δ(18)O and δD can discriminate rice cultivation areas. However, δ(13)C and δ(15)N values in Fujin and Wuchang overlapped when the differences between SS and IS were considered, thus δ(13)C and δ(15)N cannot be used to discriminate cultivation areas. This exploratory study indicate the variation of the light stable isotopes in the grains located on different panicle positions could be used to discriminate the geographical origin but still need further systematic consideration and verification.

  6. Whole-Plant Dynamic System of Nitrogen Use for Vegetative Growth and Grain Filling in Rice Plants (Oryza sativa L.) as Revealed through the Production of 350 Grains from a Germinated Seed Over 150 Days: A Review and Synthesis.

    PubMed

    Yoneyama, Tadakatsu; Tanno, Fumio; Tatsumi, Jiro; Mae, Tadahiko

    2016-01-01

    A single germinated rice (Oryza sativa L) seed can produce 350 grains with the sequential development of 15 leaves on the main stem and 7-10 leaves on four productive tillers (forming five panicles in total), using nitrogen (N) taken up from the environment over a 150-day growing season. Nitrogen travels from uptake sites to the grain through growing organ-directed cycling among sequentially developed organs. Over the past 40 years, the dynamic system for N allocation during vegetative growth and grain filling has been elucidated through studies on N and (15)N transport as well as enzymes and transporters involved. In this review, we synthesize the information obtained in these studies along the following main points: (1) During vegetative growth before grain-filling, about half of the total N in the growing organs, including young leaves, tillers, root tips and differentiating panicles is supplied via phloem from mature source organs such as leaves and roots, after turnover and remobilization of proteins, whereas the other half is newly taken up and supplied via xylem, with an efficient xylem-to-phloem transfer at stem nodes. Thus, the growth of new organs depends equally on both N sources. (2) A large fraction (as much as 80%) of the grain N is derived largely from mature organs such as leaves and stems by degradation, including the autophagy pathway of chloroplast proteins (e.g., Rubisco). (3) Mobilized proteinogenic amino acids (AA), including arginine, lysine, proline and valine, are derived mainly from protein degradation, with AA transporters playing a role in transferring these AAs across cell membranes of source and sink organs, and enabling their efficient reutilization in the latter. On the other hand, AAs such as glutamine, glutamic acid, γ-amino butyric acid, aspartic acid, and alanine are produced by assimilation of newly taken up N by roots and and transported via xylem and phloem. The formation of 350 filled grains over 50 days during the

  7. Whole-Plant Dynamic System of Nitrogen Use for Vegetative Growth and Grain Filling in Rice Plants (Oryza sativa L.) as Revealed through the Production of 350 Grains from a Germinated Seed Over 150 Days: A Review and Synthesis

    PubMed Central

    Yoneyama, Tadakatsu; Tanno, Fumio; Tatsumi, Jiro; Mae, Tadahiko

    2016-01-01

    A single germinated rice (Oryza sativa L) seed can produce 350 grains with the sequential development of 15 leaves on the main stem and 7–10 leaves on four productive tillers (forming five panicles in total), using nitrogen (N) taken up from the environment over a 150-day growing season. Nitrogen travels from uptake sites to the grain through growing organ-directed cycling among sequentially developed organs. Over the past 40 years, the dynamic system for N allocation during vegetative growth and grain filling has been elucidated through studies on N and 15N transport as well as enzymes and transporters involved. In this review, we synthesize the information obtained in these studies along the following main points: (1) During vegetative growth before grain-filling, about half of the total N in the growing organs, including young leaves, tillers, root tips and differentiating panicles is supplied via phloem from mature source organs such as leaves and roots, after turnover and remobilization of proteins, whereas the other half is newly taken up and supplied via xylem, with an efficient xylem-to-phloem transfer at stem nodes. Thus, the growth of new organs depends equally on both N sources. (2) A large fraction (as much as 80%) of the grain N is derived largely from mature organs such as leaves and stems by degradation, including the autophagy pathway of chloroplast proteins (e.g., Rubisco). (3) Mobilized proteinogenic amino acids (AA), including arginine, lysine, proline and valine, are derived mainly from protein degradation, with AA transporters playing a role in transferring these AAs across cell membranes of source and sink organs, and enabling their efficient reutilization in the latter. On the other hand, AAs such as glutamine, glutamic acid, γ-amino butyric acid, aspartic acid, and alanine are produced by assimilation of newly taken up N by roots and and transported via xylem and phloem. The formation of 350 filled grains over 50 days during the

  8. Oryza sativa (Rice) Hull Extract Inhibits Lipopolysaccharide-Induced Inflammatory Response in RAW264.7 Macrophages by Suppressing Extracellular Signal-regulated Kinase, c-Jun N-terminal Kinase, and Nuclear Factor-κB Activation

    PubMed Central

    Ha, Sang Keun; Sung, Jeehye; Choi, Inwook; Kim, Yoonsook

    2016-01-01

    Background: Rice (Oryza sativa) is a major cereal crop in many Asian countries and an important staple food source. Rice hulls have been reported to possess antioxidant activities. Materials and Methods: In this study, we evaluated the antiinflammatory effects of rice hull extract and associated signal transduction mechanisms in lipopolysaccharide (LPS)-stimulated RAW 264.7 macrophages. Results: We found that rice hull extract inhibited nitric oxide (NO) and prostaglandin E2 by suppressing the expression of inducible NO synthase and cyclooxygenase-2, respectively. The release of interleukin-1β and tumor necrosis factor-α was also reduced in a dose-dependent manner. Furthermore, rice hull extract attenuated the activation of nuclear factor-kappa B (NF-κB), as well as the phosphorylation of mitogen-activated protein kinases, extracellular signal-regulated kinase (ERK), and c-Jun N-terminal kinase (JNK), in LPS-stimulated RAW264.7 cells. Conclusion: This suggests that rice hull extract decreases the production of inflammatory mediators by downregulating ERK and JNK and the NF-κB signal pathway in RAW 264.7 cells. SUMMARY Rice hull extract inhibits the lipopolysaccharide-induced inflammatory response in RAW264.7 macrophages.Rice hull extract inhibited nitric oxide and prostaglandin E2 by suppressing the expression of inducible NO synthase and cyclooxygenase-2, respectively.Rice hull extract exerted anti-inflammatory effect through inhibition of nuclear factor-kappa B, extracellular signal-regulated kinase and c-Jun N-terminal kinase signaling pathways.Rice hull extract may provide a potential therapeutic approach for inflammatory diseases. Abbreviations used: COX-2: cyclooxygenase-2, ERK: extracellular signal-regulated kinase, IκB: inhibitory kappa B, IL-1β: interleukin-1β, iNOS: inducible NO synthase, JNK: c-Jun N-terminal kinase, LPS: lipopolysaccharide, MAPKs: mitogen-activated protein kinases, NF-κB: nuclear factor-κB, NO: nitric oxide, PGE2: prostaglandin

  9. 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

  10. 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.

  11. Leaf hydraulic conductance is coordinated with leaf morpho-anatomical traits and nitrogen status in the genus Oryza.

    PubMed

    Xiong, Dongliang; Yu, Tingting; Zhang, Tong; Li, Yong; Peng, Shaobing; Huang, Jianliang

    2015-02-01

    Leaf hydraulic conductance (K leaf) is a major determinant of photosynthetic rate in plants. Previous work has assessed the relationships between leaf morpho-anatomical traits and K leaf with woody species, but there has been very little focus on cereal crops. The genus Oryza, which includes rice (Oryza sativa) and wild species (such as O. rufipogon cv. Griff), is ideal material for identifying leaf features associated with K leaf and gas exchange. Leaf morpho-anatomical traits, K leaf, leaf N content per leaf area, and CO2 diffusion efficiency were investigated in 11 Oryza cultivars. K leaf was positively correlated with leaf thickness and related traits, and therefore positively correlated with leaf mass per area and leaf N content per leaf area, and negatively with inter-veinal distance. K leaf was also positively correlated with leaf area and its related traits, and therefore negatively correlated with the proportion of minor vein length per area. In addition, coordination between K leaf and CO2 diffusion conductance in leaves was observed. We conclude that leaf morpho-anatomical traits and N content per leaf area strongly influence K leaf. Our results suggest that more detailed anatomical and structural studies are needed to elucidate the impacts of leaf feature traits on K leaf and gas exchange in grasses.

  12. A dose-response relationship for marketable yield reduction of two lettuce (Lactuca sativa L.) cultivars exposed to tropospheric ozone in Southern Europe.

    PubMed

    Marzuoli, Riccardo; Finco, Angelo; Chiesa, Maria; Gerosa, Giacomo

    2016-12-27

    The present study investigated the response to ozone (O3) of two cultivars (cv.'Romana' and cv. 'Canasta') of irrigated lettuce grown in an open-top chamber (OTC) experiment in Mediterranean conditions. Two different levels of O3 were applied, ambient O3 in non-filtered OTCs (NF-OTCs) and -40% of ambient O3 in charcoal-filtered OTCs (CF-OTCs), during four consecutive growing cycles. At the end of each growing cycle, the marketable yield (fresh biomass) was assessed while during the growing periods, measurements of the stomatal conductance at leaf level were performed and used to define a stomatal conductance model for calculation of the phytotoxic ozone dose (POD) absorbed by the plants.Results showed that O3 caused statistically significant yield reductions in the first and in the last growing cycle. In general, the marketable yield of the NF-OTC plants was always lower than the CF-OTC plants for both cultivars, with mean reductions of -18.5 and -14.5% for 'Romana' and 'Canasta', respectively. On the contrary, there was no statistically significant difference in marketable yield due to the cultivar factor or to the interaction between O3 and cultivar in any of the growing cycle performed.Dose-response relationships for the marketable relative yield based on the POD values were calculated according to different flux threshold values (Y). The best regression fit was obtained using an instantaneous flux threshold of 6 nmol O3 m(-2) s(-1) (POD6); the same value was obtained also for other crops. According to the generic lettuce dose-response relationship, an O3 critical level of 1 mmol O3 m(-2) of POD6 for a 15% of marketable yield loss was found.

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

    PubMed

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

    2015-09-20

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

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

    PubMed

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

    2015-02-01

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

  15. Characterization of the hrpF pathogenicity peninsula of Xanthomonas oryzae pv. oryzae.

    PubMed

    Sugio, Akiko; Yang, Bing; White, Frank F

    2005-06-01

    The hrp gene cluster of Xanthomonas spp. contains genes for the assembly and function of a type III secretion system (TTSS). The hrpF genes reside in a region between hpaB and the right end of the hrp cluster. The region of the hrpF gene of Xanthomonas oryzae pv. oryzae is bounded by two IS elements and also contains a homolog of hpaF of X. campestris pv. vesicatoria and two newly identified genes, hpa3 and hpa4. A comparison of the hrp gene clusters of different species of Xanthomonas revealed that the hrpF region is a constant yet more variable peninsula of the hrp pathogenicity island. Mutations in hpaF, hpa3, and hpa4 had no effect on virulence, whereas hrpF mutants were severely reduced in virulence on susceptible rice cultivars. The hrpF genes from X. campestris pv. vesicatoria, X. campestris pv. campestris, and X. axonopodis pv. citri each were capable of restoring virulence to the hrpF mutant of X. oryzae pv. oryzae. Correspondingly, none of the Xanthomonas pathovars with hrpF from X. oryzae pv. oryzae elicited a hypersensitive reaction in their respective hosts. Therefore, no evidence was found for hrpF as a host-specialization factor. In contrast to the loss of Bs3-dependent reactions by hrpF mutants of X. campestris pv. vesicatoria, hrpF mutants of X. oryzae pv. oryzae with either avrXa10 or avrXa7 elicited hypersensitive reactions in rice cultivars with the corresponding R genes. A double hrpFxoo-hpa1 mutant also elicited an Xa10-dependent resistance reaction. Thus, loss of hrpF, hpal, or both may reduce delivery or effectiveness of type III effectors. However, the mutations did not completely prevent the delivery of effectors from X. oryzae pv. oryzae into the host cells.

  16. African rice (Oryza glaberrima): History and future potential

    PubMed Central

    Linares, Olga F.

    2002-01-01

    The African species of rice (Oryza glaberrima) was cultivated long before Europeans arrived in the continent. At present, O. glaberrima is being replaced by the introduced Asian species of rice, Oryza sativa. Some West African farmers, including the Jola of southern Senegal, still grow African rice for use in ritual contexts. The two species of rice have recently been crossed, producing a promising hybrid. PMID:12461173

  17. Seasonal CH4 and N2O emissions and plant growth characteristics of several cultivars in direct seeded rice systems

    NASA Astrophysics Data System (ADS)

    Simmonds, M.; Anders, M. M.; Adviento-Borbe, M. A.; Van Kessel, C.; McClung, A.; Linquist, B.

    2014-12-01

    Understanding cultivar effects on field greenhouse gas (GHG) emissions in rice (Oryza sativa L.) systems is needed to improve the accuracy of predictive models used for estimating GHG emissions, and to determine to what extent choice of cultivar may have on GHG mitigation. We compared CH4 and N2O emissions, global warming potential (GWP = N2O + CH4), yield-scaled GWP (GWPY = GWP Mg-1 grain), and plant growth characteristics of 8 cultivars within 4 study sites in California and Arkansas. Seasonal CH4 emissions differed between cultivars by a factor of 2.1 and 1.3 at one California and one Arkansas site, respectively. Nitrous oxide emissions were negligible, comprised <10% of GWP, and were not different among cultivars. When sites and cultivars were pooled, and data were normalized to site averages, there was a positive correlation (r = 0.33) between root biomass at heading and seasonal CH4 emissions, but no correlation with shoot biomass at heading, or grain or straw biomass at maturity. Although differences in GWP and GWPY were observed, the consistency of some of the trends was variable across sites, indicating the importance of the genotype x environment interaction. While no high-yielding and low CH4-emitting cultivars were identified at the California sites, among the Southern varieties tested at the Arkansas site, the lowest emitting cultivar had the highest yield. This highlights the potential for breeding high-yielding varieties with low GWP, the ideal scenario to achieve low GWPY due to simultaneously mitigating GHG emissions and improving global food security.

  18. De Novo Assemblies of Three Oryza glaberrima Accessions Provide First Insights about Pan-Genome of African Rices

    PubMed Central

    Monat, Cécile; Pera, Bérengère; Ndjiondjop, Marie-Noelle; Sow, Mounirou; Tranchant-Dubreuil, Christine; Bastianelli, Leila; Ghesquière, Alain

    2017-01-01

    Oryza glaberrima is one of the two cultivated species of rice, and harbors various interesting agronomic traits, especially in biotic and abiotic resistance, compared with its Asian cousin O. sativa. A previous reference genome was published but newer studies highlighted some missing parts. Moreover, global species diversity is known nowadays to be represented by more than one single individual. For that purpose, we sequenced, assembled and annotated de novo three different cultivars from O. glaberrima. After validating our assemblies, we were able to better solve complex regions than the previous assembly and to provide a first insight in pan-genomic divergence between individuals. The three assemblies shown large common regions, but almost 25% of the genome present collinearity breakpoints or are even individual specific. PMID:28173009

  19. Metabolic variation between japonica and indica rice cultivars as revealed by non-targeted metabolomics

    PubMed Central

    Hu, Chaoyang; Shi, Jianxin; Quan, Sheng; Cui, Bo; Kleessen, Sabrina; Nikoloski, Zoran; Tohge, Takayuki; Alexander, Danny; Guo, Lining; Lin, Hong; Wang, Jing; Cui, Xiao; Rao, Jun; Luo, Qian; Zhao, Xiangxiang; Fernie, Alisdair R.; Zhang, Dabing

    2014-01-01

    Seed metabolites are critically important both for plant development and human nutrition; however, the natural variation in their levels remains poorly characterized. Here we profiled 121 metabolites in mature seeds of a wide panel Oryza sativa japonica and indica cultivars, revealing correlations between the metabolic phenotype and geographic origin of the rice seeds. Moreover, japonica and indica subspecies differed significantly not only in the relative abundances of metabolites but also in their corresponding metabolic association networks. These findings provide important insights into metabolic adaptation in rice subgroups, bridging the gap between genome and phenome, and facilitating the identification of genetic control of metabolic properties that can serve as a basis for the future improvement of rice quality via metabolic engineering. PMID:24861081

  20. Ultraviolet B-sensitive rice cultivar deficient in cyclobutyl pyrimidine dimer repair

    SciTech Connect

    Hidema, Jun; Kumagai, Tadashi; Sutherland, J.C.; Sutherland, B.M.

    1997-01-01

    Repair of cyclobutyl pyrimidine dimers (CPDs) in DNA is essential in most organisms to prevent biological damage by ultraviolet (UV) light. In higher plants tested thus far, UV-sensitive strains had higher initial damage levels or deficient repair of nondimer DNA lesions but normal CPD repair. This suggested that CPDs might not be important for biological lesions. The photosynthetic apparatus has also been proposed as a critical target. We have analyzed CPD induction and repair in the UV-sensitive rice (Oryza sativa L.) cultivar Norin 1 and its close relative UV-resistant Sasanishiki using alkaline agarose gel electrophoresis. Norin 1 is deficient in cyclobutyl pyrimidine dimer photoreactivation and excision; thus, UV sensitivity correlates with deficient dimer repair. 38 refs., 3 figs.

  1. Effect of Sesbania rostrata on Hirschmanniella oryzae in Flooded Rice

    PubMed Central

    Germani, G.; Reversat, G.; Luc, M.

    1983-01-01

    Microplot experiments on flooded soil infested with Hirschmanniella oryzae were conducted to investigate the influence of the legum Sesbania rostrata as a rotation crop with rice, Oryza sativa L. cv. Moroberekan. To avoid a green manure effect from S. rostrata, all aerial parts were removed at harvest. The dry weight of paddy, culms and leaves, and number of culms of rice following Sesbania were 214%, 158%, and 121% greater, respectively, than those following rice. Ripening of the paddy occurred earlier if rice followed Sesbania. The beneficial effect of Sesbania may have been due to the trap-crop action of Sesbania against H. oryzae. PMID:19295801

  2. Whole genomic sequencing of RT98 mitochondria derived from Oryza rufipogon and northern blot analysis to uncover a cytoplasmic male sterility-associated gene.

    PubMed

    Igarashi, Keisuke; Kazama, Tomohiko; Motomura, Keiji; Toriyama, Kinya

    2013-02-01

    Cytoplasmic male sterility (CMS) is a maternally inherited trait resulting in the failure to produce functional pollen and is often observed when an alien cytoplasm is transferred into a cultivated species. An RT98A CMS line and an RT98C fertility restorer line were obtained by successive backcrossing between Oryza rufipogon W1109 and Oryza sativa cultivar Taichung 65. To uncover the CMS-associated mitochondrial genes, we determined the complete sequence of the RT98-CMS mitochondrial genome using next-generation pyrosequencing, and searched new open reading frames (orfs) absent in a reported mitochondrial genome of O. sativa Nipponbare. Then, six candidates were selected for the CMS-associated genes based on the criteria in which they were chimeric in structure or encoded a peptide with transmembrane domains. One of the candidates, orf113, showed different transcript sizes between RT98A and RT98C on Northern blot analysis. The orf113 gene was shown to be co-transcribed with atp4 and cox3 encoding ATP synthase F0 subunit 4 and Cyt c oxidase subunit 3, respectively, and their transcripts were distinctly processed in the presence of a fertility restorer gene. Our results indicate that orf113 is a CMS-associated gene of RT98-CMS.

  3. Dorsoventral asymmetry of photosynthesis and photoinhibition in flag leaves of two rice cultivars that differ in nitrogen response and leaf angle.

    PubMed

    Kumagai, Etsushi; Hamaoka, Norimitsu; Araki, Takuya; Ueno, Osamu

    2014-08-01

    Rice is believed to show photosynthetic symmetry between adaxial and abaxial leaf sides. To verify this, we re-examined dorsoventral asymmetry in photosynthesis, chlorophyll fluorescence and anatomical traits in flag leaves of two Oryza sativa cultivars that differ in nitrogen (N) response and in leaf angle: 'Akenohoshi', a cultivar that can adapt to low-N (LN), with low leaf angle (more erect leaves), and 'Shirobeniya', a cultivar that is unable to adapt to LN, with higher leaf angle. Plants were grown under standard-N (SN) and LN conditions. LN leaves of both cultivars became more erect than SN, but LN Akenohoshi still had more erect ones than Shirobeniya. Contrary to results of previous studies, leaves of both cultivars showed an asymmetry in photosynthetic rate between adaxial and abaxial sides (higher on the adaxial side) under SN. SN leaves of both cultivars showed lower susceptibility to photoinhibition on the adaxial side than on the abaxial side. However, leaves of Akenohoshi showed less asymmetry in these traits under LN than under SN, whereas leaves of Shirobeniya had similar degrees of asymmetry in these traits under both SN and LN. Both cultivars also showed dorsoventral asymmetry in anatomical traits of mesophyll tissue regardless of N level, but the degree of asymmetry was lower in LN Akenohoshi. These data reveal that rice leaves exhibit dorsoventral asymmetry in photosynthetic and anatomical features, and that the degree of asymmetry varies with cultivar and N level. It is suggested that lower leaf angles (particularly in Akenohoshi) in the presence of LN represent a light acclimation to prevent photoinhibition.

  4. Whole Genome Sequencing of Elite Rice Cultivars as a Comprehensive Information Resource for Marker Assisted Selection

    PubMed Central

    Duitama, Jorge; Silva, Alexander; Sanabria, Yamid; Cruz, Daniel Felipe; Quintero, Constanza; Ballen, Carolina; Lorieux, Mathias; Scheffler, Brian; Farmer, Andrew; Torres, Edgar; Oard, James; Tohme, Joe

    2015-01-01

    Current advances in sequencing technologies and bioinformatics revealed the genomic background of rice, a staple food for the poor people, and provided the basis to develop large genomic variation databases for thousands of cultivars. Proper analysis of this massive resource is expected to give novel insights into the structure, function, and evolution of the rice genome, and to aid the development of rice varieties through marker assisted selection or genomic selection. In this work we present sequencing and bioinformatics analyses of 104 rice varieties belonging to the major subspecies of Oryza sativa. We identified repetitive elements and recurrent copy number variation covering about 200 Mbp of the rice genome. Genotyping of over 18 million polymorphic locations within O. sativa allowed us to reconstruct the individual haplotype patterns shaping the genomic background of elite varieties used by farmers throughout the Americas. Based on a reconstruction of the alleles for the gene GBSSI, we could identify novel genetic markers for selection of varieties with high amylose content. We expect that both the analysis methods and the genomic information described here would be of great use for the rice research community and for other groups carrying on similar sequencing efforts in other crops. PMID:25923345

  5. Molecular analysis of the hrp gene cluster in Xanthomonas oryzae pathovar oryzae KACC10859.

    PubMed

    Cho, Hee-Jung; Park, Young-Jin; Noh, Tae-Hwan; Kim, Yeong-Tae; Kim, Jeong-Gu; Song, Eun-Sung; Lee, Dong-Hee; Lee, Byoung-Moo

    2008-06-01

    Xanthomonas oryzae pathovar oryzae is the causal agent of rice bacterial blight. The plant pathogenic bacterium X. oryzae pv. oryzae expresses a type III secretion system that is necessary for both the pathogenicity in susceptible hosts and the induction of the hypersensitive response in resistant plants. This specialized protein transport system is encoded by a 32.18kb hrp (hypersensitive response and pathogenicity) gene cluster. The hrp gene cluster is composed of nine hrp, nine hrc (hrp conserved) and eight hpa (hrp-associated) genes and is controlled by HrpG and HrpX, which are known as regulators of the hrp gene cluster. Before mutational analysis of these hrp genes, the transcriptional linkages of the core region of the hrp gene cluster from hpaB to hrcC of the X. oryzae pv. oryzae KACC10859 was determined and the non-polarity of EZTn5 insertional mutagenesis was demonstrated by reverse transcription polymerase chain reaction. Pathogenicity assays of these non-polar hrp mutants were carried out on the susceptible rice cultivar, Milyang-23. According to the results of these assays, all hrp-hrc, except hrpF, and hpaB mutants lost their pathogenicity, which indicates that most hrp-hrc genes encode essential pathogenicity factors. On the other hand, most hpa mutants showed decreased virulence in a different pattern, i.e., hpa genes are not essential but are important for pathogenicity.

  6. Genetic Isolation, Divergence And Gene Flow In O. sativa

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Knowledge about the structure and evolutionary history of naturally occurring variation in crops and their wild relatives provides insights into the complex process of domestication and new opportunities for utilizing novel alleles in crop improvement. Domesticated Asian rice (Oryza sativa L.) is co...

  7. Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A

    PubMed Central

    Salzberg, Steven L; Sommer, Daniel D; Schatz, Michael C; Phillippy, Adam M; Rabinowicz, Pablo D; Tsuge, Seiji; Furutani, Ayako; Ochiai, Hirokazu; Delcher, Arthur L; Kelley, David; Madupu, Ramana; Puiu, Daniela; Radune, Diana; Shumway, Martin; Trapnell, Cole; Aparna, Gudlur; Jha, Gopaljee; Pandey, Alok; Patil, Prabhu B; Ishihara, Hiromichi; Meyer, Damien F; Szurek, Boris; Verdier, Valerie; Koebnik, Ralf; Dow, J Maxwell; Ryan, Robert P; Hirata, Hisae; Tsuyumu, Shinji; Won Lee, Sang; Ronald, Pamela C; Sonti, Ramesh V; Van Sluys, Marie-Anne; Leach, Jan E; White, Frank F; Bogdanove, Adam J

    2008-01-01

    Background Xanthomonas oryzae pv. oryzae causes bacterial blight of rice (Oryza sativa L.), a major disease that constrains production of this staple crop in many parts of the world. We report here on