Ocimum sanctum leaf extract induces drought stress tolerance in rice

PubMed Central

Pandey, Veena; Ansari, M.W.; Tula, Suresh; Sahoo, R.K.; Bains, Gurdeep; Kumar, J.; Tuteja, Narendra; Shukla, Alok

2016-01-01

ABSTRACT Ocimum leaves are highly enriched in antioxidant components. Thus, its leaf extract, if applied in plants, is believed to efficiently scavenge ROS, thereby preventing oxidative damage under drought stress. Thus, the present study was performed in kharif 2013 and rabi 2014 season to evaluate the effect of aqueous leaf extract of Ocimum sanctum against drought stress in 2 rice genotype under glass house conditions. Here we show that various morpho- physiological (chlorophyll fluorescence, leaf rolling score, leaf tip burn, number of senesced leaves and total dry matter) and biochemical parameters (proline, malondialdehyde and superoxide dismutase content) were amended by Ocimum treatment in both the seasons. Application of Ocimum extract increased expression of dehydrin genes, while reducing expression of aquaporin genes in drought stressed rice plant. Thus, application of Ocimum leaf extract under drought stress can be suggested as a promising strategy to mitigate drought stress in economical, accessible and ecofriendly manner. PMID:26890603

Analysis of the differential gene and protein expression profile of the rolled leaf mutant of transgenic rice (Oryza sativa L.).

PubMed

Zhu, Qiuqiang; Yu, Shuguang; Chen, Guanshui; Ke, Lanlan; Pan, Daren

2017-01-01

The importance of leaf rolling in rice (Oryza sativa L.) has been widely recognized. Although several studies have investigated rice leaf rolling and identified some related genes, knowledge of the molecular mechanism underlying rice leaf rolling, especially outward leaf rolling, is limited. Therefore, in this study, differential proteomics and gene expression profiling were used to analyze rolled leaf mutant of transgenic rice in order to investigate differentially expressed genes and proteins related to rice leaf rolling. To this end, 28 differentially expressed proteins related to rolling leaf traits were isolated and identified. Digital expression profiling detected 10 genes related to rice leaf rolling. Some of the proteins and genes detected are involved in lipid metabolism, which is related to the development of bulliform cells, such as phosphoinositide phospholipase C, Mgll gene, and At4g26790 gene. The "omics"-level techniques were useful for simultaneously isolating several proteins and genes related to rice leaf rolling. In addition, the results of the analysis of differentially expressed proteins and genes were closely consistent with those from a corresponding functional analysis of cellular mechanisms; our study findings might form the basis for further research on the molecular mechanisms underlying rice leaf rolling.

Defense Responses in Rice Induced by Silicon Amendment against Infestation by the Leaf Folder Cnaphalocrocis medinalis

PubMed Central

Han, Yongqiang; Li, Pei; Gong, Shaolong; Yang, Lang; Wen, Lizhang; Hou, Maolin

2016-01-01

Silicon (Si) amendment to plants can confer enhanced resistance to herbivores. In the present study, the physiological and cytological mechanisms underlying the enhanced resistance of plants with Si addition were investigated for one of the most destructive rice pests in Asian countries, the rice leaf folder, Cnaphalocrocis medinalis (Guenée). Activities of defense-related enzymes, superoxide dismutase, peroxidase, catalase, phenylalanine ammonia-lyase, and polyphenol oxidase, and concentrations of malondialdehyde and soluble protein in leaves were measured in rice plants with or without leaf folder infestation and with or without Si amendment at 0.32 g Si/kg soil. Silicon amendment significantly reduced leaf folder larval survival. Silicon addition alone did not change activities of defense-related enzymes and malondialdehyde concentration in rice leaves. With leaf folder infestation, activities of the defense-related enzymes increased and malondialdehyde concentration decreased in plants amended with Si. Soluble protein content increased with Si addition when the plants were not infested, but was reduced more in the infested plants with Si amendment than in those without Si addition. Regardless of leaf folder infestation, Si amendment significantly increased leaf Si content through increases in the number and width of silica cells. Our results show that Si addition enhances rice resistance to the leaf folder through priming the feeding stress defense system, reduction in soluble protein content and cell silicification of rice leaves. PMID:27124300

Leaf-FISH: Microscale Imaging of Bacterial Taxa on Phyllosphere

PubMed Central

Peredo, Elena L.; Simmons, Sheri L.

2018-01-01

Molecular methods for microbial community characterization have uncovered environmental and plant-associated factors shaping phyllosphere communities. Variables undetectable using bulk methods can play an important role in shaping plant-microbe interactions. Microscale analysis of bacterial dynamics in the phyllosphere requires imaging techniques specially adapted to the high autoflouresence and 3-D structure of the leaf surface. We present an easily-transferable method (Leaf-FISH) to generate high-resolution tridimensional images of leaf surfaces that allows simultaneous visualization of multiple bacterial taxa in a structurally informed context, using taxon-specific fluorescently labeled oligonucleotide probes. Using a combination of leaf pretreatments coupled with spectral imaging confocal microscopy, we demonstrate the successful imaging bacterial taxa at the genus level on cuticular and subcuticular leaf areas. Our results confirm that different bacterial species, including closely related isolates, colonize distinct microhabitats in the leaf. We demonstrate that highly related Methylobacterium species have distinct colonization patterns that could not be predicted by shared physiological traits, such as carbon source requirements or phytohormone production. High-resolution characterization of microbial colonization patterns is critical for an accurate understanding of microbe-microbe and microbe-plant interactions, and for the development of foliar bacteria as plant-protective agents. PMID:29375531

Gravimorphism in rice and barley: promotion of leaf elongation by vertical inversion in agravitropically growing plants.

PubMed

Abe, K; Takahashi, H; Suge, H

1998-12-01

We have compared shoot responses of agravitropic rice and barley plants to vertical inversion with those of normal ones. When rice plants were vertically inverted, the main stems of a japonica type of rice, cv. Kamenoo, showed negative gravitropism at nodes 2-15 of both elongated and non-elongated internodes. However, shoots of lazy line of rice, lazy-Kamenoo, bent gravitropically at nodes 11-15 only elongated internodes but not at nodes 2-10 of non-elongated ones. Thus, shoots of Kamenoo responded gravitropically at all stages of growth, whereas shoots of lazy-Kamenoo did not show gravitropic response before heading. In Kamenoo plants, lengths of both leaf-sheath and leaf-blade were shortened by vertical inversion, but those of the vertically inverted plants of lazy-Kamenoo were significantly longer than the plants in an upright position. When agravitropic and normal plants of barley were vertically inverted, the same results as in rice were obtained; elongation of both leaf-sheath and leaf-blade was inhibited in normal barley plants, Chikurin-Ibaragi No. 1, but significantly stimulated in agravitropic plants of serpentina barley. These results suggest that vertical inversion of rice and barley plants enhances the elongation growth of leaves in the absence of tropistic response.

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

PubMed

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

2016-12-01

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

Increasing leaf vein density by mutagenesis: laying the foundations for C4 rice.

PubMed

Feldman, Aryo B; Murchie, Erik H; Leung, Hei; Baraoidan, Marietta; Coe, Robert; Yu, Su-May; Lo, Shuen-Fang; Quick, William P

2014-01-01

A high leaf vein density is both an essential feature of C4 photosynthesis and a foundation trait to C4 evolution, ensuring the optimal proportion and proximity of mesophyll and bundle sheath cells for permitting the rapid exchange of photosynthates. Two rice mutant populations, a deletion mutant library with a cv. IR64 background (12,470 lines) and a T-DNA insertion mutant library with a cv. Tainung 67 background (10,830 lines), were screened for increases in vein density. A high throughput method with handheld microscopes was developed and its accuracy was supported by more rigorous microscopy analysis. Eight lines with significantly increased leaf vein densities were identified to be used as genetic stock for the global C4 Rice Consortium. The candidate population was shown to include both shared and independent mutations and so more than one gene controlled the high vein density phenotype. The high vein density trait was found to be linked to a narrow leaf width trait but the linkage was incomplete. The more genetically robust narrow leaf width trait was proposed to be used as a reliable phenotypic marker for finding high vein density variants in rice in future screens.

Genetic dissection and validation of candidate genes for flag leaf size in rice (Oryza sativa L.).

PubMed

Tang, Xinxin; Gong, Rong; Sun, Wenqiang; Zhang, Chaopu; Yu, Sibin

2018-04-01

Two major loci with functional candidate genes were identified and validated affecting flag leaf size, which offer desirable genes to improve leaf architecture and photosynthetic capacity in rice. Leaf size is a major determinant of plant architecture and yield potential in crops. However, the genetic and molecular mechanisms regulating leaf size remain largely elusive. In this study, quantitative trait loci (QTLs) for flag leaf length and flag leaf width in rice were detected with high-density single nucleotide polymorphism genotyping of a chromosomal segment substitution line (CSSL) population, in which each line carries one or a few chromosomal segments from the japonica cultivar Nipponbare in a common background of the indica variety Zhenshan 97. In total, 14 QTLs for flag leaf length and nine QTLs for flag leaf width were identified in the CSSL population. Among them, qFW4-2 for flag leaf width was mapped to a 37-kb interval, with the most likely candidate gene being the previously characterized NAL1. Another major QTL for both flag leaf width and length was delimited by substitution mapping to a small region of 13.5 kb that contains a single gene, Ghd7.1. Mutants of Ghd7.1 generated using CRISPR/CAS9 approach showed reduced leaf size. Allelic variation analyses also validated Ghd7.1 as a functional candidate gene for leaf size, photosynthetic capacity and other yield-related traits. These results provide useful genetic information for the improvement of leaf size and yield in rice breeding programs.

Genetics and breeding of bacterial leaf spot resistance

USDA-ARS?s Scientific Manuscript database

Bacterial leaf spot (BLS) caused by the pathogen Xanthomonas campestris pv. vitians (Xcv) is a globally important disease of whole head and baby leaf lettuce that reduces crop yield and quality. Host resistance is the most feasible method to reduce disease losses. Screening Lactuca accessions has id...

Interaction between Vaccinium bracteatum Thunb. leaf pigment and rice proteins.

PubMed

Wang, Li; Xu, Yuan; Zhou, Sumei; Qian, Haifeng; Zhang, Hui; Qi, Xiguang; Fan, Meihua

2016-03-01

In this study, we investigated the interaction of Vaccinium bracteatum Thunb. leaf (VBTL) pigment and rice proteins. In the presence of rice protein, VBTL pigment antioxidant activity and free polyphenol content decreased by 67.19% and 68.11%, respectively, and L(∗) of the protein-pigment complex decreased significantly over time. L(∗) values of albumin, globulin and glutelin during 60-min pigment exposure decreased by 55.00, 57.14, and 54.30%, respectively, indicating that these proteins had bound to the pigment. A significant difference in protein surface hydrophobicity was observed between rice proteins and pigment-protein complexes, indicating that hydrophobic interaction is a major binding mechanism between VBTL pigment and rice proteins. A significant difference in secondary structures between proteins and protein-pigment complexes was also uncovered, indicating that hydrogen bonding may be another mode of interaction between VBTL pigment and rice proteins. Our results indicate that VBTL pigment can stain rice proteins with hydrophobic and hydrogen interactions. Copyright © 2015 Elsevier Ltd. All rights reserved.

SP-LL-37, human antimicrobial peptide, enhances disease resistance in transgenic rice.

PubMed

Lee, In Hye; Jung, Yu-Jin; Cho, Yong Gu; Nou, Ill Sup; Huq, Md Amdadul; Nogoy, Franz Marielle; Kang, Kwon-Kyoo

2017-01-01

Human LL-37 is a multifunctional antimicrobial peptide of cathelicidin family. It has been shown in recent studies that it can serve as a host's defense against influenza A virus. We now demonstrate in this study how signal peptide LL-37 (SP-LL-37) can be used in rice resistance against bacterial leaf blight and blast. We synthesized LL-37 peptide and subcloned in a recombinant pPZP vector with pGD1 as promoter. SP-LL-37 was introduced into rice plants by Agrobacterium mediated transformation. Stable expression of SP-LL-37 in transgenic rice plants was confirmed by RT-PCR and ELISA analyses. Subcellular localization of SP-LL-37-GFP fusion protein showed evidently in intercellular space. Our data on testing for resistance to bacterial leaf blight and blast revealed that the transgenic lines are highly resistant compared to its wildtype. Our results suggest that LL-37 can be further explored to improve wide-spectrum resistance to biotic stress in rice.

A maize resistance gene functions against bacterial streak disease in rice.

PubMed

Zhao, Bingyu; Lin, Xinghua; Poland, Jesse; Trick, Harold; Leach, Jan; Hulbert, Scot

2005-10-25

Although cereal crops all belong to the grass family (Poacea), most of their diseases are specific to a particular species. Thus, a given cereal species is typically resistant to diseases of other grasses, and this nonhost resistance is generally stable. To determine the feasibility of transferring nonhost resistance genes (R genes) between distantly related grasses to control specific diseases, we identified a maize R gene that recognizes a rice pathogen, Xanthomonas oryzae pv. oryzicola, which causes bacterial streak disease. Bacterial streak is an important disease of rice in Asia, and no simply inherited sources of resistance have been identified in rice. Although X. o. pv. oryzicola does not cause disease on maize, we identified a maize gene, Rxo1, that conditions a resistance reaction to a diverse collection of pathogen strains. Surprisingly, Rxo1 also controls resistance to the unrelated pathogen Burkholderia andropogonis, which causes bacterial stripe of sorghum and maize. The same gene thus controls resistance reactions to both pathogens and nonpathogens of maize. Rxo1 has a nucleotide-binding site-leucine-rich repeat structure, similar to many previously identified R genes. Most importantly, Rxo1 functions after transfer as a transgene to rice, demonstrating the feasibility of nonhost R gene transfer between cereals and providing a valuable tool for controlling bacterial streak disease.

Draft genome sequence of rice orange leaf phytoplasma from Guangdong, China

USDA-ARS?s Scientific Manuscript database

The genome of rice orange leaf phytoplasma strain LD1 from Luoding City, Guangdong, P. R. China, was sequenced. The draft LD1genome is 599,264 bp with GC content of 28.2%, 647 predicted open reading frames and 33 RNA genes....

A maize resistance gene functions against bacterial streak disease in rice

PubMed Central

Zhao, Bingyu; Lin, Xinghua; Poland, Jesse; Trick, Harold; Leach, Jan; Hulbert, Scot

2005-01-01

Although cereal crops all belong to the grass family (Poacea), most of their diseases are specific to a particular species. Thus, a given cereal species is typically resistant to diseases of other grasses, and this nonhost resistance is generally stable. To determine the feasibility of transferring nonhost resistance genes (R genes) between distantly related grasses to control specific diseases, we identified a maize R gene that recognizes a rice pathogen, Xanthomonas oryzae pv. oryzicola, which causes bacterial streak disease. Bacterial streak is an important disease of rice in Asia, and no simply inherited sources of resistance have been identified in rice. Although X. o. pv. oryzicola does not cause disease on maize, we identified a maize gene, Rxo1, that conditions a resistance reaction to a diverse collection of pathogen strains. Surprisingly, Rxo1 also controls resistance to the unrelated pathogen Burkholderia andropogonis, which causes bacterial stripe of sorghum and maize. The same gene thus controls resistance reactions to both pathogens and nonpathogens of maize. Rxo1 has a nucleotide-binding site-leucine-rich repeat structure, similar to many previously identified R genes. Most importantly, Rxo1 functions after transfer as a transgene to rice, demonstrating the feasibility of nonhost R gene transfer between cereals and providing a valuable tool for controlling bacterial streak disease. PMID:16230639

Carbon nanomaterials alter plant physiology and soil bacterial community composition in a rice-soil-bacterial ecosystem.

PubMed

Hao, Yi; Ma, Chuanxin; Zhang, Zetian; Song, Youhong; Cao, Weidong; Guo, Jing; Zhou, Guopeng; Rui, Yukui; Liu, Liming; Xing, Baoshan

2018-01-01

The aim of this study was to compare the toxicity effects of carbon nanomaterials (CNMs), namely fullerene (C 60 ), reduced graphene oxide (rGO) and multi-walled carbon nanotubes (MWCNTs), on a mini-ecosystem of rice grown in a loamy potted soil. We measured plant physiological and biochemical parameters and examined bacterial community composition in the CNMs-treated plant-soil system. After 30 days of exposure, all the three CNMs negatively affected the shoot height and root length of rice, significantly decreased root cortical cells diameter and resulted in shrinkage and deformation of cells, regardless of exposure doses (50 or 500 mg/kg). Additionally, at the high exposure dose of CNM, the concentrations of four phytohormones, including auxin, indoleacetic acid, brassinosteroid and gibberellin acid 4 in rice roots significantly increased as compared to the control. At the high exposure dose of MWCNTs and C 60 , activities of the antioxidant enzymes superoxide dismutase (SOD) and peroxidase (POD) in roots increased significantly. High-throughput sequencing showed that three typical CNMs had little effect on shifting the predominant soil bacterial species, but the presence of CNMs significantly altered the composition of the bacterial community. Our results indicate that different CNMs indeed resulted in environmental toxicity to rice and soil bacterial community in the rhizosphere and suggest that CNMs themselves and their incorporated products should be reasonably used to control their release/discharge into the environment to prevent their toxic effects on living organisms and the potential risks to food safety. Copyright © 2017 Elsevier Ltd. All rights reserved.

A hairy-leaf gene, BLANKET LEAF, of wild Oryza nivara increases photosynthetic water use efficiency in rice.

PubMed

Hamaoka, Norimitsu; Yasui, Hideshi; Yamagata, Yoshiyuki; Inoue, Yoko; Furuya, Naruto; Araki, Takuya; Ueno, Osamu; Yoshimura, Atsushi

2017-12-01

High water use efficiency is essential to water-saving cropping. Morphological traits that affect photosynthetic water use efficiency are not well known. We examined whether leaf hairiness improves photosynthetic water use efficiency in rice. A chromosome segment introgression line (IL-hairy) of wild Oryza nivara (Acc. IRGC105715) with the genetic background of Oryza sativa cultivar 'IR24' had high leaf pubescence (hair). The leaf hairs developed along small vascular bundles. Linkage analysis in BC 5 F 2 and F 3 populations showed that the trait was governed by a single gene, designated BLANKET LEAF (BKL), on chromosome 6. IL-hairy plants had a warmer leaf surface in sunlight, probably due to increased boundary layer resistance. They had a lower transpiration rate under moderate and high light intensities, resulting in higher photosynthetic water use efficiency. Introgression of BKL on chromosome 6 from O. nivara improved photosynthetic water use efficiency in the genetic background of IR24.

Suppression of the rice fatty-acid desaturase gene OsSSI2 enhances resistance to blast and leaf blight diseases in rice.

PubMed

Jiang, Chang-Jie; Shimono, Masaki; Maeda, Satoru; Inoue, Haruhiko; Mori, Masaki; Hasegawa, Morifumi; Sugano, Shoji; Takatsuji, Hiroshi

2009-07-01

Fatty acids and their derivatives play important signaling roles in plant defense responses. It has been shown that suppressing a gene for stearoyl acyl carrier protein fatty-acid desaturase (SACPD) enhances the resistance of Arabidopsis (SSI2) and soybean to multiple pathogens. In this study, we present functional analyses of a rice homolog of SSI2 (OsSSI2) in disease resistance of rice plants. A transposon insertion mutation (Osssi2-Tos17) and RNAi-mediated knockdown of OsSSI2 (OsSSI2-kd) reduced the oleic acid (18:1) level and increased that of stearic acid (18:0), indicating that OsSSI2 is responsible for fatty-acid desaturase activity. These plants displayed spontaneous lesion formation in leaf blades, retarded growth, slight increase in endogenous free salicylic acid (SA) levels, and SA/benzothiadiazole (BTH)-specific inducible genes, including WRKY45, a key regulator of SA/BTH-induced resistance, in rice. Moreover, the OsSSI2-kd plants showed markedly enhanced resistance to the blast fungus Magnaporthe grisea and leaf-blight bacteria Xanthomonas oryzae pv. oryzae. These results suggest that OsSSI2 is involved in the negative regulation of defense responses in rice, as are its Arabidopsis and soybean counterparts. Microarray analyses identified 406 genes that were differentially expressed (>or=2-fold) in OsSSI2-kd rice plants compared with wild-type rice and, of these, approximately 39% were BTH responsive. Taken together, our results suggest that induction of SA-responsive genes, including WRKY45, is likely responsible for enhanced disease resistance in OsSSI2-kd rice plants.

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

PubMed

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

2017-02-01

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

XA21-specific induction of stress-related genes following Xanthomonas infection of detached rice leaves.

PubMed

Thomas, Nicholas C; Schwessinger, Benjamin; Liu, Furong; Chen, Huamin; Wei, Tong; Nguyen, Yen P; Shaker, Isaac W F; Ronald, Pamela C

2016-01-01

The rice XA21 receptor kinase confers robust resistance to the bacterial pathogen Xanthomonas oryzae pv. oryzae ( Xoo ). We developed a detached leaf infection assay to quickly and reliably measure activation of the XA21-mediated immune response using genetic markers. We used RNA sequencing of elf18 treated EFR:XA21:GFP plants to identify candidate genes that could serve as markers for XA21 activation. From this analysis, we identified eight genes that are up-regulated in both in elf18 treated EFR:XA21:GFP rice leaves and Xoo infected XA21 rice leaves. These results provide a rapid and reliable method to assess bacterial-rice interactions.

Leaf gas films contribute to rice (Oryza sativa) submergence tolerance during saline floods.

PubMed

Herzog, Max; Konnerup, Dennis; Pedersen, Ole; Winkel, Anders; Colmer, Timothy David

2018-05-01

Floods and salinization of agricultural land adversely impact global rice production. We investigated whether gas films on leaves of submerged rice delay salt entry during saline submergence. Two-week-old plants with leaf gas films (+GF) or with gas films experimentally removed (-GF) were submerged in artificial floodwater with 0 or 50 mm NaCl for up to 16 d. Gas films were present >9 d on GF plants after which gas films were diminished. Tissue ion analysis (Na + , Cl - and K + ) showed that gas films caused some delay of Na + entry, as leaf Na + concentration was 36-42% higher in -GF leaves than +GF leaves on days 1-5. However, significant net uptakes of Na + and Cl - , and K + net loss, occurred despite the presence of gas films, indicating the likely presence of some leaf-to-floodwater contact, so that the gas layer must not have completely separated the leaf surfaces from the water. Natural loss and removal of gas films resulted in severe declines in growth, underwater photosynthesis, chlorophyll a and tissue porosity. Submergence was more detrimental to leaf P N and growth than the additional effect of 50 mm NaCl, as salt did not significantly affect underwater P N at 200 μm CO 2 nor growth. © 2016 John Wiley & Sons Ltd.

Molecular breeding of transgenic rice plants expressing a bacterial chlorocatechol dioxygenase gene.

PubMed

Shimizu, Masami; Kimura, Tetsuya; Koyama, Takayoshi; Suzuki, Katsuhisa; Ogawa, Naoto; Miyashita, Kiyotaka; Sakka, Kazuo; Ohmiya, Kunio

2002-08-01

The cbnA gene encoding the chlorocatechol dioxygenase gene from Ralstonia eutropha NH9 was introduced into rice plants. The cbnA gene was expressed in transgenic rice plants under the control of a modified cauliflower mosaic virus 35S promoter. Western blot analysis using anti-CbnA protein indicated that the cbnA gene was expressed in leaf tissue, roots, culms, and seeds. Transgenic rice calluses expressing the cbnA gene converted 3-chlorocatechol to 2-chloromucote efficiently. Growth and morphology of the transgenic rice plants expressing the cbnA gene were not distinguished from those of control rice plants harboring only a Ti binary vector. It is thus possible to breed transgenic plants that degrade chloroaromatic compounds in soil and surface water.

Temperature Thresholds and Thermal Requirements for the Development of the Rice Leaf Folder, Cnaphalocrocis medinalis

PubMed Central

Padmavathi, Chintalapati; Katti, Gururaj; Sailaja, V.; Padmakumari, A.P.; Jhansilakshmi, V.; Prabhakar, M.; Prasad, Y.G.

2013-01-01

The rice leaf folder, Cnaphalocrocis medinalis Guenée (Lepidoptera: Pyralidae) is a predominant foliage feeder in all the rice ecosystems. The objective of this study was to examine the development of leaf folder at 7 constant temperatures (18, 20, 25, 30, 32, 34, 35° C) and to estimate temperature thresholds and thermal constants for the forecasting models based on heat accumulation units, which could be developed for use in forecasting. The developmental periods of different stages of rice leaf folder were reduced with increases in temperature from 18 to 34° C. The lower threshold temperatures of 11.0, 10.4, 12.8, and 11.1° C, and thermal constants of 69, 270, 106, and 455 degree days, were estimated by linear regression analysis for egg, larva, pupa, and total development, respectively. Based on the thermodynamic non-linear optimSSI model, intrinsic optimum temperatures for the development of egg, larva, and pupa were estimated at 28.9, 25.1 and 23.7° C, respectively. The upper and lower threshold temperatures were estimated as 36.4° C and 11.2° C for total development, indicating that the enzyme was half active and half inactive at these temperatures. These estimated thermal thresholds and degree days could be used to predict the leaf folder activity in the field for their effective management. PMID:24205891

Evaluating Leaf and Canopy Reflectance of Stressed Rice Plants to Monitor Arsenic Contamination.

PubMed

Bandaru, Varaprasad; Daughtry, Craig S; Codling, Eton E; Hansen, David J; White-Hansen, Susan; Green, Carrie E

2016-06-18

Arsenic contamination is a serious problem in rice cultivated soils of many developing countries. Hence, it is critical to monitor and control arsenic uptake in rice plants to avoid adverse effects on human health. This study evaluated the feasibility of using reflectance spectroscopy to monitor arsenic in rice plants. Four arsenic levels were induced in hydroponically grown rice plants with application of 0, 5, 10 and 20 µmol·L(-1) sodium arsenate. Reflectance spectra of upper fully expanded leaves were acquired over visible and infrared (NIR) wavelengths. Additionally, canopy reflectance for the four arsenic levels was simulated using SAIL (Scattering by Arbitrarily Inclined Leaves) model for various soil moisture conditions and leaf area indices (LAI). Further, sensitivity of various vegetative indices (VIs) to arsenic levels was assessed. Results suggest that plants accumulate high arsenic amounts causing plant stress and changes in reflectance characteristics. All leaf spectra based VIs related strongly with arsenic with coefficient of determination (r²) greater than 0.6 while at canopy scale, background reflectance and LAI confounded with spectral signals of arsenic affecting the VIs' performance. Among studied VIs, combined index, transformed chlorophyll absorption reflectance index (TCARI)/optimized soil adjusted vegetation index (OSAVI) exhibited higher sensitivity to arsenic levels and better resistance to soil backgrounds and LAI followed by red edge based VIs (modified chlorophyll absorption reflectance index (MCARI) and TCARI) suggesting that these VIs could prove to be valuable aids for monitoring arsenic in rice fields.

Development of practical diagnostic methods for monitoring rice bacterial panicle blight disease and evaluation of rice germplasm for resistance

USDA-ARS?s Scientific Manuscript database

A study was initiated to understand Burkholderia glumae, the major causal agent for bacterial panicle blight disease of rice; to develop practical diagnostic methods for monitoring the disease; and to evaluate rice germplasm for resistance. Burkholderia glumae was frequently isolated from infected p...

Development of practical diagnostic methods for monitoring rice bacterial panicle blight disease and evaluation of rice germplasm for resistance

USDA-ARS?s Scientific Manuscript database

A study was initiated to understand Burkholderia glumae (major causal agent for bacterial panicle blight disease of rice) to develop practical diagnostic methods for monitoring the disease; and to evaluate rice germplasm for resistance. B. glumae was frequently isolated from symptomatic panicles on...

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

PubMed

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

2010-06-01

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

Genetic analysis of rice mutants responsible for narrow leaf phenotype and reduced vein number.

PubMed

Kubo, Fumika Clara; Yasui, Yukiko; Kumamaru, Toshihiro; Sato, Yutaka; Hirano, Hiro-Yuki

2017-03-17

Leaves are a major site for photosynthesis and a key determinant of plant architecture. Rice produces thin and slender leaves, which consist of the leaf blade and leaf sheath separated by the lamina joint. Two types of vasculature, the large and small vascular bundles, run in parallel, together with a strong structure, the midrib. In this paper, we examined the function of four genes that regulate the width of the leaf blade and the vein number: NARROW LEAF1 (NAL1), NAL2, NAL3 and NAL7. We backcrossed original mutants of these genes with the standard wild-type rice, Taichung 65. We then compared the effect of each mutation on similar genetic backgrounds and examined genetic interactions of these genes. The nal1 single mutation and the nal2 nal3 double mutation showed a severe effect on leaf width, resulting in very narrow leaves. Although vein number was also reduced in the nal1 and nal2 nal3 mutants, the small vein number was more strongly reduced than the large vein number. In contrast, the nal7 mutation showed a milder effect on leaf width and vein number, and both the large and small veins were similarly affected. Thus, the genes responsible for narrow leaf phenotype seem to play distinct roles. The nal7 mutation showed additive effects on both leaf width and vein number, when combined with the nal1 single or the nal2 nal3 double mutation. In addition, observations of inner tissues revealed that cell differentiation was partially compromised in the nal2 nal3 nal7 mutant, consistent with the severe reduction in leaf width in this triple mutant.

Leaf Photosynthetic Parameters Related to Biomass Accumulation in a Global Rice Diversity Survey1[OPEN

PubMed Central

Zheng, Guangyong; Hamdani, Saber; Essemine, Jemaa; Song, Qingfeng; Wang, Hongru

2017-01-01

Mining natural variations is a major approach to identify new options to improve crop light use efficiency. So far, successes in identifying photosynthetic parameters positively related to crop biomass accumulation through this approach are scarce, possibly due to the earlier emphasis on properties related to leaf instead of canopy photosynthetic efficiency. This study aims to uncover rice (Oryza sativa) natural variations to identify leaf physiological parameters that are highly correlated with biomass accumulation, a surrogate of canopy photosynthesis. To do this, we systematically investigated 14 photosynthetic parameters and four morphological traits in a rice population, which consists of 204 U.S. Department of Agriculture-curated minicore accessions collected globally and 11 elite Chinese rice cultivars in both Beijing and Shanghai. To identify key components responsible for the variance of biomass accumulation, we applied a stepwise feature-selection approach based on linear regression models. Although there are large variations in photosynthetic parameters measured in different environments, we observed that photosynthetic rate under low light (Alow) was highly related to biomass accumulation and also exhibited high genomic inheritability in both environments, suggesting its great potential to be used as a target for future rice breeding programs. Large variations in Alow among modern rice cultivars further suggest the great potential of using this parameter in contemporary rice breeding for the improvement of biomass and, hence, yield potential. PMID:28739819

Comparative study of endophytic and endophytic diazotrophic bacterial communities across rice landraces grown in the highlands of northern Thailand.

PubMed

Rangjaroen, Chakrapong; Rerkasem, Benjavan; Teaumroong, Neung; Sungthong, Rungroch; Lumyong, Saisamorn

2014-01-01

Communities of bacterial endophytes within the rice landraces cultivated in the highlands of northern Thailand were studied using fingerprinting data of 16S rRNA and nifH genes profiling by polymerase chain reaction-denaturing gradient gel electrophoresis. The bacterial communities' richness, diversity index, evenness, and stability were varied depending on the plant tissues, stages of growth, and rice cultivars. These indices for the endophytic diazotrophic bacteria within the landrace rice Bue Wah Bo were significantly the lowest. The endophytic bacteria revealed greater diversity by cluster analysis with seven clusters compared to the endophytic diazotrophic bacteria (three clusters). Principal component analysis suggested that the endophytic bacteria showed that the community structures across the rice landraces had a higher stability than those of the endophytic diazotrophic bacteria. Uncultured bacteria were found dominantly in both bacterial communities, while higher generic varieties were observed in the endophytic diazotrophic bacterial community. These differences in bacterial communities might be influenced either by genetic variation in the rice landraces or the rice cultivation system, where the nitrogen input affects the endophytic diazotrophic bacterial community.

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

PubMed

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

2016-03-01

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

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

PubMed

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

2007-01-01

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

[Dynamics and combined injuries of main pest species in rice cropping zones of Yunnan, Southwest China].

PubMed

Dong, Kun; Dong, Yan; Wang, Hai-Long; Zhang, Li-Min; Zan, Qing-An; Chen, Bin; Li, Zheng-Yue

2014-01-01

A series of rice pest injuries (due to pathogens, insects, and weeds) were surveyed in 286 farmers' fields for major rice varieties of three rice cropping zones of Yunnan Province, Southwest China. The composition and dynamics of main pest species were analyzed, and the trend of rice pest succession in Yunnan was discussed based upon landmark publications. The results showed that the three rice cropping zones had different pest characteristics as regard to main species, dynamics and combined injuries. Sheath rot, bacterial leaf blight, rice stripe, leaf hoppers, armyworms and stem borers were serious in the japonica rice zone. Sheath blight and rice stripe were serious in the japonica-indica interlacing zone. Leaf blast, sheath blight, leaf folders and weeds above rice crop canopy were serious in the indica rice zone. False smut, plant hoppers and weeds below rice crop canopy were ubiquitous and serious in the three kinds of rice cropping zones. Many kinds of weed infestation emerged in the whole rice cropping seasons. Echinochloa crusgalli, Sagittaria pygmaea, Potamogeton distinctus and Spirodela polyrhiza were the main species of weeds in the rice cropping zones of Yunnan. Overall, levels of combined injuries due to pests in the japonica rice zone and the indica rice zone were higher than that in the japonica-indica interlacing zone. In terms of the trend of rice pest succession in Yunnan, injuries due to false smut, sheath blight and plant hoppers seemed to be in a worse tendency in all rice cropping zones of Yunnan, while dominants species of weeds in the paddy fields are shifting from the annual weeds to the perennial malignant weeds.

Fluid drag reduction and efficient self-cleaning with rice leaf and butterfly wing bioinspired surfaces

NASA Astrophysics Data System (ADS)

Bixler, Gregory D.; Bhushan, Bharat

2013-08-01

Researchers are continually inspired by living nature to solve complex challenges. For example, unique surface characteristics of rice leaves and butterfly wings combine the shark skin (anisotropic flow leading to low drag) and lotus leaf (superhydrophobic and self-cleaning) effects, producing the so-called rice and butterfly wing effect. In this paper, we present an overview of rice leaf and butterfly wing fluid drag and self-cleaning studies. In addition, we examine two other promising aquatic surfaces in nature known for such properties, including fish scales and shark skin. Morphology, drag, self-cleaning, contact angle, and contact angle hysteresis data are presented to understand the role of wettability, viscosity, and velocity. Liquid repellent coatings are utilized to recreate or combine various effects. Discussion is provided along with conceptual models describing the role of surface structures related to low drag, self-cleaning, and antifouling properties. Modeling provides design guidance when developing novel low drag and self-cleaning surfaces for applications in the medical, marine, and industrial fields.

Transcriptional profile of genes involved in ascorbate glutathione cycle in senescing leaves for an early senescence leaf (esl) rice mutant.

PubMed

Li, Zhaowei; Su, Da; Lei, Bingting; Wang, Fubiao; Geng, Wei; Pan, Gang; Cheng, Fangmin

2015-03-15

To clarify the complex relationship between ascorbate-glutathione (AsA-GSH) cycle and H2O2-induced leaf senescence, the genotype-dependent difference in some senescence-related physiological parameters and the transcript levels and the temporal patterns of genes involved in the AsA-GSH cycle during leaf senescence were investigated using two rice genotypes, namely, the early senescence leaf (esl) mutant and its wild type. Meanwhile, the triggering effect of exogenous H2O2 on the expression of OsAPX genes was examined using detached leaves. The results showed that the esl mutant had higher H2O2 level than its wild type at the initial stage of leaf senescence. At transcriptional level, the association of expression of various genes involved in the AsA-GSH cycle with leaf senescence was isoform dependent. For OsAPXs, the transcripts of two cytosolic OsAPX genes (OsAPX1 and OsAPX2), thylakoid-bound OsAPX8, chloroplastic OsAPX7 and peroxisomal OsAPX4 exhibited remarkable genotype-dependent variation in their expression levels and temporal patterns during leaf senescence, there were significantly increasing transcripts of OsAXP1 and OsAPX7, severely repressed transcripts of OsAPX4 and OsAPX8 for the esl rice at the initial leaf senescence. In contrast, the repressing transcript of OsAPX8 was highly sensitive to the increasing H2O2 level in the senescing rice leaves, while higher H2O2 concentration resulted in the enhancing transcripts of two cytosolic OsAPX genes, OsAPX7 transcript was greatly variable with different H2O2 concentrations and incubating duration, suggesting that the different OsAPXs isoforms played a complementary role in perceiving and scavenging H2O2 accumulation at various H2O2 concentrations during leaf senescence. Higher H2O2 level, increased AsA level, higher activities of APX and glutathione reductase (GR), and relatively stable GSH content during the entire sampling period in the leaves of esl mutant implied that a close interrelationship existed

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

PubMed

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

2018-06-01

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

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

PubMed Central

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

2016-01-01

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

Baby leaf lettuce germplasm enhancement: developing diverse populations with resistance to bacterial leaf spot caused by Xanthomonas campestris pv. vitians

USDA-ARS?s Scientific Manuscript database

Baby leaf lettuce cultivars with resistance to bacterial leaf spot (BLS) caused by Xanthomonas campestris pv. vitians (Xcv) are needed to reduce crop losses. The objectives of this research were to assess the genetic diversity for BLS resistance in baby leaf lettuce cultivars and to select early gen...

Proteomic Analysis Reveals Coordinated Regulation of Anthocyanin Biosynthesis through Signal Transduction and Sugar Metabolism in Black Rice Leaf.

PubMed

Chen, Linghua; Huang, Yining; Xu, Ming; Cheng, Zuxin; Zheng, Jingui

2017-12-15

Black rice ( Oryza sativa L.) is considered to be a healthy food due to its high content of anthocyanins in the pericarp. The synthetic pathway of anthocyanins in black rice grains has been identified, however, the proteomic profile of leaves during grain development is still unclear. Here, isobaric Tags Relative and Absolute Quantification (iTRAQ) MS/MS was carried out to identify statistically significant changes of leaf proteome in the black rice during grain development. Throughout three sequential developmental stages, a total of 3562 proteins were detected and 24 functional proteins were differentially expressed 3-10 days after flowering (DAF). The detected proteins are known to be involved in various biological processes and most of these proteins were related to gene expression regulatory (33.3%), signal transduction (16.7%) and developmental regulation and hormone-like proteins (12.5%). The coordinated changes were consistent with changes in regulatory proteins playing a leading role in leaves during black rice grain development. This indicated that signal transduction between leaves and grains may have an important role in anthocyanin biosynthesis and accumulation during grain development of black rice. In addition, four identified up-regulated proteins associated with starch metabolism suggested that the remobilization of nutrients for starch synthesis plays a potential role in anthocyanin biosynthesis of grain. The mRNA transcription for eight selected proteins was validated with quantitative real-time PCR. Our results explored the proteomics of the coordination between leaf and grain in anthocyanins biosynthesis of grain, which might be regulated by signal transduction and sugar metabolism in black rice leaf.

Proteomic Analysis Reveals Coordinated Regulation of Anthocyanin Biosynthesis through Signal Transduction and Sugar Metabolism in Black Rice Leaf

PubMed Central

Chen, Linghua; Huang, Yining; Xu, Ming; Cheng, Zuxin; Zheng, Jingui

2017-01-01

Black rice (Oryza sativa L.) is considered to be a healthy food due to its high content of anthocyanins in the pericarp. The synthetic pathway of anthocyanins in black rice grains has been identified, however, the proteomic profile of leaves during grain development is still unclear. Here, isobaric Tags Relative and Absolute Quantification (iTRAQ) MS/MS was carried out to identify statistically significant changes of leaf proteome in the black rice during grain development. Throughout three sequential developmental stages, a total of 3562 proteins were detected and 24 functional proteins were differentially expressed 3–10 days after flowering (DAF). The detected proteins are known to be involved in various biological processes and most of these proteins were related to gene expression regulatory (33.3%), signal transduction (16.7%) and developmental regulation and hormone-like proteins (12.5%). The coordinated changes were consistent with changes in regulatory proteins playing a leading role in leaves during black rice grain development. This indicated that signal transduction between leaves and grains may have an important role in anthocyanin biosynthesis and accumulation during grain development of black rice. In addition, four identified up-regulated proteins associated with starch metabolism suggested that the remobilization of nutrients for starch synthesis plays a potential role in anthocyanin biosynthesis of grain. The mRNA transcription for eight selected proteins was validated with quantitative real-time PCR. Our results explored the proteomics of the coordination between leaf and grain in anthocyanins biosynthesis of grain, which might be regulated by signal transduction and sugar metabolism in black rice leaf. PMID:29244752

CLD1/SRL1 modulates leaf rolling by affecting cell wall formation, epidermis integrity and water homeostasis in rice.

PubMed

Li, Wen-Qiang; Zhang, Min-Juan; Gan, Peng-Fei; Qiao, Lei; Yang, Shuai-Qi; Miao, Hai; Wang, Gang-Feng; Zhang, Mao-Mao; Liu, Wen-Ting; Li, Hai-Feng; Shi, Chun-Hai; Chen, Kun-Ming

2017-12-01

Leaf rolling is considered as one of the most important agronomic traits in rice breeding. It has been previously reported that SEMI-ROLLED LEAF 1 (SRL1) modulates leaf rolling by regulating the formation of bulliform cells in rice (Oryza sativa); however, the regulatory mechanism underlying SRL1 has yet to be further elucidated. Here, we report the functional characterization of a novel leaf-rolling mutant, curled leaf and dwarf 1 (cld1), with multiple morphological defects. Map-based cloning revealed that CLD1 is allelic with SRL1, and loses function in cld1 through DNA methylation. CLD1/SRL1 encodes a glycophosphatidylinositol (GPI)-anchored membrane protein that modulates leaf rolling and other aspects of rice growth and development. The cld1 mutant exhibits significant decreases in cellulose and lignin contents in secondary cell walls of leaves, indicating that the loss of function of CLD1/SRL1 affects cell wall formation. Furthermore, the loss of CLD1/SRL1 function leads to defective leaf epidermis such as bulliform-like epidermal cells. The defects in leaf epidermis decrease the water-retaining capacity and lead to water deficits in cld1 leaves, which contribute to the main cause of leaf rolling. As a result of the more rapid water loss and lower water content in leaves, cld1 exhibits reduced drought tolerance. Accordingly, the loss of CLD1/SRL1 function causes abnormal expression of genes and proteins associated with cell wall formation, cuticle development and water stress. Taken together, these findings suggest that the functional roles of CLD1/SRL1 in leaf-rolling regulation are closely related to the maintenance of cell wall formation, epidermal integrity and water homeostasis. © 2017 The Authors The Plant Journal © 2017 John Wiley & Sons Ltd.

Efficacy of bacillus biocontrol agents for management of sheath blight and narrow brown leaf spot in organic rice

USDA-ARS?s Scientific Manuscript database

Organic rice production has significantly increased in the U. S. over the last decade. Growers lack effective tools to manage sheath blight, caused by Rhizoctonia solani, and narrow brown leaf spot (NBLS), caused by Cercospora janseana, two major diseases affecting organic rice production. An experi...

Bacterial Leaf Spot of Lettuce: Request for Samples

USDA-ARS?s Scientific Manuscript database

Bacterial leaf spot of lettuce caused by by Xanthomonas campestris pv. vitians has been affecting coastal California crops for many years and has become a chronic problem. Differences in pathogen genotypes have been demonstrated and correlated to disease responses on resistant and susceptible cultiv...

Tree Leaf Bacterial Community Structure and Diversity Differ along a Gradient of Urban Intensity

PubMed Central

Messier, Christian; Kembel, Steven W.

2017-01-01

ABSTRACT Tree leaf-associated microbiota have been studied in natural ecosystems but less so in urban settings, where anthropogenic pressures on trees could impact microbial communities and modify their interaction with their hosts. Additionally, trees act as vectors spreading bacterial cells in the air in urban environments due to the density of microbial cells on aerial plant surfaces. Characterizing tree leaf bacterial communities along an urban gradient is thus key to understand the impact of anthropogenic pressures on urban tree-bacterium interactions and on the overall urban microbiome. In this study, we aimed (i) to characterize phyllosphere bacterial communities of seven tree species in urban environments and (ii) to describe the changes in tree phyllosphere bacterial community structure and diversity along a gradient of increasing urban intensity and at two degrees of tree isolation. Our results indicate that, as anthropogenic pressures increase, urban leaf bacterial communities show a reduction in the abundance of the dominant class in the natural plant microbiome, the Alphaproteobacteria. Our work in the urban environment here reveals that the structures of leaf bacterial communities differ along the gradient of urban intensity. The diversity of phyllosphere microbial communities increases at higher urban intensity, also displaying a greater number and variety of associated indicator taxa than the low and medium urban gradient sites. In conclusion, we find that urban environments influence tree bacterial community composition, and our results suggest that feedback between human activity and plant microbiomes could shape urban microbiomes. IMPORTANCE In natural forests, tree leaf surfaces host diverse bacterial communities whose structure and composition are primarily driven by host species identity. Tree leaf bacterial diversity has also been shown to influence tree community productivity, a key function of terrestrial ecosystems. However, most urban

Tree Leaf Bacterial Community Structure and Diversity Differ along a Gradient of Urban Intensity.

PubMed

Laforest-Lapointe, Isabelle; Messier, Christian; Kembel, Steven W

2017-01-01

Tree leaf-associated microbiota have been studied in natural ecosystems but less so in urban settings, where anthropogenic pressures on trees could impact microbial communities and modify their interaction with their hosts. Additionally, trees act as vectors spreading bacterial cells in the air in urban environments due to the density of microbial cells on aerial plant surfaces. Characterizing tree leaf bacterial communities along an urban gradient is thus key to understand the impact of anthropogenic pressures on urban tree-bacterium interactions and on the overall urban microbiome. In this study, we aimed (i) to characterize phyllosphere bacterial communities of seven tree species in urban environments and (ii) to describe the changes in tree phyllosphere bacterial community structure and diversity along a gradient of increasing urban intensity and at two degrees of tree isolation. Our results indicate that, as anthropogenic pressures increase, urban leaf bacterial communities show a reduction in the abundance of the dominant class in the natural plant microbiome, the Alphaproteobacteria . Our work in the urban environment here reveals that the structures of leaf bacterial communities differ along the gradient of urban intensity. The diversity of phyllosphere microbial communities increases at higher urban intensity, also displaying a greater number and variety of associated indicator taxa than the low and medium urban gradient sites. In conclusion, we find that urban environments influence tree bacterial community composition, and our results suggest that feedback between human activity and plant microbiomes could shape urban microbiomes. IMPORTANCE In natural forests, tree leaf surfaces host diverse bacterial communities whose structure and composition are primarily driven by host species identity. Tree leaf bacterial diversity has also been shown to influence tree community productivity, a key function of terrestrial ecosystems. However, most urban microbiome

Brassinosteroid insensitive 1-associated kinase 1 (OsI-BAK1) is associated with grain filling and leaf development in rice.

PubMed

Khew, Choy-Yuen; Teo, Chin-Jit; Chan, Wai-Sun; Wong, Hann-Ling; Namasivayam, Parameswari; Ho, Chai-Ling

2015-06-15

Brassinosteroid Insensitive 1 (BRI1)-Associated Kinase I (BAK1) has been reported to interact with BRI1 for brassinosteroid (BR) perception and signal transduction that regulate plant growth and development. The aim of this study is to investigate the functions of a rice OsBAK1 homologue, designated as OsI-BAK1, which is highly expressed after heading. Silencing of OsI-BAK1 in rice plants produced a high number of undeveloped green and unfilled grains compared to the untransformed plants. Histological analyses demonstrated that embryos were either absent or retarded in their development in these unfilled rice grains of OsI-BAK1 RNAi plants. Down regulation of OsI-BAK1 caused a reduction in cell number and enlargement in leaf bulliform cells. Furthermore, transgenic rice plants overexpressing OsI-BAK1 were demonstrated to have corrugated and twisted leaves probably due to increased cell number that caused abnormal bulliform cell structure which were enlarged and plugged deep into leaf epidermis. The current findings suggest that OsI-BAK1 may play an important role in the developmental processes of rice grain filling and leaf cell including the bulliform cells. Copyright © 2015 Elsevier GmbH. All rights reserved.

An anti-bacterial approach to nanoscale roughening of biomimetic rice-like pattern PP by thermal annealing

NASA Astrophysics Data System (ADS)

Jafari Nodoushan, Emad; Ebrahimi, Nadereh Golshan; Ayazi, Masoumeh

2017-11-01

In this paper, we introduced thermal annealing treatment as an effective way of increasing the nanoscale roughness of a semi-crystalline polymer surface. Annealing treatment applied to a biomimetic microscale pattern of rice leaf to achieve a superhydrophobic surface with a hierarchical roughness. Resulted surfaces was characterized by XRD, AFM and FE-SEM instruments and showed an increase of roughness and cristallinity within both time and temperature of treatment. These two parameters also impact on measured static contact angle up to 158°. Bacterial attachment potency has an inverse relationship with the similarity of surface pattern dimensions and bacterial size and due to that, thermal annealing could be an effective way to create anti-bacterial surface beyond its effect on water repellency. Point in case, the anti-bacterial properties of produced water-repellence surfaces of PP were measured and counted colonies of both gram-negative (E. coli) and gram-positive (S. aureus) bacteria reduced with the nature of PP and hierarchical pattern on that. Anti-bacterial characterization of the resulted surface reveals a stunning reduction in adhesion of gram-positive bacteria to the surface. S. aureus reduction rates equaled to 95% and 66% when compared to control blank plate and smooth surface of PP. Moreover, it also could affect the other type of bacteria, gram-negative (E. coli). In the latter case, adhesion reduction rates calculated 66% and 53% when against to the same controls, respectively.

Suppression of bacterial infection in rice by treatment with a sulfated peptide.

PubMed

Wei, Tong; Chern, Mawsheng; Liu, Furong; Ronald, Pamela C

2016-12-01

The rice XA21 receptor kinase confers robust resistance to bacterial blight disease caused by Xanthomonas oryzae pv. oryzae (Xoo). A tyrosine-sulfated peptide from Xoo, called RaxX, triggers XA21-mediated immune responses, including the production of ethylene and reactive oxygen species and the induction of defence gene expression. It has not been tested previously whether these responses confer effective resistance to Xoo. Here, we describe a newly established post-inoculation treatment assay that facilitates investigations into the effect of the sulfated RaxX peptide in planta. In this assay, rice plants were inoculated with a virulent strain of Xoo and then treated with the RaxX peptide 2 days after inoculation. We found that post-inoculation treatment of XA21 plants with the sulfated RaxX peptide suppresses the development of Xoo infection in XA21 rice plants. The treated plants display restricted lesion development and reduced bacterial growth. Our findings demonstrate that exogenous application of sulfated RaxX activates XA21-mediated immunity in planta, and provides a potential strategy for the control of bacterial disease in the field. © 2016 BSPP and John Wiley & Sons Ltd.

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

PubMed

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

2009-07-01

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

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

PubMed

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

2018-01-01

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

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

PubMed Central

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

2018-01-01

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

Metabolic Profiling and Physiological Analysis of a Novel Rice Introgression Line with Broad Leaf Size

PubMed Central

Zhao, Xiuqin; Zhang, Guilian; Wang, Yun; Zhang, Fan; Wang, Wensheng; Zhang, Wenhao; Fu, Binying; Xu, Jianlong; Li, Zhikang

2015-01-01

A rice introgression line, NIL-SS1, and its recurrent parent, Teqing, were used to investigate the influence of the introgression segment on plant growth. The current research showed NIL-SS1 had an increased flag leaf width, total leaf area, spikelet number per panicle and grain yield, but a decreased photosynthetic rate. The metabolite differences in NIL-SS1 and Teqing at different developmental stages were assessed using gas chromatography—mass spectrometry technology. Significant metabolite differences were observed across the different stages. NIL-SS1 increased the plant leaf nitrogen content, and the greatest differences between NIL-SS1 and Teqing occurred at the booting stage. Compared to Teqing, the metabolic phenotype of NIL-SS1 at the booting stage has closer association with those at the flowering stage. The introgression segment induced more active competition for sugars and organic acids (OAs) from leaves to the growing young spikes, which resulted in more spikelet number per plant (SNP). The results indicated the introgression segment could improve rice grain yield by increasing the SNP and total leaf area per plant, which resulted from the higher plant nitrogen content across growth stages and stronger competition for sugars and OAs of young spikes at the booting stage. PMID:26713754

Morphological and molecular characterization of Magnaporthe oryzae (fungus) from infected rice leaf samples

NASA Astrophysics Data System (ADS)

Muni, Nurulhidayah Mat; Nadarajah, Kalaivani

2014-09-01

Magnaporthe oryzae is a plant-pathogenic fungus that causes a serious disease affecting rice called rice blast. Outbreaks of rice blast have been a threat to the global production of rice. This fungal disease is estimated to cause production losses of US55 million each year in South and Southeast Asia. It has been used as a primary model for elucidating various aspects of the host-pathogen interaction with its host. We have isolated five isolates of Magnaporthe oryzae from diseased leaf samples obtained from the field at Kompleks Latihan MADA, Kedah, Malaysia. We have identified the isolates using morphological and microscopic studies on the fungal spores and the lesions on the diseased leaves. Amplification of the internal transcribed spacer (ITS) was carried out with universal primers ITS1 and ITS4. The sequence of each isolates showed at least 99% nucleotide identity with the corresponding sequence in GenBank for Magnaporthe oryzae.

SEMI-ROLLED LEAF1 Encodes a Putative Glycosylphosphatidylinositol-Anchored Protein and Modulates Rice Leaf Rolling by Regulating the Formation of Bulliform Cells1[W][OA

PubMed Central

Xiang, Jing-Jing; Zhang, Guang-Heng; Qian, Qian; Xue, Hong-Wei

2012-01-01

Leaf rolling is an important agronomic trait in rice (Oryza sativa) breeding and moderate leaf rolling maintains the erectness of leaves and minimizes shadowing between leaves, leading to improved photosynthetic efficiency and grain yields. Although a few rolled-leaf mutants have been identified and some genes controlling leaf rolling have been isolated, the molecular mechanisms of leaf rolling still need to be elucidated. Here we report the isolation and characterization of SEMI-ROLLED LEAF1 (SRL1), a gene involved in the regulation of leaf rolling. Mutants srl1-1 (point mutation) and srl1-2 (transferred DNA insertion) exhibit adaxially rolled leaves due to the increased numbers of bulliform cells at the adaxial cell layers, which could be rescued by complementary expression of SRL1. SRL1 is expressed in various tissues and is expressed at low levels in bulliform cells. SRL1 protein is located at the plasma membrane and predicted to be a putative glycosylphosphatidylinositol-anchored protein. Moreover, analysis of the gene expression profile of cells that will become epidermal cells in wild type but probably bulliform cells in srl1-1 by laser-captured microdissection revealed that the expression of genes encoding vacuolar H+-ATPase (subunits A, B, C, and D) and H+-pyrophosphatase, which are increased during the formation of bulliform cells, were up-regulated in srl1-1. These results provide the transcript profile of rice leaf cells that will become bulliform cells and demonstrate that SRL1 regulates leaf rolling through inhibiting the formation of bulliform cells by negatively regulating the expression of genes encoding vacuolar H+-ATPase subunits and H+-pyrophosphatase, which will help to understand the mechanism regulating leaf rolling. PMID:22715111

Microwave Backscatter and Attenuation Dependence of Leaf Area Index for Flooded Rice Fields

NASA Technical Reports Server (NTRS)

Durden, Stephen L.; Morrissey, Leslie A.; Livingston, Gerald P.

1995-01-01

Wetlands are important for their role in global climate as a source of methane and other reduced trace gases. As part of an effort to determine whether radar is suitable for wetland vegetation monitoring, we have studied the dependence of microwave backscatter and attenuation on leaf area index (LAI) for flooded rice fields. We find that the radar return from a flooded rice field does show dependence on LAI. In particular, the C-band VV cross section per unit area decreases with increasing LAI. A simple model for scattering from rice fields is derived and fit to the observed HH and VV data. The model fit provides insight into the relation of backscatter to LAI and is also used to calculate the canopy path attenuation as a function of LAI.

The Brown Midrib Leaf (bml) Mutation in Rice (Oryza sativa L.) Causes Premature Leaf Senescence and the Induction of Defense Responses.

PubMed

Akhter, Delara; Qin, Ran; Nath, Ujjal Kumar; Alamin, Md; Jin, Xiaoli; Shi, Chunhai

2018-04-09

Isolating and characterizing mutants with altered senescence phenotypes is one of the ways to understand the molecular basis of leaf aging. Using ethyl methane sulfonate mutagenesis, a new rice ( Oryza sativa ) mutant, brown midrib leaf ( bml ), was isolated from the indica cultivar 'Zhenong34'. The bml mutants had brown midribs in their leaves and initiated senescence prematurely, at the onset of heading. The mutants had abnormal cells with degraded chloroplasts and contained less chlorophyll compared to the wild type (WT). The bml mutant showed excessive accumulation of reactive oxygen species (ROS), increased activities of superoxide dismutase, catalase, and malondialdehyde, upregulation of senescence-induced STAY-GREEN genes and senescence-related transcription factors, and down regulation of photosynthesis-related genes. The levels of abscisic acid (ABA) and jasmonic acid (JA) were increased in bml with the upregulation of some ABA and JA biosynthetic genes. In pathogen response, bml demonstrated higher resistance against Xanthomonas oryzae pv. oryzae and upregulation of four pathogenesis-related genes compared to the WT. A genetic study confirmed that the bml trait was caused by a single recessive nuclear gene ( BML ). A map-based cloning using insertion/deletion markers confirmed that BML was located in the 57.32kb interval between the L5IS7 and L5IS11 markers on the short arm of chromosome 5. A sequence analysis of the candidate region identified a 1 bp substitution (G to A) in the 5'-UTR (+98) of bml . BML is a candidate gene associated with leaf senescence, ROS regulation, and disease response, also involved in hormone signaling in rice. Therefore, this gene might be useful in marker-assisted backcrossing/gene editing to improve rice cultivars.

[Effects of alkaline fertilizer on cadmium content in rice and paddy soil.

PubMed

Zhang, Liang Liang; Fan, Xiao Lin; Zhang, Li Dan; Liu, Fang

2016-03-01

A field plot trial was conducted at Songbai Village, Chenzhou, Hunan Province to exa-mine the effects of alkaline fertilizer with and without combination application of bacterial regent on cadmium accumulation in rice and paddy soil. Compared with the conventional fertilizer, the alkaline fertilizer reduced the available cadmium content in soil at the tillering, filling and the harvest stages by 8.3%, 6.7% and 16.4% respectively. Compared with the Cd content in soil before transplanting, it was reduced by 7.2% at harvest time in alkaline fertilizer treatment, while increased by 11.0% in the conventional fertilizer treatment. The available cadmium content in soil was increased by 1.2% to 23.3% by bacterial regent. Compared with the conventional fertilizer, the cadmium content of root, stem sheath, leaf, grain and brown rice of the alkaline fertilizer treatment reduced by 54.9%, 56.6%, 41.8%, 62.7% and 67.6% respectively. The alkaline fertilizer treatment combined with bacterial regent increased the cadmium content of brown rice by 63.2%. It was concluded that the alkaline fertilizer could significantly reduce the available cadmium content in both soil and the different organs of the rice, however, when it was combined with bacterial regent together, the effect of alkaline fertilizer to reduce Cd content of brown rice would be declined.

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

PubMed Central

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

2012-01-01

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

Germplasm Evaluation for Resistance and Monitoring Bacterial Panicle Blight Disease of Rice in Arkansas, 2016

USDA-ARS?s Scientific Manuscript database

Bacterial panicle blight (BPB), caused by a bacterial pathogen, mainly Burkholderia glumae, has posed a higher level of threat to rice production worldwide in recent years. Here we report the response of over 300 entries evaluated by artificially inoculating with a bacterial suspension under field c...

Overexpression of microRNA319 impacts leaf morphogenesis and leads to enhanced cold tolerance in rice (Oryza sativa L.).

PubMed

Yang, Chunhua; Li, Dayong; Mao, Donghai; Liu, Xue; Ji, Chengjun; Li, Xiaobing; Zhao, Xianfeng; Cheng, Zhukuan; Chen, Caiyan; Zhu, Lihuang

2013-12-01

MicroRNA319 (miR319) family is one of the conserved microRNA (miRNA) families among diverse plant species. It has been reported that miR319 regulates plant development in dicotyledons, but little is known at present about its functions in monocotyledons. In rice (Oryza sativa L.), the MIR319 gene family comprises two members, Osa-MIR319a and Osa-MIR319b. Here, we report an expression pattern analysis and a functional characterization of the two Osa-MIR319 genes in rice. We found that overexpressing Osa-MIR319a and Osa-MIR319b in rice both resulted in wider leaf blades. Leaves of osa-miR319 overexpression transgenic plants showed an increased number of longitudinal small veins, which probably accounted for the increased leaf blade width. In addition, we observed that overexpressing osa-miR319 led to enhanced cold tolerance (4 °C) after chilling acclimation (12 °C) in transgenic rice seedlings. Notably, under both 4 and 12 °C low temperatures, Osa-MIR319a and Osa-MIR319b were down-regulated while the expression of miR319-targeted genes was induced. Furthermore, genetically down-regulating the expression of either of the two miR319-targeted genes, OsPCF5 and OsPCF8, in RNA interference (RNAi) plants also resulted in enhanced cold tolerance after chilling acclimation. Our findings in this study demonstrate that miR319 plays important roles in leaf morphogenesis and cold tolerance in rice. © 2013 John Wiley & Sons Ltd.

Characterization and fine mapping of a light-dependent leaf lesion mimic mutant 1 in rice.

PubMed

Wang, Jing; Ye, Bangquan; Yin, Junjie; Yuan, Can; Zhou, Xiaogang; Li, Weitao; He, Min; Wang, Jichun; Chen, Weilan; Qin, Peng; Ma, Bintian; Wang, Yuping; Li, Shigui; Chen, Xuewei

2015-12-01

Plants that spontaneously produce lesion mimics or spots, without any signs of obvious adversity, such as pesticide and mechanical damage, or pathogen infection, are so-called lesion mimic mutants (lmms). In rice, many lmms exhibit enhanced resistance to pathogens, which provides a unique opportunity to uncover the molecular mechanism underlying lmms. We isolated a rice light-dependent leaf lesion mimic mutant 1 (llm1). Lesion spots appeared in the leaves of the llm1 mutant at the tillering stage. Furthermore, the mutant llm1 had similar agronomic traits to wild type rice. Trypan blue and diamiobenzidine staining analyses revealed that the lesion spot formation on the llm1 mutant was due to programmed cell death and reactive oxygen species. The chloroplasts were severely damaged in the llm1 mutant, suggesting that chloroplast damage was associated with the formation of lesion spots in llm1. More importantly, llm1 exhibited enhanced resistance to bacterial blight pathogens within increased expression of pathogenesis related genes (PRs). Using a map-based cloning approach, we delimited the LLM1 locus to a 121-kb interval between two simple sequence repeat markers, RM17470 and RM17473, on chromosome 4. We sequenced the candidate genes on the interval and found that a base mutation had substituted adenine phosphate for thymine in the last exon of LOC_Os04g52130, which led to an amino acid change (Asp(388) to Val) in the llm1 mutant. Our investigation showed that the putative coproporphyrinogen III oxidase (CPOX) encoded by LOC_Os04g52130 was produced by LLM1 and that amino acid Asp(388) was essential for CPOX function. Our study provides the basis for further investigations into the mechanism underlying lesion mimic initiation associated with LLM1. Copyright © 2015 Elsevier Masson SAS. All rights reserved.

Rice leaf growth and water potential are resilient to evaporative demand and soil water deficit once the effects of root system are neutralized.

PubMed

Parent, Boris; Suard, Benoît; Serraj, Rachid; Tardieu, François

2010-08-01

Rice is known to be sensitive to soil water deficit and evaporative demand, with a greatest sensitivity of lowland-adapted genotypes. We have analysed the responses of plant water relations and of leaf elongation rate (LER) to soil water status and evaporative demand in seven rice genotypes belonging to different species, subspecies, either upland- or lowland-adapted. In the considered range of soil water potential (0 to -0.6 MPa), stomatal conductance was controlled in such a way that the daytime leaf water potential was similar in well-watered, droughted or flooded conditions (isohydric behaviour). A low sensitivity of LER to evaporative demand was observed in the same three conditions, with small differences between genotypes and lower sensitivity than in maize. The sensitivity of LER to soil water deficit was similar to that of maize. A tendency towards lower sensitivities was observed in upland than lowland genotypes but with smaller differences than expected. We conclude that leaf water status and leaf elongation of rice are not particularly sensitive to water deficit. The main origin of drought sensitivity in rice may be its poor root system, whose effect was alleviated in the study presented here by growing plants in pots whose soil was entirely colonized by roots of all genotypes.

Transgenic rice expressing Allium sativum leaf agglutinin (ASAL) exhibits high-level resistance against major sap-sucking pests

PubMed Central

Yarasi, Bharathi; Sadumpati, Vijayakumar; Immanni, China Pasalu; Vudem, Dasavantha Reddy; Khareedu, Venkateswara Rao

2008-01-01

Background Rice (Oryza sativa) productivity is adversely impacted by numerous biotic and abiotic factors. An approximate 52% of the global production of rice is lost annually owing to the damage caused by biotic factors, of which ~21% is attributed to the attack of insect pests. In this paper we report the isolation, cloning and characterization of Allium sativum leaf agglutinin (asal) gene, and its expression in elite indica rice cultivars using Agrobacterium-mediated genetic transformation method. The stable transgenic lines, expressing ASAL, showed explicit resistance against major sap-sucking pests. Results Allium sativum leaf lectin gene (asal), coding for mannose binding homodimeric protein (ASAL) from garlic plants, has been isolated and introduced into elite indica rice cultivars susceptible to sap-sucking insects, viz., brown planthopper (BPH), green leafhopper (GLH) and whitebacked planthopper (WBPH). Embryogenic calli of rice were co-cultivated with Agrobacterium harbouring pSB111 super-binary vector comprising garlic lectin gene asal along with the herbicide resistance gene bar, both under the control of CaMV35S promoter. PCR and Southern blot analyses confirmed stable integration of transgenes into the genomes of rice plants. Northern and western blot analyses revealed expression of ASAL in different transgenic rice lines. In primary transformants, the level of ASAL protein, as estimated by enzyme-linked immunosorbent assay, varied between 0.74% and 1.45% of the total soluble proteins. In planta insect bioassays on transgenic rice lines revealed potent entomotoxic effects of ASAL on BPH, GLH and WBPH insects, as evidenced by significant decreases in the survival, development and fecundity of the insects. Conclusion In planta insect bioassays were carried out on asal transgenic rice lines employing standard screening techniques followed in conventional breeding for selection of insect resistant plants. The ASAL expressing rice plants, bestowed with high

Transgenic rice expressing Allium sativum leaf agglutinin (ASAL) exhibits high-level resistance against major sap-sucking pests.

PubMed

Yarasi, Bharathi; Sadumpati, Vijayakumar; Immanni, China Pasalu; Vudem, Dasavantha Reddy; Khareedu, Venkateswara Rao

2008-10-14

Rice (Oryza sativa) productivity is adversely impacted by numerous biotic and abiotic factors. An approximate 52% of the global production of rice is lost annually owing to the damage caused by biotic factors, of which approximately 21% is attributed to the attack of insect pests. In this paper we report the isolation, cloning and characterization of Allium sativum leaf agglutinin (asal) gene, and its expression in elite indica rice cultivars using Agrobacterium-mediated genetic transformation method. The stable transgenic lines, expressing ASAL, showed explicit resistance against major sap-sucking pests. Allium sativum leaf lectin gene (asal), coding for mannose binding homodimeric protein (ASAL) from garlic plants, has been isolated and introduced into elite indica rice cultivars susceptible to sap-sucking insects, viz., brown planthopper (BPH), green leafhopper (GLH) and whitebacked planthopper (WBPH). Embryogenic calli of rice were co-cultivated with Agrobacterium harbouring pSB111 super-binary vector comprising garlic lectin gene asal along with the herbicide resistance gene bar, both under the control of CaMV35S promoter. PCR and Southern blot analyses confirmed stable integration of transgenes into the genomes of rice plants. Northern and western blot analyses revealed expression of ASAL in different transgenic rice lines. In primary transformants, the level of ASAL protein, as estimated by enzyme-linked immunosorbent assay, varied between 0.74% and 1.45% of the total soluble proteins. In planta insect bioassays on transgenic rice lines revealed potent entomotoxic effects of ASAL on BPH, GLH and WBPH insects, as evidenced by significant decreases in the survival, development and fecundity of the insects. In planta insect bioassays were carried out on asal transgenic rice lines employing standard screening techniques followed in conventional breeding for selection of insect resistant plants. The ASAL expressing rice plants, bestowed with high entomotoxic

Identification and characterization of a gibberellin-regulated protein, which is ASR5, in the basal region of rice leaf sheaths.

PubMed

Takasaki, Hironori; Mahmood, Tariq; Matsuoka, Makoto; Matsumoto, Hiroshi; Komatsu, Setsuko

2008-04-01

Gibberellins (GAs) regulate growth and development in higher plants. To identify GA-regulated proteins during rice leaf sheath elongation, a proteomic approach was used. Proteins from the basal region of leaf sheath in rice seedling treated with GA(3) were analyzed by fluorescence two-dimensional difference gel electrophoresis. The levels of abscisic acid-stress-ripening-inducible 5 protein (ASR5), elongation factor-1 beta, translationally controlled tumor protein, fructose-bisphosphate aldolase and a novel protein increased; whereas the level of RuBisCO subunit binding-protein decreased by GA(3) treatment. ASR5 out of these six proteins was significantly regulated by GA(3) at the protein level but not at the mRNA level in the basal region of leaf sheaths. Since this protein is regulated not only by abscisic acid but also by GA(3), these results indicate that ASR5 might be involved in plant growth in addition to stress in the basal regions of leaf sheaths.

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

PubMed

Ohsumi, Akihiro; Hamasaki, Akihiro; Nakagawa, Hiroshi; Yoshida, Hiroe; Shiraiwa, Tatsuhiko; Horie, Takeshi

2007-02-01

Identification of physiological traits associated with leaf photosynthetic rate (Pn) is important for improving potential productivity of rice (Oryza sativa). The objectives of this study were to develop a model which can explain genotypic variation and ontogenetic change of Pn in rice under optimal conditions as a function of leaf nitrogen content per unit area (N) and stomatal conductance (g(s)), and to quantify the effects of interaction between N and g(s) on the variation of Pn. Pn, N and g(s) were measured at different developmental stages for the topmost fully expanded leaves in ten rice genotypes with diverse backgrounds grown in pots (2002) and in the field (2001 and 2002). A model of Pn that accounts for carboxylation and CO diffusion processes, and assumes that the ratio of internal conductance to g(s) is constant, was constructed, and its goodness of fit was examined. Considerable genotypic differences in Pn were evident for rice throughout development in both the pot and field experiments. The genotypic variation of Pn was correlated with that of g(s) at a given stage, and the change of Pn with plant development was closely related to the change of N. The variation of g(s) among genotypes was independent of that of N. The model explained well the variation in Pn of the ten genotypes grown under different conditions at different developmental stages. Conclusions The response of Pn to increased N differs with g(s), and the increase in Pn of genotypes with low g(s) is smaller than that of genotypes with high g(s). Therefore, simultaneous improvements of these two traits are essential for an effective breeding of rice genotypes with increased Pn.

Bacterial DNA Detected in Japanese Rice Wines and the Fermentation Starters.

PubMed

Terasaki, Momoka; Fukuyama, Akari; Takahashi, Yurika; Yamada, Masato; Nishida, Hiromi

2017-12-01

As Japanese rice wine (sake) brewing is not done aseptically, bacterial contamination is conceivable during the process of sake production. There are two types of the fermentation starter, sokujo-moto and yamahai-moto (kimoto). We identified bacterial DNA found in various sakes, the sokujo-moto and the yamahai-moto making just after sake yeast addition. Each sake has a unique variety of bacterial DNA not observed in other sakes. Although most bacterial DNA sequences detected in the sokujo-moto were found in sakes of different sake breweries, most bacterial DNA sequences detected in the yamahai-moto at the early stage of the starter fermentation were not detected in any sakes. Our findings demonstrate that various bacteria grow and then die during the process of sake brewing, as indicated by the presence of trace levels of bacterial DNA.

Bacterial Leaf Spot of Parsley: Characterization of a New Disease

USDA-ARS?s Scientific Manuscript database

Since 2002, a severe leaf spot disease on parsley has occurred throughout central coastal California and particularly in Monterey County. Two different bacterial pathogens (Pseudomonas syringae pv. apii, and P. syringae pv. coriandricola) have been associated these outbreaks on parsley. Our research...

OsMYB103L, an R2R3-MYB transcription factor, influences leaf rolling and mechanical strength in rice (Oryza sativa L.).

PubMed

Yang, Chunhua; Li, Dayong; Liu, Xue; Ji, Chengjun; Hao, Lili; Zhao, Xianfeng; Li, Xiaobing; Chen, Caiyan; Cheng, Zhukuan; Zhu, Lihuang

2014-06-06

The shape of grass leaves possesses great value in both agronomy and developmental biology research. Leaf rolling is one of the important traits in rice (Oryza sativa L.) breeding. MYB transcription factors are one of the largest gene families and have important roles in plant development, metabolism and stress responses. However, little is known about their functions in rice. In this study, we report the functional characterization of a rice gene, OsMYB103L, which encodes an R2R3-MYB transcription factor. OsMYB103L was localized in the nucleus with transactivation activity. Overexpression of OsMYB103L in rice resulted in a rolled leaf phenotype. Further analyses showed that expression levels of several cellulose synthase genes (CESAs) were significantly increased, as was the cellulose content in OsMYB103L overexpressing lines. Knockdown of OsMYB103L by RNA interference led to a decreased level of cellulose content and reduced mechanical strength in leaves. Meanwhile, the expression levels of several CESA genes were decreased in these knockdown lines. These findings suggest that OsMYB103L may target CESA genes for regulation of cellulose synthesis and could potentially be engineered for desirable leaf shape and mechanical strength in rice.

Influence of plant species and environmental conditions on epiphytic and endophytic pink-pigmented facultative methylotrophic bacterial populations associated with field-grown rice cultivars.

PubMed

Madhaiyan, Munusamy; Poonguzhali, Selvaraj; Sa, Tongmin

2007-10-01

The total methylotrophic population associated with rice plants from different cultivars was enumerated at three different stages: vegetative, flowering, and harvesting. The bacterial population in the leaf, rhizosphere soil, endophytic in the stem and roots, and epiphytic in the florets and grains were determined from four rice cultivars, Il-mi, Nam-pyeoung, O-dae, and Dong-jin, sampled from three different field sites. The methylotrophic bacteria isolated on AMS media containing 0.5% methanol as the sole carbon source uniformly showed three distinct morphologies, which were recorded as separate groups and their distribution among the various samples was determined using the ecophysiological index. The growth stage at the time of sampling had a more significant effect on the methylotrophic population and their distribution than the field site or cultivar. A similar effect was also observed for the PPFMs, where their population in different plant parts increased from V10 to R4 and then decreased towards stage R9. A canonical discriminant analysis of the PPFM population from different parts of rice showed clear variations among the cultivars, sampled sites, and growth stages, although the variations were more prominent among the growth stages.

Safety assessment of genetically modified rice expressing human serum albumin from urine metabonomics and fecal bacterial profile.

PubMed

Qi, Xiaozhe; Chen, Siyuan; Sheng, Yao; Guo, Mingzhang; Liu, Yifei; He, Xiaoyun; Huang, Kunlun; Xu, Wentao

2015-02-01

The genetically modified (GM) rice expressing human serum albumin (HSA) is used for non-food purposes; however, its food safety assessment should be conducted due to the probability of accidental mixture with conventional food. In this research, Sprague Dawley rats were fed diets containing 50% (wt/wt) GM rice expressing HSA or non-GM rice for 90 days. Urine metabolites were detected by (1)H NMR to examine the changes of the metabolites in the dynamic process of metabolism. Fecal bacterial profiles were detected by denaturing gradient gel electrophoresis to reflect intestinal health. Additionally, short chain fatty acids and fecal enzymes were investigated. The results showed that compared with rats fed the non-GM rice, some significant differences were observed in rats fed with the GM rice; however, these changes were not significantly different from the control diet group. Additionally, the gut microbiota was associated with blood indexes and urine metabolites. In conclusion, the GM rice diet is as safe as the traditional daily diet. Furthermore, urine metabonomics and fecal bacterial profiles provide a non-invasive food safety assessment rat model for genetically modified crops that are used for non-food/feed purposes. Fecal bacterial profiles have the potential for predicting the change of blood indexes in future. Copyright © 2014 Elsevier Ltd. All rights reserved.

Leaf Morphology and Ultrastructure Responses to Elevated O3 in Transgenic Bt (cry1Ab/cry1Ac) Rice and Conventional Rice under Fully Open-Air Field Conditions

PubMed Central

Li, Chunyan; Liu, Biao; Li, Chunhua; Zeng, Qing; Hao, Mingzhuo; Han, Zhengmin; Zhu, Jianguo; Li, Xiaogang; Shen, Wenjing

2013-01-01

Background Elevated tropospheric ozone severely affects not only yield but also the morphology, structure and physiological functions of plants. Because of concerns regarding the potential environmental risk of transgenic crops, it is important to monitor changes in transgenic insect-resistant rice under the projected high tropospheric ozone before its commercial release. Methodology/Principal Findings Using a free-air concentration enrichment (FACE) system, we investigated the changes in leaf morphology and leaf ultrastructure of two rice varieties grown in plastic pots, transgenic Bt Shanyou 63 (Bt-SY63, carrying a fusion gene of cry1Ab and cry1Ac) and its non-transgenic counterpart (SY63), in elevated O3 (E-O3) versus ambient O3 (A-O3) after 64-DAS (Days after seeding), 85-DAS and 102-DAS. Our results indicated that E-O3 had no significant effects on leaf length, leaf width, leaf area, stomatal length and stomatal density for both Bt-SY63 and SY63. E-O3 increased the leaf thickness of Bt-SY63, but decreased that of SY63. O3 stress caused early swelling of the thylakoids of chloroplasts, a significant increase in the proportion of total plastoglobule area in the entire cell area (PCAP) and a significant decrease in the proportion of total starch grain area in the entire cell area (SCAP), suggesting that E-O3 accelerated the leaf senescence of the two rice genotypes. Compared with SY63, E-O3 caused early swelling of the thylakoids of chloroplasts and more substantial breakdown of chloroplasts in Bt-SY63. Conclusions/Significance Our results suggest that the incorporation of cry1Ab/Ac into SY63 could induce unintentional changes in some parts of plant morphology and that O3 stress results in greater leaf damage to Bt-SY63 than to SY63, with the former coupled with higher O3 sensitivity in CCAP (the proportions of total chloroplast area in the entire cell area), PCAP and SCAP. This study provides valuable baseline information for the prospective commercial release

Culturable bacterial endophytes isolated from Mangrove tree (Rhizophora apiculata Blume) enhance seedling growth in Rice.

PubMed

Deivanai, Subramanian; Bindusara, Amitraghata Santhanam; Prabhakaran, Guruswamy; Bhore, Subhash Janardhan

2014-07-01

Endophytic bacteria do have several potential applications in medicine and in other various sectors of biotechnology including agriculture. Bacterial endophytes need to be explored for their potential applications in agricultural biotechnology. One of the potential applications of bacterial endophytes in agricultural is to enhance the growth of the agricultural crops. Hence, this study was undertaken to explore the plant growth promoting potential application of bacterial endophytes. The objective of this study was to examine the effect of endophytic bacteria from mangrove tree (Rhizophora apiculata Blume) for their efficacy in promoting seedling growth in rice. Eight endophytic bacterial isolates (EBIs) isolated from twig and petiole tissues of the mangrove were identified based on their 16S ribosomal ribonucleic acid (rRNA) gene sequence homology. Separately, surface sterilized paddy seeds were treated with cell-free broth and cell suspension of the EBIs. Rice seedlings were analyzed by various bioassays and data was recorded. The gene sequences of the isolates were closely related to two genera namely, Bacillus and Pantoea. Inoculation of EBIs from R. apiculata with rice seeds resulted in accelerated root and shoot growth with significant increase in chlorophyll content. Among the isolates, Pantoea ananatis (1MSE1) and Bacillus amyloliquefaciens (3MPE1) had shown predominance of activity. Endophytic invasion was recognized by the non-host by rapid accumulation of reactive oxygen species (ROS) and was counteracted by the production of hydrogen peroxide (H2O2) and lipid peroxide. The results demonstrated that EBIs from mangrove tree can increase the fitness of the rice seedlings under controlled conditions. These research findings could be useful to enhance the seedling growth and could serve as foundation in further research on enhancing the growth of the rice crop using endophytic bacteria.

Characterizing endophytic competence and plant growth promotion of bacterial endophytes inhabiting the seed endosphere of Rice.

PubMed

Walitang, Denver I; Kim, Kiyoon; Madhaiyan, Munusamy; Kim, Young Kee; Kang, Yeongyeong; Sa, Tongmin

2017-10-26

Rice (Oryza sativa L. ssp. indica) seeds as plant microbiome present both an opportunity and a challenge to colonizing bacterial community living in close association with plants. Nevertheless, the roles and activities of bacterial endophytes remain largely unexplored and insights into plant-microbe interaction are compounded by its complexity. In this study, putative functions or physiological properties associated with bacterial endophytic nature were assessed. Also, endophytic roles in plant growth and germination that may allow them to be selectively chosen by plants were also studied. The cultivable seed endophytes were dominated by Proteobacteria particularly class Gammaproteobacteria. Highly identical type strains were isolated from the seed endosphere regardless of the rice host's physiological tolerance to salinity. Among the type strains, Flavobacterium sp., Microbacterium sp. and Xanthomonas sp. were isolated from the salt-sensitive and salt-tolerant cultivars. PCA-Biplot ordination also showed that specific type strains isolated from different rice cultivars have distinguishing similar characteristics. Flavobacterium sp. strains are phosphate solubilizers and indole-3-acetic acid producers with high tolerance to salinity and osmotic stress. Pseudomonas strains are characterized as high siderophore producers while Microbacterium sp. and Xanthomonas sp. strains have very high pectinase and cellulase activity. Among the physiological traits of the seed endophytes, bacterial pectinase and cellulase activity are positively correlated as well as salt and osmotic tolerance. Overall characterization shows that majority of the isolates could survive in 4-8% salt concentration as well as in 0.6 M and 1.2 M sucrose solution. The activities of catalase, pectinase and cellulase were also observed in almost all of the isolates indicating the importance of these characteristics for survival and colonization into the seed endosphere. Seed bacterial endophytes also

Introgression of two chromosome regions for leaf photosynthesis from an indica rice into the genetic background of a japonica rice

PubMed Central

Hirasawa, Tadashi

2014-01-01

Increases in rates of individual leaf photosynthesis (P n) are critical for future increases of rice yields. A previous study, using introgression lines derived from a cross between indica cultivar Habataki, with one of the highest recorded values of P n, and the Japanese elite cultivar Koshihikari, identified four QTLs (qCAR4, qCAR5, qCAR8, and qCAR11) that affect P n. The present study examined the combined effect of qCAR4 and qCAR8 on P n in the genetic background of Koshihikari. The pyramided near-isogenic line NIL(qCAR4+qCAR8) showed higher P n than both NIL(qCAR4) and NIL(qCAR8), equivalent to that of Habataki despite being due to only two out of the four QTLs. The high P n of NIL(qCAR4+qCAR8) may be attributable to the high leaf nitrogen content, which may have been inherited from NIL(qCAR4), to the large hydraulic conductance due to the large root surface area from NIL(qCAR4), and to the high hydraulic conductivity from NIL(qCAR8). It might be also attributable to high mesophyll conductance, which may have been inherited from NIL(qCAR4). The induction of mesophyll conductance and the high leaf nitrogen content and high hydraulic conductivity could not be explained in isolation from the Koshihikari background. These results suggest that QTL pyramiding is a useful approach in rice breeding aimed at increasing P n. PMID:24591053

Bacterial brown leaf spot of citrus, a new disease caused by Burkholderia andropogonis

USDA-ARS?s Scientific Manuscript database

A new bacterial disease of citrus was recently identified in Florida and named as bacterial brown leaf spot (BBLS) of citrus. BBLS-infected citrus displayed flat, circular and brownish lesions with water-soaked margins surrounded by a chlorotic halo on leaves. Based on Biolog carbon source metabolic...

Rapid and simple procedure for homogenizing leaf tissues suitable for mini-midi-scale DNA extraction in rice.

PubMed

Yi, Gihwan; Choi, Jun-Ho; Lee, Jong-Hee; Jeong, Unggi; Nam, Min-Hee; Yun, Doh-Won; Eun, Moo-Young

2005-01-01

We describe a rapid and simple procedure for homogenizing leaf samples suitable for mini/midi-scale DNA preparation in rice. The methods used tungsten carbide beads and general vortexer for homogenizing leaf samples. In general, two samples can be ground completely within 11.3+/-1.5 sec at one time. Up to 20 samples can be ground at a time using a vortexer attachment. The yields of the DNA ranged from 2.2 to 7.6 microg from 25-150 mg of young fresh leaf tissue. The quality and quantity of DNA was compatible for most of PCR work and RFLP analysis.

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.

A novel protein RLS1 with NB-ARM domains is involved in chloroplast degradation during leaf senescence in rice.

PubMed

Jiao, Bin-Bin; Wang, Jian-Jun; Zhu, Xu-Dong; Zeng, Long-Jun; Li, Qun; He, Zu-Hua

2012-01-01

Leaf senescence, a type of programmed cell death (PCD) characterized by chlorophyll degradation, is important to plant growth and crop productivity. It emerges that autophagy is involved in chloroplast degradation during leaf senescence. However, the molecular mechanism(s) involved in the process is not well understood. In this study, the genetic and physiological characteristics of the rice rls1 (rapid leaf senescence 1) mutant were identified. The rls1 mutant developed small, yellow-brown lesions resembling disease scattered over the whole surfaces of leaves that displayed earlier senescence than those of wild-type plants. The rapid loss of chlorophyll content during senescence was the main cause of accelerated leaf senescence in rls1. Microscopic observation indicated that PCD was misregulated, probably resulting in the accelerated degradation of chloroplasts in rls1 leaves. Map-based cloning of the RLS1 gene revealed that it encodes a previously uncharacterized NB (nucleotide-binding site)-containing protein with an ARM (armadillo) domain at the carboxyl terminus. Consistent with its involvement in leaf senescence, RLS1 was up-regulated during dark-induced leaf senescence and down-regulated by cytokinin. Intriguingly, constitutive expression of RLS1 also slightly accelerated leaf senescence with decreased chlorophyll content in transgenic rice plants. Our study identified a previously uncharacterized NB-ARM protein involved in PCD during plant growth and development, providing a unique tool for dissecting possible autophagy-mediated PCD during senescence in plants.

Recycling coffee grounds and tea leaf wastes to improve the yield and mineral content of grains of paddy rice.

PubMed

Morikawa, Claudio K; Saigusa, M

2011-08-30

Coffee grounds and tea leaf wastes exhibit strong affinity for metals such as Fe and Zn. The objective of this experiment was to evaluate the effect of top-dressing application of Fe- and Zn-enriched coffee grounds and tea leaf wastes at the panicle initiation stage on the mineral content of rice grains and the yield of paddy rice. The Fe and Zn contents of brown rice grains increased significantly on application of both coffee and tea waste materials. The concentration of Mn was increased by top-dressing application of coffee waste material only. For Cu, no significant (P < 0.05) differences were found between the control and ferrous sulfate/zinc sulfate treatment. The application of coffee and tea waste materials led to a significant (P < 0.05) increase in the number of grains per panicle, which was reflected in increases in the total number of grains per hill and in grain yield. The top-dressing application of these materials is an excellent method to recycle coffee grounds and tea wastes from coffee shops. Use of these novel materials would not only reduce the waste going to landfill but would also benefit the mineral nutrition of rice consumers at low cost by increasing Fe and Zn levels of rice grains as well as grain yield. Copyright © 2011 Society of Chemical Industry.

Response of Leaf Water Potential, Stomatal Resistance, and Leaf Rolling to Water Stress

PubMed Central

O'Toole, John C.; Cruz, Rolando T.

1980-01-01

Numerous studies have associated increased stomatal resistance with response to water deficit in cereals. However, consideration of change in leaf form seems to have been neglected. The response of adaxial and abaxial stomatal resistance and leaf rolling in rice to decreasing leaf water potential was investigated. Two rice cultivars were subjected to control and water stress treatments in a deep (1-meter) aerobic soil. Concurrent measurements of leaf water potential, stomatal resistance, and degree of leaf rolling were made through a 29-day period after cessation of irrigation. Kinandang Patong, an upland adapted cultivar, maintained higher dawn and midday leaf water potential than IR28, a hybrid selected in irrigated conditions. This was not explained by differences in leaf diffusive resistance or leaf rolling, and is assumed to result from a difference in root system extent. Stomatal resistance increased more on the abaxial than the adaxial leaf surface in both cultivars. This was associated with a change in leaf form or rolling inward of the upper leaf surface. Both responses, increased stomatal resistance and leaf rolling, were initiated in a similar leaf water potential range (−8 to −12 bars). Leaves of IR28 became fully rolled at leaf water potential of about −22 bars; however, total leaf diffusive resistance was only about 4 to 5 seconds per centimeter (conductance 0.25 to 0.2 centimeter per second) at that stage. Leaf diffusive resistance and degree of leaf rolling were linearly related to leaf water potential. Thus, leaf rolling in rice may be used as an estimate of the other two less obvious effects of water deficit. PMID:16661206

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

USDA-ARS?s Scientific Manuscript database

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

[Effects of desulfurization waste on calcium distribution, Ca(2+)-ATPase activity, and antioxidant characteristics of rice leaf under alkali stress].

PubMed

Mao, Gui-Lian; Xu, Xing; Zeng, Jin; Yue, Zi-Hui; Yang, Shu-Juan

2012-02-01

To approach the action mechanisms of desulfurization waste on alleviating alkali stress-induced injury of rice, a pot experiment was conducted to study the variations of leaf total calcium content, calcium distribution, plasma membrane Ca(2+)-ATPase activity, and reactive oxygen content of rice seedlings under alkali stress after the application of desulfurization waste. In the control, a few calcium particulates scattered in the cell wall and chloroplasts, while applying desulfurization waste or CaSO4 increased the calcium particulates in the plasma membrane, intercellular space, cell wall, and vacuole significantly. With the increasing application rate of desulfurization waste or CaSO4, the leaf total calcium content increased, Ca(2+)-ATPase activity in plasma membrane and tonoplast presented an increasing trend, plasma membrane relative permeability, MDA content, and O2 production rate decreased, and SOD and POD activities increased. The desulfurization waste could relieve the alkali stress to rice in some extent, and the main reactive compound in the waste could be CaSO4.

Rice microstructure

USDA-ARS?s Scientific Manuscript database

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

Leaf-associated bacterial microbiota of coffee and its correlation with manganese and calcium levels on leaves.

PubMed

de Sousa, Leandro Pio de; da Silva, Marcio José da; Mondego, Jorge Maurício

2018-05-17

Coffee is one of the most valuable agricultural commodities and the plants' leaves are the primary site of infection for most coffee diseases, such as the devastating coffee leaf rust. Therefore, the use of bacterial microbiota that inhabits coffee leaves to fight infections could be an alternative agricultural method to protect against coffee diseases. Here, we report the leaf-associated bacteria in three coffee genotypes over the course of a year, with the aim to determine the diversity of bacterial microbiota. The results indicate a prevalence of Enterobacteriales in Coffea canephora, Pseudomonadales in C. arabica 'Obatã', and an intriguing lack of bacterial dominance in C. arabica 'Catuaí'. Using PERMANOVA analyses, we assessed the association between bacterial abundance in the coffee genotypes and environmental parameters such as temperature, precipitation, and mineral nutrients in the leaves. We detected a close relationship between the amount of Mn and the abundance of Pseudomonadales in 'Obatã' and the amount of Ca and the abundance of Enterobacteriales in C. canephora. We suggest that mineral nutrients can be key drivers that shape leaf microbial communities.

Leaf bacterial diversity mediates plant diversity and ecosystem function relationships.

PubMed

Laforest-Lapointe, Isabelle; Paquette, Alain; Messier, Christian; Kembel, Steven W

2017-06-01

Research on biodiversity and ecosystem functioning has demonstrated links between plant diversity and ecosystem functions such as productivity. At other trophic levels, the plant microbiome has been shown to influence host plant fitness and function, and host-associated microbes have been proposed to influence ecosystem function through their role in defining the extended phenotype of host organisms However, the importance of the plant microbiome for ecosystem function has not been quantified in the context of the known importance of plant diversity and traits. Here, using a tree biodiversity-ecosystem functioning experiment, we provide strong support for the hypothesis that leaf bacterial diversity is positively linked to ecosystem productivity, even after accounting for the role of plant diversity. Our results also show that host species identity, functional identity and functional diversity are the main determinants of leaf bacterial community structure and diversity. Our study provides evidence of a positive correlation between plant-associated microbial diversity and terrestrial ecosystem productivity, and a new mechanism by which models of biodiversity-ecosystem functioning relationships can be improved.

Jasmonate induction of the monoterpene linalool confers resistance to rice bacterial blight and its biosynthesis is regulated by JAZ protein in rice.

PubMed

Taniguchi, Shiduku; Hosokawa-Shinonaga, Yumi; Tamaoki, Daisuke; Yamada, Shoko; Akimitsu, Kazuya; Gomi, Kenji

2014-02-01

Jasmonic acid (JA) is involved in the regulation of host immunity in plants. Recently, we demonstrated that JA signalling has an important role in resistance to rice bacterial blight caused by Xanthomonas oryzae pv. oryzae (Xoo) in rice. Here, we report that many volatile compounds accumulate in response to exogenous application of JA, including the monoterpene linalool. Expression of linalool synthase was up-regulated by JA. Vapour treatment with linalool induced resistance to Xoo, and transgenic rice plants overexpressing linalool synthase were more resistance to Xoo, presumably due to the up-regulation of defence-related genes in the absence of any treatment. JA-induced accumulation of linalool was regulated by OsJAZ8, a rice jasmonate ZIM-domain protein involving the JA signalling pathway at the transcriptional level, suggesting that linalool plays an important role in JA-induced resistance to Xoo in rice. © 2013 John Wiley & Sons Ltd.

Bacterial anoxygenic photosynthesis on plant leaf surfaces.

PubMed

Atamna-Ismaeel, Nof; Finkel, Omri; Glaser, Fabian; von Mering, Christian; Vorholt, Julia A; Koblížek, Michal; Belkin, Shimshon; Béjà, Oded

2012-04-01

The aerial surface of plants, the phyllosphere, is colonized by numerous bacteria displaying diverse metabolic properties that enable their survival in this specific habitat. Recently, we reported on the presence of microbial rhodopsin harbouring bacteria on the top of leaf surfaces. Here, we report on the presence of additional bacterial populations capable of harvesting light as a means of supplementing their metabolic requirements. An analysis of six phyllosphere metagenomes revealed the presence of a diverse community of anoxygenic phototrophic bacteria, including the previously reported methylobacteria, as well as other known and unknown phototrophs. The presence of anoxygenic phototrophic bacteria was also confirmed in situ by infrared epifluorescence microscopy. The microscopic enumeration correlated with estimates based on metagenomic analyses, confirming both the presence and high abundance of these microorganisms in the phyllosphere. Our data suggest that the phyllosphere contains a phylogenetically diverse assemblage of phototrophic species, including some yet undescribed bacterial clades that appear to be phyllosphere-unique. © 2012 Society for Applied Microbiology and Blackwell Publishing Ltd.

Monitoring the efficacy of mutated Allium sativum leaf lectin in transgenic rice against Rhizoctonia solani.

PubMed

Ghosh, Prithwi; Sen, Senjuti; Chakraborty, Joydeep; Das, Sampa

2016-03-01

Rice sheath blight, caused by Rhizoctonia solani is one of the most devastating diseases of rice. It is associated with significant reduction in rice productivity worldwide. A mutant variant of mannose binding Allium sativum leaf agglutinin (mASAL) was previously reported to exhibit strong antifungal activity against R. solani. In this study, the mASAL gene has been evaluated for its in planta antifungal activity in rice plants. mASAL was cloned into pCAMBIA1301 binary vector under the control of CaMV35S promoter. It was expressed in an elite indica rice cv. IR64 by employing Agrobacterium tumefaciens-mediated transformation. Molecular analyses of transgenic plants confirmed the presence and stable integration of mASAL gene. Immunohistofluorescence analysis of various tissue sections of plant parts clearly indicated the constitutive expression of mASAL. The segregation pattern of mASAL transgene was observed in T1 progenies in a 3:1 Mendelian ratio. The expression of mASAL was confirmed in T0 and T1 plants through western blot analysis followed by ELISA. In planta bioassay of transgenic lines against R. solani exhibited an average of 55 % reduction in sheath blight percentage disease index (PDI). The present study opens up the possibility of engineering rice plants with the antifungal gene mASAL, conferring resistance to sheath blight.

Bacterial Microbiota of Rice Roots: 16S-Based Taxonomic Profiling of Endophytic and Rhizospheric Diversity, Endophytes Isolation and Simplified Endophytic Community.

PubMed

Moronta-Barrios, Felix; Gionechetti, Fabrizia; Pallavicini, Alberto; Marys, Edgloris; Venturi, Vittorio

2018-02-11

Rice is currently the most important food crop in the world and we are only just beginning to study the bacterial associated microbiome. It is of importance to perform screenings of the core rice microbiota and also to develop new plant-microbe models and simplified communities for increasing our understanding about the formation and function of its microbiome. In order to begin to address this aspect, we have performed a 16S rDNA taxonomic bacterial profiling of the rhizosphere and endorhizosphere of two high-yield rice cultivars-Pionero 2010 FL and DANAC SD20A-extensively grown in Venezuela in 2014. Fifteen putative bacterial endophytes were then isolated from surface-sterilized roots and further studied in vitro and in planta . We have then performed inoculation of rice seedlings with a simplified community composed by 10 of the isolates and we have tracked them in the course of 30 days in greenhouse cultivation. The results obtained suggest that a set was able to significantly colonize together the rice endorhizospheres, indicating possible cooperation and the ability to form a stable multispecies community. This approach can be useful in the development of microbial solutions for a more sustainable rice production.

Severe outbreak of bacterial panicle blight across Texas Rice Belt in 2010

USDA-ARS?s Scientific Manuscript database

Bacterial panicle blight symptoms have been observed in rice fields in Texas for many years, but it was not until 1996 that Burkholderia glumae was identified as the causal agent. Although it is generally considered a minor disease, there have been years where significant losses to yield and milling...

Nutrients and host attributes modulate the abundance and functional traits of phyllosphere microbiome in rice.

PubMed

Thapa, Shobit; Prasanna, Radha; Ranjan, Kunal; Velmourougane, Kulandaivelu; Ramakrishnan, Balasubramanian

2017-11-01

The abundance of phyllosphere bacterial communities of seven genotypes of rice ADT- 38, ADT-43, CR-1009, PB-1, PS-5, P-44, and PB-1509 was investigated, in relation to nutrient dynamics of rhizosphere and leaves. P-44 genotype recorded highest pigment accumulation, while genotypes CR-1009 and P-44 exhibited most number of different bacterial morphotypes, Colony forming units in two media (Nutrient agar and R2A) varied significantly and ranged from 10 6 -10 7 per g plant tissues. Among the selected 60 distinct morphotypes, IAA and siderophore producers were the dominant functional types. Biocontrol activity against Drechslera oryzae was shown by 38 isolates, while 17 and 9 isolates were potent against Rhizoctonia solani and Magnaporthe oryzae respectively. Principal Component Analysis (PCA) illustrated the significant effects of selected soil and leaf nutrients of seven rice varieties on the culturable phyllospheric population (log CFU), particularly in the R2A medium. Eigen values revealed that 83% of the variance observed could be assigned to Leaf-Fe, Leaf-Mn, chlorophyll b and soil organic carbon (OC). Quantitative PCR analyses of abundance of bacteria, cyanobacteria and archaebacteria revealed a host-specific response, with CR-1009 showing highest number of 16S rRNA copies of bacterial members, while both P-44 and PS-5 had higher cyanobacterial abundance, but lowest number of those belonging to archaebacteria. Nutritional aspects of leaf and soil influenced the abundance of bacteria and their functional attributes; this is of interest for enhancing the efficacy of foliar inoculants, thereby, improving plant growth and disease tolerance. Copyright © 2017 Elsevier GmbH. All rights reserved.

Exploring the potential of the bacterial carotene desaturase CrtI to increase the beta-carotene content in Golden Rice.

PubMed

Al-Babili, Salim; Hoa, Tran Thi Cuc; Schaub, Patrick

2006-01-01

To increase the beta-carotene (provitamin A) content and thus the nutritional value of Golden Rice, the optimization of the enzymes employed, phytoene synthase (PSY) and the Erwinia uredovora carotene desaturase (CrtI), must be considered. CrtI was chosen for this study because this bacterial enzyme, unlike phytoene synthase, was expressed at barely detectable levels in the endosperm of the Golden Rice events investigated. The low protein amounts observed may be caused by either weak cauliflower mosaic virus 35S promoter activity in the endosperm or by inappropriate codon usage. The protein level of CrtI was increased to explore its potential for enhancing the flux of metabolites through the pathway. For this purpose, a synthetic CrtI gene with a codon usage matching that of rice storage proteins was generated. Rice plants were transformed to express the synthetic gene under the control of the endosperm-specific glutelin B1 promoter. In addition, transgenic plants expressing the original bacterial gene were generated, but the endosperm-specific glutelin B1 promoter was employed instead of the cauliflower mosaic virus 35S promoter. Independent of codon optimization, the use of the endosperm-specific promoter resulted in a large increase in bacterial desaturase production in the T(1) rice grains. However, this did not lead to a significant increase in the carotenoid content, suggesting that the bacterial enzyme is sufficiently active in rice endosperm even at very low levels and is not rate-limiting. The endosperm-specific expression of CrtI did not affect the carotenoid pattern in the leaves, which was observed upon its constitutive expression. Therefore, tissue-specific expression of CrtI represents the better option.

Natural Variation in the Flag Leaf Morphology of Rice Due to a Mutation of the NARROW LEAF 1 Gene in Oryza sativa L.

PubMed

Taguchi-Shiobara, Fumio; Ota, Tatsuya; Ebana, Kaworu; Ookawa, Taiichiro; Yamasaki, Masanori; Tanabata, Takanari; Yamanouchi, Utako; Wu, Jianzhong; Ono, Nozomi; Nonoue, Yasunori; Nagata, Kazufumi; Fukuoka, Shuichi; Hirabayashi, Hideyuki; Yamamoto, Toshio; Yano, Masahiro

2015-10-01

We investigated the natural variations in the flag leaf morphology of rice. We conducted a principal component analysis based on nine flag leaf morphology traits using 103 accessions from the National Institute of Agrobiological Sciences Core Collection. The first component explained 39% of total variance, and the variable with highest loading was the width of the flag leaf (WFL). A genome-wide association analysis of 102 diverse Japanese accessions revealed that marker RM6992 on chromosome 4 was highly associated with WFL. In analyses of progenies derived from a cross between Takanari and Akenohoshi, the most significant quantitative trait locus (QTL) for WFL was in a 10.3-kb region containing the NARROW LEAF 1 (NAL1) gene, located 0.4 Mb downstream of RM6992. Analyses of chromosomal segment substitution lines indicated that a mutation (G1509A single-nucleotide mutation, causing an R233H amino acid substitution in NAL1) was present at the QTL. This explained 13 and 20% of total variability in WFL and the distance between small vascular bundles, respectively. The mutation apparently occurred during rice domestication and spread into japonica, tropical japonica, and indica subgroups. Notably, one accession, Phulba, had a NAL1 allele encoding only the N-terminal, or one-fourth, of the wild-type peptide. Given that the Phulba allele and the histidine-type allele showed essentially the same phenotype, the histidine-type allele was regarded as malfunctional. The phenotypes of transgenic plants varied depending on the ratio of histidine-type alleles to arginine-type alleles, raising the possibility that H(233)-type products function differently from and compete with R(233)-type products. Copyright © 2015 by the Genetics Society of America.

Methoprene influences reproduction and flight capacity in adults of the rice leaf roller, Cnaphalocrocis medinalis (Guenee) (Lepidoptera: Pyralidae)

USDA-ARS?s Scientific Manuscript database

Juvenile hormone (JH) influences many aspects of insect biology, including oogenesis-flight syndrome tradeoffs between migration and reproduction. Drawing on studies of many migratory insects, we posed the hypothesis that JH influences migratory capacity and oogenesis in the rice leaf roller, Cnapha...

Blue light-promoted rice leaf bending and unrolling are due to up-regulated brassinosteroid biosynthesis genes accompanied by accumulation of castasterone.

PubMed

Asahina, Masashi; Tamaki, Yuji; Sakamoto, Tomoaki; Shibata, Kyomi; Nomura, Takahito; Yokota, Takao

2014-08-01

In this study the relationship between blue light- and brassinosteroid-enhanced leaf lamina bending and unrolling in rice was investigated. Twenty-four hours (h) irradiation with white or blue light increased endogenous brassinosteroid levels, especially those of typhasterol and castasterone, in aerial tissues of rice seedlings. There was an accompanying up-regulation of transcript levels of CYP85A1/OsDWARF, encoding an enzyme catalyzing C-6 oxidation, after 6h under either white or blue light. These effects were not observed in seedlings placed under far-red or red light regimes. It was concluded that blue light up-regulates the levels of several cytochrome P450 enzymes including CYP85A1, thereby promoting the synthesis of castasterone, a biologically active brassinosteroid in rice. Based on these findings, it is considered that blue light-mediated rice leaf bending and unrolling are consequences of the enhanced biosynthesis of endogenous castasterone. In contrast to aerial tissues, brassinosteroid synthesis in roots appeared to be negatively regulated by white, blue and red light but positively controlled by far-red light. Copyright © 2014 Elsevier Ltd. All rights reserved.

OsHKT1;4-mediated Na(+) transport in stems contributes to Na(+) exclusion from leaf blades of rice at the reproductive growth stage upon salt stress.

PubMed

Suzuki, Kei; Yamaji, Naoki; Costa, Alex; Okuma, Eiji; Kobayashi, Natsuko I; Kashiwagi, Tatsuhiko; Katsuhara, Maki; Wang, Cun; Tanoi, Keitaro; Murata, Yoshiyuki; Schroeder, Julian I; Ma, Jian Feng; Horie, Tomoaki

2016-01-19

Na(+) exclusion from leaf blades is one of the key mechanisms for glycophytes to cope with salinity stress. Certain class I transporters of the high-affinity K(+) transporter (HKT) family have been demonstrated to mediate leaf blade-Na(+) exclusion upon salinity stress via Na(+)-selective transport. Multiple HKT1 transporters are known to function in rice (Oryza sativa). However, the ion transport function of OsHKT1;4 and its contribution to the Na(+) exclusion mechanism in rice remain to be elucidated. Here, we report results of the functional characterization of the OsHKT1;4 transporter in rice. OsHKT1;4 mediated robust Na(+) transport in Saccharomyces cerevisiae and Xenopus laevis oocytes. Electrophysiological experiments demonstrated that OsHKT1;4 shows strong Na(+) selectivity among cations tested, including Li(+), Na(+), K(+), Rb(+), Cs(+), and NH4 (+), in oocytes. A chimeric protein, EGFP-OsHKT1;4, was found to be functional in oocytes and targeted to the plasma membrane of rice protoplasts. The level of OsHKT1;4 transcripts was prominent in leaf sheaths throughout the growth stages. Unexpectedly however, we demonstrate here accumulation of OsHKT1;4 transcripts in the stem including internode II and peduncle in the reproductive growth stage. Moreover, phenotypic analysis of OsHKT1;4 RNAi plants in the vegetative growth stage revealed no profound influence on the growth and ion accumulation in comparison with WT plants upon salinity stress. However, imposition of salinity stress on the RNAi plants in the reproductive growth stage caused significant Na(+) overaccumulation in aerial organs, in particular, leaf blades and sheaths. In addition, (22)Na(+) tracer experiments using peduncles of RNAi and WT plants suggested xylem Na(+) unloading by OsHKT1;4. Taken together, our results indicate a newly recognized function of OsHKT1;4 in Na(+) exclusion in stems together with leaf sheaths, thus excluding Na(+) from leaf blades of a japonica rice cultivar in the

Leaf microbiota in an agroecosystem: spatiotemporal variation in bacterial community composition on field-grown lettuce

PubMed Central

Rastogi, Gurdeep; Sbodio, Adrian; Tech, Jan J; Suslow, Trevor V; Coaker, Gitta L; Leveau, Johan H J

2012-01-01

The presence, size and importance of bacterial communities on plant leaf surfaces are widely appreciated. However, information is scarce regarding their composition and how it changes along geographical and seasonal scales. We collected 106 samples of field-grown Romaine lettuce from commercial production regions in California and Arizona during the 2009–2010 crop cycle. Total bacterial populations averaged between 105 and 106 per gram of tissue, whereas counts of culturable bacteria were on average one (summer season) or two (winter season) orders of magnitude lower. Pyrosequencing of 16S rRNA gene amplicons from 88 samples revealed that Proteobacteria, Firmicutes, Bacteroidetes and Actinobacteria were the most abundantly represented phyla. At the genus level, Pseudomonas, Bacillus, Massilia, Arthrobacter and Pantoea were the most consistently found across samples, suggesting that they form the bacterial ‘core' phyllosphere microbiota on lettuce. The foliar presence of Xanthomonas campestris pv. vitians, which is the causal agent of bacterial leaf spot of lettuce, correlated positively with the relative representation of bacteria from the genus Alkanindiges, but negatively with Bacillus, Erwinia and Pantoea. Summer samples showed an overrepresentation of Enterobacteriaceae sequences and culturable coliforms compared with winter samples. The distance between fields or the timing of a dust storm, but not Romaine cultivar, explained differences in bacterial community composition between several of the fields sampled. As one of the largest surveys of leaf surface microbiology, this study offers new insights into the extent and underlying causes of variability in bacterial community composition on plant leaves as a function of time, space and environment. PMID:22534606

Leaf shedding as an anti-bacterial defense in Arabidopsis cauline leaves

PubMed Central

2017-01-01

Plants utilize an innate immune system to protect themselves from disease. While many molecular components of plant innate immunity resemble the innate immunity of animals, plants also have evolved a number of truly unique defense mechanisms, particularly at the physiological level. Plant’s flexible developmental program allows them the unique ability to simply produce new organs as needed, affording them the ability to replace damaged organs. Here we develop a system to study pathogen-triggered leaf abscission in Arabidopsis. Cauline leaves infected with the bacterial pathogen Pseudomonas syringae abscise as part of the defense mechanism. Pseudomonas syringae lacking a functional type III secretion system fail to elicit an abscission response, suggesting that the abscission response is a novel form of immunity triggered by effectors. HAESA/HAESA-like 2, INFLORESCENCE DEFICIENT IN ABSCISSION, and NEVERSHED are all required for pathogen-triggered abscission to occur. Additionally phytoalexin deficient 4, enhanced disease susceptibility 1, salicylic acid induction-deficient 2, and senescence-associated gene 101 plants with mutations in genes necessary for bacterial defense and salicylic acid signaling, and NahG transgenic plants with low levels of salicylic acid fail to abscise cauline leaves normally. Bacteria that physically contact abscission zones trigger a strong abscission response; however, long-distance signals are also sent from distal infected tissue to the abscission zone, alerting the abscission zone of looming danger. We propose a threshold model regulating cauline leaf defense where minor infections are handled by limiting bacterial growth, but when an infection is deemed out of control, cauline leaves are shed. Together with previous results, our findings suggest that salicylic acid may regulate both pathogen- and drought-triggered leaf abscission. PMID:29253890

The Evolutionary Basis of Naturally Diverse Rice Leaves Anatomy

PubMed Central

Chatterjee, Jolly; Dionora, Jacqueline; Elmido-Mabilangan, Abigail; Wanchana, Samart; Thakur, Vivek; Bandyopadhyay, Anindya; Brar, Darshan S.; Quick, William Paul

2016-01-01

Rice contains genetically and ecologically diverse wild and cultivated species that show a wide variation in plant and leaf architecture. A systematic characterization of leaf anatomy is essential in understanding the dynamics behind such diversity. Therefore, leaf anatomies of 24 Oryza species spanning 11 genetically diverse rice genomes were studied in both lateral and longitudinal directions and possible evolutionary trends were examined. A significant inter-species variation in mesophyll cells, bundle sheath cells, and vein structure was observed, suggesting precise genetic control over these major rice leaf anatomical traits. Cellular dimensions, measured along three growth axes, were further combined proportionately to construct three-dimensional (3D) leaf anatomy models to compare the relative size and orientation of the major cell types present in a fully expanded leaf. A reconstruction of the ancestral leaf state revealed that the following are the major characteristics of recently evolved rice species: fewer veins, larger and laterally elongated mesophyll cells, with an increase in total mesophyll area and in bundle sheath cell number. A huge diversity in leaf anatomy within wild and domesticated rice species has been portrayed in this study, on an evolutionary context, predicting a two-pronged evolutionary pathway leading to the ‘sativa leaf type’ that we see today in domesticated species. PMID:27792743

The Evolutionary Basis of Naturally Diverse Rice Leaves Anatomy.

PubMed

Chatterjee, Jolly; Dionora, Jacqueline; Elmido-Mabilangan, Abigail; Wanchana, Samart; Thakur, Vivek; Bandyopadhyay, Anindya; Brar, Darshan S; Quick, William Paul

2016-01-01

Rice contains genetically and ecologically diverse wild and cultivated species that show a wide variation in plant and leaf architecture. A systematic characterization of leaf anatomy is essential in understanding the dynamics behind such diversity. Therefore, leaf anatomies of 24 Oryza species spanning 11 genetically diverse rice genomes were studied in both lateral and longitudinal directions and possible evolutionary trends were examined. A significant inter-species variation in mesophyll cells, bundle sheath cells, and vein structure was observed, suggesting precise genetic control over these major rice leaf anatomical traits. Cellular dimensions, measured along three growth axes, were further combined proportionately to construct three-dimensional (3D) leaf anatomy models to compare the relative size and orientation of the major cell types present in a fully expanded leaf. A reconstruction of the ancestral leaf state revealed that the following are the major characteristics of recently evolved rice species: fewer veins, larger and laterally elongated mesophyll cells, with an increase in total mesophyll area and in bundle sheath cell number. A huge diversity in leaf anatomy within wild and domesticated rice species has been portrayed in this study, on an evolutionary context, predicting a two-pronged evolutionary pathway leading to the 'sativa leaf type' that we see today in domesticated species.

Cytological and molecular analysis of nonhost resistance in rice to wheat powdery mildew and leaf rust pathogens.

PubMed

Cheng, Yulin; Yao, Juanni; Zhang, Hongchang; Huang, Lili; Kang, Zhensheng

2015-07-01

Cereal powdery mildews caused by Blumeria graminis and cereal rusts caused by Puccinia spp. are constant disease threats that limit the production of almost all important cereal crops. Rice is an intensively grown agricultural cereal that is atypical because of its immunity to all powdery mildew and rust fungi. We analyzed the nonhost interactions between rice and the wheat powdery mildew fungus B. graminis f. sp. tritici (Bgt) and the wheat leaf rust fungus Puccinia triticina (Ptr) to identify the basis of nonhost resistance (NHR) in rice against cereal powdery mildew and rust fungi at cytological and molecular levels. No visible symptoms were observed on rice leaves inoculated with Bgt or Ptr. Microscopic observations showed that both pathogens exhibited aberrant differentiation and significantly reduced penetration frequencies on rice compared to wheat. The development of Bgt and Ptr was also completely arrested at early infection stages in cases of successful penetration into rice leaves. Attempted infection of rice by Bgt and Ptr induced similar defense responses, including callose deposition, accumulation of reactive oxygen species, and hypersensitive response in rice epidermal and mesophyll cells, respectively. Furthermore, a set of defense-related genes were upregulated in rice against Bgt and Ptr infection. Rice is an excellent monocot model for genetic and molecular studies. Therefore, our results demonstrate that rice is a useful model to study the mechanisms of NHR to cereal powdery mildew and rust fungi, which provides useful information for the development of novel and durable strategies to control these important pathogens.

Lower responsiveness of canopy evapotranspiration rate than of leaf stomatal conductance to open-air CO2 elevation in rice.

PubMed

Shimono, Hiroyuki; Nakamura, Hirofumi; Hasegawa, Toshihiro; Okada, Masumi

2013-08-01

An elevated atmospheric CO2 concentration ([CO2 ]) can reduce stomatal conductance of leaves for most plant species, including rice (Oryza sativa L.). However, few studies have quantified seasonal changes in the effects of elevated [CO2 ] on canopy evapotranspiration, which integrates the response of stomatal conductance of individual leaves with other responses, such as leaf area expansion, changes in leaf surface temperature, and changes in developmental stages, in field conditions. We conducted a field experiment to measure seasonal changes in stomatal conductance of the uppermost leaves and in the evapotranspiration, transpiration, and evaporation rates using a lysimeter method. The study was conducted for flooded rice under open-air CO2 elevation. Stomatal conductance decreased by 27% under elevated [CO2 ], averaged throughout the growing season, and evapotranspiration decreased by an average of 5% during the same period. The decrease in daily evapotranspiration caused by elevated [CO2 ] was more significantly correlated with air temperature and leaf area index (LAI) rather than with other parameters of solar radiation, days after transplanting, vapor-pressure deficit and FAO reference evapotranspiration. This indicates that higher air temperatures, within the range from 16 to 27 °C, and a larger LAI, within the range from 0 to 4 m(2)  m(-2) , can increase the magnitude of the decrease in evapotranspiration rate caused by elevated [CO2 ]. The crop coefficient (i.e. the evapotranspiration rate divided by the FAO reference evapotranspiration rate) was 1.24 at ambient [CO2 ] and 1.17 at elevated [CO2 ]. This study provides the first direct measurement of the effects of elevated [CO2 ] on rice canopy evapotranspiration under open-air conditions using the lysimeter method, and the results will improve future predictions of water use in rice fields. © 2013 John Wiley & Sons Ltd.

Do transgenesis and marker-assisted backcross breeding produce substantially equivalent plants? A comparative study of transgenic and backcross rice carrying bacterial blight resistant gene Xa21.

PubMed

Gao, Lifen; Cao, Yinghao; Xia, Zhihui; Jiang, Guanghuai; Liu, Guozhen; Zhang, Weixiong; Zhai, Wenxue

2013-10-29

The potential impact of genetically modified (GM) plants on human health has attracted much attention worldwide, and the issue remains controversial. This is in sharp contrast to the broad acceptance of plants produced by breeding through Marker Assisted Backcrossing (MAB). Focusing on transcriptome variation and perturbation to signaling pathways, we assessed the molecular and biological aspects of substantial equivalence, a general principle for food safety endorsed by the Food and Agricultural Organization and the World Health Organization, between a transgenic crop and a plant from MAB breeding. We compared a transgenic rice line (DXT) and a MAB rice line (DXB), both of which contain the gene Xa21 providing resistance to bacterial leaf blight. By using Next-Generation sequencing data of DXT, DXB and their parental line (D62B), we compared the transcriptome variation of DXT and DXB. Remarkably, DXT had 43% fewer differentially expressed genes (DEGs) than DXB. The genes exclusively expressed in DXT and in DXB have pathogen and stress defense functions. Functional categories of DEGs in DXT were comparable to that in DXB, and seven of the eleven pathways significantly affected by transgenesis were also perturbed by MAB breeding. These results indicated that the transgenic rice and rice from MAB breeding are substantial equivalent at the transcriptome level, and paved a way for further study of transgenic rice, e.g., understanding the chemical and nutritional properties of the DEGs identified in the current study.

Do transgenesis and marker-assisted backcross breeding produce substantially equivalent plants? - A comparative study of transgenic and backcross rice carrying bacterial blight resistant gene Xa21

PubMed Central

2013-01-01

Background The potential impact of genetically modified (GM) plants on human health has attracted much attention worldwide, and the issue remains controversial. This is in sharp contrast to the broad acceptance of plants produced by breeding through Marker Assisted Backcrossing (MAB). Results Focusing on transcriptome variation and perturbation to signaling pathways, we assessed the molecular and biological aspects of substantial equivalence, a general principle for food safety endorsed by the Food and Agricultural Organization and the World Health Organization, between a transgenic crop and a plant from MAB breeding. We compared a transgenic rice line (DXT) and a MAB rice line (DXB), both of which contain the gene Xa21 providing resistance to bacterial leaf blight. By using Next-Generation sequencing data of DXT, DXB and their parental line (D62B), we compared the transcriptome variation of DXT and DXB. Remarkably, DXT had 43% fewer differentially expressed genes (DEGs) than DXB. The genes exclusively expressed in DXT and in DXB have pathogen and stress defense functions. Functional categories of DEGs in DXT were comparable to that in DXB, and seven of the eleven pathways significantly affected by transgenesis were also perturbed by MAB breeding. Conclusions These results indicated that the transgenic rice and rice from MAB breeding are substantial equivalent at the transcriptome level, and paved a way for further study of transgenic rice, e.g., understanding the chemical and nutritional properties of the DEGs identified in the current study. PMID:24165682

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.

Non-nodulated bacterial leaf symbiosis promotes the evolutionary success of its host plants in the coffee family (Rubiaceae).

PubMed

Verstraete, Brecht; Janssens, Steven; Rønsted, Nina

2017-08-01

Every plant species on Earth interacts in some way or another with microorganisms and it is well known that certain forms of symbiosis between different organisms can drive evolution. Within some clades of Rubiaceae (coffee family), a specific plant-bacteria interaction exists in which non-pathological endophytes are present in the leaves of their hosts. It is hypothesized that the bacterial endophytes, either alone or by interacting with the host, provide chemical protection against herbivory or pathogens by producing toxic or otherwise advantageous secondary metabolites. If the bacteria indeed have a direct beneficial influence on their hosts, it is reasonable to assume that the endophytes may increase the fitness of their hosts and therefore it is probable that their presence also has an influence on the long-term evolution of the particular plant lineages. In this study, the possible origin in time of non-nodulated bacterial leaf symbiosis in the Vanguerieae tribe of Rubiaceae is elucidated and dissimilarities in evolutionary dynamics between species with endophytes versus species without are investigated. Bacterial leaf symbiosis is shown to have most probably originated in the Late Miocene, a period when the savannah habitat is believed to have expanded on the African continent and herbivore pressure increased. The presence of bacterial leaf endophytes appears to be restricted to Old World lineages so far. Plant lineages with leaf endophytes show a significantly higher speciation rate than plant lineages without endophytes, while there is only a small difference in extinction rate. The transition rate shows that evolving towards having endophytes is twice as fast as evolving towards not having endophytes, suggesting that leaf symbiosis must be beneficial for the host plants. We conclude that the presence of bacterial leaf endophytes may also be an important driver for speciation of host plants. Copyright © 2017 Elsevier Inc. All rights reserved.

Culture dependent and independent analysis of bacterial communities associated with commercial salad leaf vegetables.

PubMed

Jackson, Colin R; Randolph, Kevin C; Osborn, Shelly L; Tyler, Heather L

2013-12-01

Plants harbor a diverse bacterial community, both as epiphytes on the plant surface and as endophytes within plant tissue. While some plant-associated bacteria act as plant pathogens or promote plant growth, others may be human pathogens. The aim of the current study was to determine the bacterial community composition of organic and conventionally grown leafy salad vegetables at the point of consumption using both culture-dependent and culture-independent methods. Total culturable bacteria on salad vegetables ranged from 8.0 × 10(3) to 5.5 × 10(8) CFU g(-1). The number of culturable endophytic bacteria from surface sterilized plants was significantly lower, ranging from 2.2 × 10(3) to 5.8 × 10(5) CFU g(-1). Cultured isolates belonged to six major bacterial phyla, and included representatives of Pseudomonas, Pantoea, Chryseobacterium, and Flavobacterium. Eleven different phyla and subphyla were identified by culture-independent pyrosequencing, with Gammaproteobacteria, Betaproteobacteria, and Bacteroidetes being the most dominant lineages. Other bacterial lineages identified (e.g. Firmicutes, Alphaproteobacteria, Acidobacteria, and Actinobacteria) typically represented less than 1% of sequences obtained. At the genus level, sequences classified as Pseudomonas were identified in all samples and this was often the most prevalent genus. Ralstonia sequences made up a greater portion of the community in surface sterilized than non-surface sterilized samples, indicating that it was largely endophytic, while Acinetobacter sequences appeared to be primarily associated with the leaf surface. Analysis of molecular variance indicated there were no significant differences in bacterial community composition between organic versus conventionally grown, or surface-sterilized versus non-sterilized leaf vegetables. While culture-independent pyrosequencing identified significantly more bacterial taxa, the dominant taxa from pyrosequence data were also detected by traditional

Culture dependent and independent analysis of bacterial communities associated with commercial salad leaf vegetables

PubMed Central

2013-01-01

Background Plants harbor a diverse bacterial community, both as epiphytes on the plant surface and as endophytes within plant tissue. While some plant-associated bacteria act as plant pathogens or promote plant growth, others may be human pathogens. The aim of the current study was to determine the bacterial community composition of organic and conventionally grown leafy salad vegetables at the point of consumption using both culture-dependent and culture-independent methods. Results Total culturable bacteria on salad vegetables ranged from 8.0 × 103 to 5.5 × 108 CFU g-1. The number of culturable endophytic bacteria from surface sterilized plants was significantly lower, ranging from 2.2 × 103 to 5.8 × 105 CFU g-1. Cultured isolates belonged to six major bacterial phyla, and included representatives of Pseudomonas, Pantoea, Chryseobacterium, and Flavobacterium. Eleven different phyla and subphyla were identified by culture-independent pyrosequencing, with Gammaproteobacteria, Betaproteobacteria, and Bacteroidetes being the most dominant lineages. Other bacterial lineages identified (e.g. Firmicutes, Alphaproteobacteria, Acidobacteria, and Actinobacteria) typically represented less than 1% of sequences obtained. At the genus level, sequences classified as Pseudomonas were identified in all samples and this was often the most prevalent genus. Ralstonia sequences made up a greater portion of the community in surface sterilized than non-surface sterilized samples, indicating that it was largely endophytic, while Acinetobacter sequences appeared to be primarily associated with the leaf surface. Analysis of molecular variance indicated there were no significant differences in bacterial community composition between organic versus conventionally grown, or surface-sterilized versus non-sterilized leaf vegetables. While culture-independent pyrosequencing identified significantly more bacterial taxa, the dominant taxa from pyrosequence data were also detected by

Coordination of Leaf Photosynthesis, Transpiration, and Structural Traits in Rice and Wild Relatives (Genus Oryza).

PubMed

Giuliani, Rita; Koteyeva, Nuria; Voznesenskaya, Elena; Evans, Marc A; Cousins, Asaph B; Edwards, Gerald E

2013-07-01

The genus Oryza, which includes rice (Oryza sativa and Oryza glaberrima) and wild relatives, is a useful genus to study leaf properties in order to identify structural features that control CO(2) access to chloroplasts, photosynthesis, water use efficiency, and drought tolerance. Traits, 26 structural and 17 functional, associated with photosynthesis and transpiration were quantified on 24 accessions (representatives of 17 species and eight genomes). Hypotheses of associations within, and between, structure, photosynthesis, and transpiration were tested. Two main clusters of positively interrelated leaf traits were identified: in the first cluster were structural features, leaf thickness (Thick(leaf)), mesophyll (M) cell surface area exposed to intercellular air space per unit of leaf surface area (S(mes)), and M cell size; a second group included functional traits, net photosynthetic rate, transpiration rate, M conductance to CO(2) diffusion (g(m)), stomatal conductance to gas diffusion (g(s)), and the g(m)/g(s) ratio.While net photosynthetic rate was positively correlated with gm, neither was significantly linked with any individual structural traits. The results suggest that changes in gm depend on covariations of multiple leaf (S(mes)) and M cell (including cell wall thickness) structural traits. There was an inverse relationship between Thick(leaf) and transpiration rate and a significant positive association between Thick(leaf) and leaf transpiration efficiency. Interestingly, high g(m) together with high g(m)/g(s) and a low S(mes)/g(m) ratio (M resistance to CO(2) diffusion per unit of cell surface area exposed to intercellular air space) appear to be ideal for supporting leaf photosynthesis while preserving water; in addition, thick M cell walls may be beneficial for plant drought tolerance.

Facile fabrication of rice husk based silicon dioxide nanospheres loaded with silver nanoparticles as a rice antibacterial agent

PubMed Central

Cui, Jianghu; Liang, You; Yang, Desong; Liu, Yingliang

2016-01-01

Bacterial leaf blight of rice caused by Xanthomonas oryzae pv. oryzae (Xoo) is a major disease of rice, leading to reduction in production by 10–50%. In order to control this disease, various chemical bactericides have been used. Wide and prolonged application of chemical bactericides resulted in the resistant strain of Xoo that was isolated from rice. To address this problem, we were searching for an environmentally friendly alternative to the commonly used chemical bactericides. In this work, we demonstrate that silicon dioxide nanospheres loaded with silver nanoparticles (SiO2-Ag) can be prepared by using rice husk as base material precursor. The results of the antibacterial tests showed that SiO2-Ag composites displayed antibacterial activity against Xoo. At cellular level, the cell wall/membrane was damaged and intercellular contents were leaked out by slow-releasing of silver ions from SiO2-Ag composites. At molecular level, this composite induced reactive oxygen species production and inhibited DNA replication. Based on the results above, we proposed the potential antibacterial mechanism of SiO2-Ag composites. Moreover, the cytotoxicity assay indicated that the composites showed mild toxicity with rice cells. Thus, this work provided a new strategy to develop biocide derived from residual biomass. PMID:26888152

Bacterial Leaf Scorch Affects New Jersey State Tree (Pest Alert)

Treesearch

USDA Forest Service; Northeastern Area, State and Private Forestry

2000-01-01

Recent surveys indicate that Bacterial Leaf Scorch (BLS) of northern red oak is widespread within New Jersey (see map) with many communities experiencing a high disease incidence. BLS is considered a threat not only to the state tree, northern red oak, but also to pin and scarlet oaks and other urban trees such as sycamore and elm. The disease in oaks has been observed...

A Rice CPYC-Type Glutaredoxin OsGRX20 in Protection against Bacterial Blight, Methyl Viologen and Salt Stresses.

PubMed

Ning, Xi; Sun, Yao; Wang, Changchun; Zhang, Weilin; Sun, Meihao; Hu, Haitao; Liu, Jianzhong; Yang, Ling

2018-01-01

Glutaredoxins (GRXs) belong to the antioxidants involved in the cellular stress responses. In spite of the identification 48 GRX genes in rice genomes, the biological functions of most of them remain unknown. Especially, the biological roles of members of GRX family in disease resistance are still lacking. Our proteomic analysis found that OsGRX20 increased by 2.7-fold after infection by bacterial blight. In this study, we isolated and characterized the full-length nucleotide sequences of the rice OsGRX20 gene, which encodes a GRX family protein with CPFC active site of CPYC-type class. OsGRX20 protein was localized in nucleus and cytosol, and its transcripts were expressed predominantly in leaves. Several stress- and hormone-related motifs putatively acting as regulatory elements were found in the OsGRX20 promoter. Real-time quantitative PCR analysis indicated that OsGRX20 was expressed at a significantly higher level in leaves of a resistant or tolerant rice genotype, Yongjing 50A, than in a sensitive genotype, Xiushui 11, exposed to bacterial blight, methyl viologen, heat, and cold. Its expression could be induced by salt, PEG-6000, 2,4-D, salicylic acid, jasmonic acid, and abscisic acid treatments in Yongjing 50A. Overexpression of OsGRX20 in rice Xiushui 11 significantly enhanced its resistance to bacterial blight attack, and tolerance to methyl viologen and salt stresses. In contrast, interference of OsGRX20 in Yongjing 50A led to increased susceptibility to bacterial blight, methyl viologen and salt stresses. OsGRX20 restrained accumulation of superoxide radicals in aerial tissue during methyl viologen treatment. Consistently, alterations in OsGRX20 expression affect the ascorbate/dehydroascorbate ratio and the abundance of transcripts encoding four reactive oxygen species scavenging enzymes after methyl viologen-induced stress. Our results demonstrate that OsGRX20 functioned as a positive regulator in rice tolerance to multiple stresses, which may be of

Stomatal conductance, mesophyll conductance, and transpiration efficiency in relation to leaf anatomy in rice and wheat genotypes under drought.

PubMed

Ouyang, Wenjing; Struik, Paul C; Yin, Xinyou; Yang, Jianchang

2017-11-02

Increasing leaf transpiration efficiency (TE) may provide leads for growing rice like dryland cereals such as wheat (Triticum aestivum). To explore avenues for improving TE in rice, variations in stomatal conductance (gs) and mesophyll conductance (gm) and their anatomical determinants were evaluated in two cultivars from each of lowland, aerobic, and upland groups of Oryza sativa, one cultivar of O. glaberrima, and two cultivars of T. aestivum, under three water regimes. The TE of upland rice, O. glaberrima, and wheat was more responsive to the gm/gs ratio than that of lowland and aerobic rice. Overall, the explanatory power of the particular anatomical trait varied among species. Low stomatal density mostly explained the low gs in drought-tolerant rice, whereas rice genotypes with smaller stomata generally responded more strongly to drought. Compared with rice, wheat had a higher gm, which was associated with thicker mesophyll tissue, mesophyll and chloroplasts more exposed to intercellular spaces, and thinner cell walls. Upland rice, O. glaberrima, and wheat cultivars minimized the decrease in gm under drought by maintaining high ratios of chloroplasts to exposed mesophyll cell walls. Rice TE could be improved by increasing the gm/gs ratio via modifying anatomical traits. © The Author 2017. Published by Oxford University Press on behalf of the Society for Experimental Biology.

Influences of Plant Species, Season and Location on Leaf Endophytic Bacterial Communities of Non-Cultivated Plants

PubMed Central

Ding, Tao; Melcher, Ulrich

2016-01-01

Bacteria are known to be associated endophytically with plants. Research on endophytic bacteria has identified their importance in food safety, agricultural production and phytoremediation. However, the diversity of endophytic bacterial communities and the forces that shape their compositions in non-cultivated plants are largely uncharacterized. In this study, we explored the diversity, community structure, and dynamics of endophytic bacteria in different plant species in the Tallgrass Prairie Preserve of northern Oklahoma, USA. High throughput sequencing of amplified segments of bacterial rDNA from 81 samples collected at four sampling times from five plant species at four locations identified 335 distinct OTUs at 97% sequence similarity, representing 16 phyla. Proteobacteria was the dominant phylum in the communities, followed by the phyla Bacteriodetes and Actinobacteria. Bacteria from four classes of Proteobacteria were detected with Alphaproteobacteria as the dominant class. Analysis of molecular variance revealed that host plant species and collecting date had significant influences on the compositions of the leaf endophytic bacterial communities. The proportion of Alphaproteobacteria was much higher in the communities from Asclepias viridis than from other plant species and differed from month to month. The most dominant bacterial groups identified in LDA Effect Size analysis showed host-specific patterns, indicating mutual selection between host plants and endophytic bacteria and that leaf endophytic bacterial compositions were dynamic, varying with the host plant’s growing season in three distinct patterns. In summary, next generation sequencing has revealed variations in the taxonomic compositions of leaf endophytic bacterial communities dependent primarily on the nature of the plant host species. PMID:26974817

Influences of Plant Species, Season and Location on Leaf Endophytic Bacterial Communities of Non-Cultivated Plants.

PubMed

Ding, Tao; Melcher, Ulrich

2016-01-01

Bacteria are known to be associated endophytically with plants. Research on endophytic bacteria has identified their importance in food safety, agricultural production and phytoremediation. However, the diversity of endophytic bacterial communities and the forces that shape their compositions in non-cultivated plants are largely uncharacterized. In this study, we explored the diversity, community structure, and dynamics of endophytic bacteria in different plant species in the Tallgrass Prairie Preserve of northern Oklahoma, USA. High throughput sequencing of amplified segments of bacterial rDNA from 81 samples collected at four sampling times from five plant species at four locations identified 335 distinct OTUs at 97% sequence similarity, representing 16 phyla. Proteobacteria was the dominant phylum in the communities, followed by the phyla Bacteriodetes and Actinobacteria. Bacteria from four classes of Proteobacteria were detected with Alphaproteobacteria as the dominant class. Analysis of molecular variance revealed that host plant species and collecting date had significant influences on the compositions of the leaf endophytic bacterial communities. The proportion of Alphaproteobacteria was much higher in the communities from Asclepias viridis than from other plant species and differed from month to month. The most dominant bacterial groups identified in LDA Effect Size analysis showed host-specific patterns, indicating mutual selection between host plants and endophytic bacteria and that leaf endophytic bacterial compositions were dynamic, varying with the host plant's growing season in three distinct patterns. In summary, next generation sequencing has revealed variations in the taxonomic compositions of leaf endophytic bacterial communities dependent primarily on the nature of the plant host species.

Leaf Hydraulic Vulnerability Triggers the Decline in Stomatal and Mesophyll Conductance during drought in Rice (Oryza sativa).

PubMed

Wang, Xiaoxiao; Du, Tingting; Huang, Jianliang; Peng, Shaobing; Xiong, Dongliang

2018-05-18

Understanding the physiological responses of crops to drought is important for ensuring sustained crop productivity under climate change, which is expected to exacerbate drought frequencies and intensities. Drought responses involve multiple traits, but the correlations between these traits are poorly understood. Using a variety of techniques, we estimated the changes in gas exchange, leaf hydraulic conductance (Kleaf), and leaf turgor in rice (Oryza sativa) in response to both short- and long-term soil drought and performed a photosynthetic limitation analysis to quantify the contributions of each limiting factor to the resultant overall decrease in photosynthesis during drought. Biomass, leaf area and leaf width significantly decreased during the two-week drought treatment, but leaf mass per area and leaf vein density increased. Light-saturated photosynthetic rate (A) declined dramatically during soil drought, mainly due to the decrease in stomatal conductance (gs) and mesophyll conductance (gm). Stomatal modeling suggested that the decline in Kleaf explained most of the decrease in stomatal closure during the drought treatment, and may also trigger the drought-related decrease of gs and gm. The results of this study provide insight into the regulation of carbon assimilation under drought conditions.

Integrating marker-assisted background analysis with foreground selection for pyramiding bacterial blight resistance genes into Basmati rice.

PubMed

Baliyan, Nikita; Malik, Rekha; Rani, Reema; Mehta, Kirti; Vashisth, Urvashi; Dhillon, Santosh; Boora, Khazan Singh

2018-01-01

Bacterial leaf blight (BB), caused by the bacterium Xanthomonas oryzae pv. Oryzae (Xoo), is the major constraint amongst rice diseases in India. CSR-30 is a very popular high-yielding, salt-tolerant Basmati variety widely grown in Haryana, India, but highly susceptible to BB. In the present study, we have successfully introgressed three BB resistance genes (Xa21, xa13 and xa5) from BB-resistant donor variety IRBB-60 into the BB-susceptible Basmati variety CSR-30 through marker-assisted selection (MAS) exercised with stringent phenotypic selection without compromising the Basmati traits. Background analysis using 131 polymorphic SSR markers revealed that recurrent parent genome (RPG) recovery ranged up to 97.1% among 15 BC 3 F 1 three-gene-pyramided genotypes. Based on agronomic evaluation, BB reaction, aroma, percentage recovery of RPG, and grain quality evaluation, four genotypes, viz., IC-R28, IC-R68, IC-R32, and IC-R42, were found promising and advanced to BC 3 F 2 generation. Copyright © 2017 Académie des sciences. Published by Elsevier Masson SAS. All rights reserved.

Effects of forest management practices in temperate beech forests on bacterial and fungal communities involved in leaf litter degradation.

PubMed

Purahong, Witoon; Kapturska, Danuta; Pecyna, Marek J; Jariyavidyanont, Katalee; Kaunzner, Jennifer; Juncheed, Kantida; Uengwetwanit, Tanaporn; Rudloff, Renate; Schulz, Elke; Hofrichter, Martin; Schloter, Michael; Krüger, Dirk; Buscot, François

2015-05-01

Forest management practices (FMPs) significantly influence important ecological processes and services in Central European forests, such as leaf litter decomposition and nutrient cycling. Changes in leaf litter diversity, and thus, its quality as well as microbial community structure and function induced by different FMPs were hypothesized to be the main drivers causing shifts in decomposition rates and nutrient release in managed forests. In a litterbag experiment lasting 473 days, we aimed to investigate the effects of FMPs (even-aged timber management, selective logging and unmanaged) on bacterial and fungal communities involved in leaf litter degradation over time. Our results showed that microbial communities in leaf litter were strongly influenced by both FMPs and sampling date. The results from nonmetric multidimensional scaling (NMDS) ordination revealed distinct patterns of bacterial and fungal successions over time in leaf litter. We demonstrated that FMPs and sampling dates can influence a range of factors, including leaf litter quality, microbial macronutrients, and pH, which significantly correlate with microbial community successions.

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

PubMed Central

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

2018-01-01

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

Bacterial succession and the dynamics of volatile compounds during the fermentation of Chinese rice wine from Shaoxing region.

PubMed

Liu, Shuang Ping; Mao, Jian; Liu, Yun Ya; Meng, Xiang Yong; Ji, Zhong Wei; Zhou, Zhi Lei; Ai-lati, Aisikaer

2015-12-01

Shaoxing rice wine is one of the most typical representatives of Chinese rice wine. It is brewed under non-sterile condition with various microorganism growing at the same time and forms a special flavor. The aims of this study was to monitor the bacterial succession by MiSeq pyrosequencing and the volatile compound dynamics by HS-SPME/GC–MS during brewing process. Moreover, the volatile compounds and bacterial community were analyzed by partial least squares regression to evaluate the effect of bacteria on volatile compounds formation. The results showed that there were ten dominating genera during Shaoxing rice wine fermentation process. Ten genera, Bacillus, Leuconostoc, Lactococcus, Weissella, Thermoactinomyces, Pseudomonas, Saccharopolyspora, Staphylococcus, Enterobacter and Lactobacillus, were identified as the main bacteria. The Bacillus and Lactobacillus dominated the Chinese rice wine ecosystems. In addition, a total of 64 volatile compounds were identified, mainly esters, alcohols, carbonyl compound and phenols. Pseudomonas were involved in synthesis of a wide variety of volatile compounds. Thermoactinomyces, Bacillus and Lactococcus also played critical roles in the formation of volatile compounds.

Direct suppression of a rice bacterial blight (Xanthomonas oryzae pv. oryzae) by monoterpene (S)-limonene.

PubMed

Lee, Gun Woong; Chung, Moon-Soo; Kang, Mihyung; Chung, Byung Yeoup; Lee, Sungbeom

2016-05-01

Rice bacterial blight, caused by Xanthomonas oryzae pv. oryzae (Xoo), is a severe disease of rice plants. Upon pathogen infection, rice biosynthesizes phytoalexins, including diterpenoids such as momilactones, phytocassanes, and oryzalexins. However, information on headspace volatiles in response to Xoo infection is limited. We have examined headspace volatile terpenes, induced by the infection of Xoo, and investigated their biological roles in the rice plant. Monoterpenes α-thujene, α-pinene, sabinene, myrcene, α-terpene, and (S)-limonene and sesquiterpenes cyclosativene, α-copaene, and β-elemene were detected from 1-week-old Xoo-infected rice seedlings, by solid-phase microextraction-gas chromatography-mass spectrometry. All monoterpenes were constitutively released from rice seedlings before Xoo infection. However, (S)-limonene emission was further elicited after exposure of the seedlings to Xoo in coincidence with upregulation of limonene synthase gene (OsTPS20) transcripts. Only the stereospecific (S)-limonene [and not (R)-limonene or other monoterpenes] severely inhibited Xoo growth, as confirmed by disc diffusion and liquid culture assays. Rice seedlings showed suppressed pathogenic symptoms suggestive of resistance to Xoo infection after foliar treatment with (S)-limonene. Collectively, our findings suggest that (S)-limonene is a volatile phytoanticipin, which plays a significant role in suppressing Xoo growth in rice seedlings.

Bacterial leaf scorch distribution and isothermal lines (PROJECT NC-EM-08-02)

Treesearch

Gerard C. Adams; Mursel Catall; James Walla; Ann B. Gould

2013-01-01

Bacterial leaf scorch (BLS) of shade trees is the common name for a disease caused by Xylella fastidiosa, a xylem-inhabiting bacterium that has fastidious nutritional requirements and is difficult to culture or verify by culturing. Forest trees including oak, sycamore, elm, planetree, sweetgum, mulberry and maple are species susceptible to ...

Surviving floods: leaf gas films improve O₂ and CO₂ exchange, root aeration, and growth of completely submerged rice.

PubMed

Pedersen, Ole; Rich, Sarah Meghan; Colmer, Timothy David

2009-04-01

When completely submerged, the leaves of some species retain a surface gas film. Leaf gas films on submerged plants have recently been termed 'plant plastrons', analogous with the plastrons of aquatic insects. In aquatic insects, surface gas layers (i.e. plastrons) enlarge the gas-water interface to promote O₂ uptake when under water; however, the function of leaf gas films has rarely been considered. The present study demonstrates that gas films on leaves of completely submerged rice facilitate entry of O₂ from floodwaters when in darkness and CO₂ entry when in light. O₂ microprofiles showed that the improved gas exchange was not caused by differences in diffusive boundary layers adjacent to submerged leaves with or without gas films; instead, reduced resistance to gas exchange was probably due to the enlarged water-gas interface (cf. aquatic insects). When gas films were removed artificially, underwater net photosynthesis declined to only 20% of the rate with gas films present, such that, after 7 days of complete submergence, tissue sugar levels declined, and both shoot and root growth were reduced. Internal aeration of roots in anoxic medium, when shoots were in aerobic floodwater in darkness or when in light, was improved considerably when leaf gas films were present. Thus, leaf gas films contribute to the submergence tolerance of rice, in addition to those traits already recognized, such as the shoot-elongation response, aerenchyma and metabolic adjustments to O₂ deficiency and oxidative stress. © 2009 The Authors. Journal compilation © 2009 Blackwell Publishing Ltd.

Characterization of N2-fixing plant growth promoting endophytic and epiphytic bacterial community of Indian cultivated and wild rice (Oryza spp.) genotypes.

PubMed

Banik, Avishek; Mukhopadhaya, Subhra Kanti; Dangar, Tushar Kanti

2016-03-01

The diversity of endophytic and epiphytic diazotrophs in different parts of rice plants has specificity to the niche (i.e. leaf, stem and root) of different genotypes and nutrient availability of the organ. Inoculation of the indigenous, polyvalent diazotrophs can facilitate and sustain production of non-leguminous crops like rice. Therefore, N2-fixing plant growth promoting bacteria (PGPB) were isolated from different parts of three Indian cultivated [Oryza sativa L. var. Sabita (semi deep/deep water)/Swarna (rain fed shallow lowland)/Swarna-Sub1(submergence tolerant)] and a wild (O. eichingeri) rice genotypes which respond differentially to nitrogenous fertilizers. Thirty-five isolates from four rice genotypes were categorized based on acetylene reduction assay on nitrogenase activity, biochemical tests, BIOLOG and 16S rRNA gene sequencing. The bacteria produced 9.36-155.83 nmole C2H4 mg(-1) dry bacteria h(-1) and among them nitrogenase activity of 11 potent isolates was complemented by nifH-sequence analysis. Phylogenetic analysis based on 16S rDNA sequencing divided them into five groups (shared 95-100 % sequence homology with type strains) belonging to five classes-alpha (Ancylobacter, Azorhizobium, Azospirillum, Rhizobium, Bradyrhizobium, Sinorhizobium, Novosphingobium, spp.), beta (Burkholderia sp.), gamma (Acinetobacter, Aeromonas, Azotobacter, Enterobacter, Klebsiella, Pantoea, Pseudomonas, Stenotrophomonas spp.) Proteobacteria, Bacilli (Bacillus, Paenibacillus spp.) and Actinobacteria (Microbacterium sp.). Besides, all bacterial strains possessed the intrinsic PGP traits of like indole (0.44-7.4 µg ml(-1)), ammonia (0.18-6 mmol ml(-1)), nitrite (0.01-3.4 mol ml(-1)), and siderophore (from 0.16-0.57 μmol ml(-1)) production. Inoculation of rice (cv. Swarna) seedlings with selected isolates had a positive impact on plant growth parameters like shoot and root elongation which was correlated with in vitro PGP attributes. The results indicated that the

A proteomic analysis of leaf sheaths from rice.

PubMed

Shen, Shihua; Matsubae, Masami; Takao, Toshifumi; Tanaka, Naoki; Komatsu, Setsuko

2002-10-01

The proteins extracted from the leaf sheaths of rice seedlings were separated by 2-D PAGE, and analyzed by Edman sequencing and mass spectrometry, followed by database searching. Image analysis revealed 352 protein spots on 2-D PAGE after staining with Coomassie Brilliant Blue. The amino acid sequences of 44 of 84 proteins were determined; for 31 of these proteins, a clear function could be assigned, whereas for 12 proteins, no function could be assigned. Forty proteins did not yield amino acid sequence information, because they were N-terminally blocked, or the obtained sequences were too short and/or did not give unambiguous results. Fifty-nine proteins were analyzed by mass spectrometry; all of these proteins were identified by matching to the protein database. The amino acid sequences of 19 of 27 proteins analyzed by mass spectrometry were similar to the results of Edman sequencing. These results suggest that 2-D PAGE combined with Edman sequencing and mass spectrometry analysis can be effectively used to identify plant proteins.

Bacterial community variations in an alfalfa-rice rotation system revealed by 16S rRNA gene 454-pyrosequencing.

PubMed

Lopes, Ana R; Manaia, Célia M; Nunes, Olga C

2014-03-01

Crop rotation is a practice harmonized with the sustainable rice production. Nevertheless, the implications of this empirical practice are not well characterized, mainly in relation to the bacterial community composition and structure. In this study, the bacterial communities of two adjacent paddy fields in the 3rd and 4th year of the crop rotation cycle and of a nonseeded subplot were characterized before rice seeding and after harvesting, using 454-pyrosequencing of the 16S rRNA gene. Although the phyla Acidobacteria, Proteobacteria, Chloroflexi, Actinobacteria and Bacteroidetes predominated in all the samples, there were variations in relative abundance of these groups. Samples from the 3rd and 4th years of the crop rotation differed on the higher abundance of groups of presumable aerobic bacteria and of presumable anaerobic and acidobacterial groups, respectively. Members of the phylum Nitrospira were more abundant after rice harvest than in the previously sampled period. Rice cropping was positively correlated with the abundance of members of the orders Acidobacteriales and 'Solibacterales' and negatively with lineages such as Chloroflexi 'Ellin6529'. Studies like this contribute to understand variations occurring in the microbial communities in soils under sustainable rice production, based on real-world data. © 2013 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

Quantifying seasonal variation of leaf area index using near-infrared digital camera in a rice paddy

NASA Astrophysics Data System (ADS)

Hwang, Y.; Ryu, Y.; Kim, J.

2017-12-01

Digital camera has been widely used to quantify leaf area index (LAI). Numerous simple and automatic methods have been proposed to improve the digital camera based LAI estimates. However, most studies in rice paddy relied on arbitrary thresholds or complex radiative transfer models to make binary images. Moreover, only a few study reported continuous, automatic observation of LAI over the season in rice paddy. The objective of this study is to quantify seasonal variations of LAI using raw near-infrared (NIR) images coupled with a histogram shape-based algorithm in a rice paddy. As vegetation highly reflects the NIR light, we installed NIR digital camera 1.8 m above the ground surface and acquired unsaturated raw format images at one-hour intervals between 15 to 80 º solar zenith angles over the entire growing season in 2016 (from May to September). We applied a sub-pixel classification combined with light scattering correction method. Finally, to confirm the accuracy of the quantified LAI, we also conducted direct (destructive sampling) and indirect (LAI-2200) manual observations of LAI once per ten days on average. Preliminary results show that NIR derived LAI agreed well with in-situ observations but divergence tended to appear once rice canopy is fully developed. The continuous monitoring of LAI in rice paddy will help to understand carbon and water fluxes better and evaluate satellite based LAI products.

Investigating alternative strategies for managing bacterial angular leaf spot in strawberry nursery production

USDA-ARS?s Scientific Manuscript database

The focus of this article is to discuss some of the approaches we have tested for managing the bacterial pathogen Xanthomonas fragariae in infected strawberry nursery stock. X. fragariae causes angular leaf spot (ALS) in strawberry. The pathogen is transmitted to production fields almost exclusively...

Shared flowering phenology, insect pests, and pathogens among wild, weedy, and cultivated rice in the Mekong Delta, Vietnam: implications for transgenic rice.

PubMed

Cohen, Michael B; Arpaia, Salvatore; Lan, La Pham; Chau, Luong Minh; Snow, Allison A

2008-01-01

Many varieties of transgenic rice are under development in countries where wild and weedy relatives co-occur with the crop. To evaluate possible risks associated with pollen-mediated transgene dispersal, we conducted a two-year survey in Vietnam to examine overlapping flowering periods of rice (Oryza sativa L.), weedy rice (O. sativa), and wild rice (O. rufipogon Griff.), all of which are inter-fertile. We surveyed populations in two regions of the Mekong Delta, northern and southern, and at three sites in each of three habitats per region: fresh water, saline water, and acid sulfate soil. Weedy rice frequently flowered simultaneously with neighboring cultivated rice plants. Flowering was more seasonal in wild rice and often peaked in November and December. Peak flowering times of wild rice overlapped with adjacent rice fields at all of the saline sites and half of the acid sulfate sites. The longer flowering season of wild rice ensured that crop-to-wild gene flow was possible in fresh water habitats as well. Our second objective was to determine whether wild and weedy rice populations are exposed to pests that could be targeted by future transgenes, which may then provide fitness benefits. These populations shared many pathogen and insect herbivore species with cultivated rice (leaffolder, locust, cricket, planthoppers, rice bug, stem borer, sheath blight, blast, bacterial leaf blight, and brown spot). Damage by leaffolders and locusts was the most frequently observed insect feeding damage on all three rice types. Indicator species analysis revealed that most of the insect herbivores were associated with particular habitats, demonstrating the importance of broad geographic sampling for transgenic rice risk assessment. These survey data and the strong likelihood of gene flow from cultivated rice suggest that further studies are needed to examine the effects of transgenic traits such as resistance to pests on the abundance of wild and weedy rice.

Gibberellin-regulated gene in the basal region of rice leaf sheath encodes basic helix-loop-helix transcription factor.

PubMed

Komatsu, Setsuko; Takasaki, Hironori

2009-07-01

Genes regulated by gibberellin (GA) during leaf sheath elongation in rice seedlings were identified using the transcriptome approach. mRNA from the basal regions of leaf sheaths treated with GA3 was analyzed by high-coverage gene expression profiling. 33,004 peaks were detected, and 30 transcripts showed significant changes in the presence of GA3. Among these, basic helix-loop-helix transcription factor (AK073385) was significantly upregulated. Quantitative PCR analysis confirmed that expression of AK073385 was controlled by GA3 in a time- and dose-dependent manner. Basic helix-loop-helix transcription factor (AK073385) is therefore involved in the regulation of gene expression by GA3.

Do all leaf photosynthesis parameters of rice acclimate to elevated CO2 , elevated temperature, and their combination, in FACE environments?

PubMed

Cai, Chuang; Li, Gang; Yang, Hailong; Yang, Jiaheng; Liu, Hong; Struik, Paul C; Luo, Weihong; Yin, Xinyou; Di, Lijun; Guo, Xuanhe; Jiang, Wenyu; Si, Chuanfei; Pan, Genxing; Zhu, Jianguo

2018-04-01

Leaf photosynthesis of crops acclimates to elevated CO 2 and temperature, but studies quantifying responses of leaf photosynthetic parameters to combined CO 2 and temperature increases under field conditions are scarce. We measured leaf photosynthesis of rice cultivars Changyou 5 and Nanjing 9108 grown in two free-air CO 2 enrichment (FACE) systems, respectively, installed in paddy fields. Each FACE system had four combinations of two levels of CO 2 (ambient and enriched) and two levels of canopy temperature (no warming and warmed by 1.0-2.0°C). Parameters of the C 3 photosynthesis model of Farquhar, von Caemmerer and Berry (the FvCB model), and of a stomatal conductance (g s ) model were estimated for the four conditions. Most photosynthetic parameters acclimated to elevated CO 2 , elevated temperature, and their combination. The combination of elevated CO 2 and temperature changed the functional relationships between biochemical parameters and leaf nitrogen content for Changyou 5. The g s model significantly underestimated g s under the combination of elevated CO 2 and temperature by 19% for Changyou 5 and by 10% for Nanjing 9108 if no acclimation was assumed. However, our further analysis applying the coupled g s -FvCB model to an independent, previously published FACE experiment showed that including such an acclimation response of g s hardly improved prediction of leaf photosynthesis under the four combinations of CO 2 and temperature. Therefore, the typical procedure that crop models using the FvCB and g s models are parameterized from plants grown under current ambient conditions may not result in critical errors in projecting productivity of paddy rice under future global change. © 2017 John Wiley & Sons Ltd.

Mapped Clone and Functional Analysis of Leaf-Color Gene Ygl7 in a Rice Hybrid (Oryza sativa L. ssp. indica)

PubMed Central

Deng, Xiao-juan; Zhang, Hai-qing; Wang, Yue; He, Feng; Liu, Jin-ling; Xiao, Xiao; Shu, Zhi-feng; Li, Wei; Wang, Guo-huai; Wang, Guo-liang

2014-01-01

Leaf-color is an effective marker to identify the hybridization of rice. Leaf-color related genes function in chloroplast development and the photosynthetic pigment biosynthesis of higher plants. The ygl7 (yellow-green leaf 7) is a mutant with spontaneous yellow-green leaf phenotype across the whole lifespan but with no change to its yield traits. We cloned gene Ygl7 (Os03g59640) which encodes a magnesium-chelatase ChlD protein. Expression of ygl7 turns green-leaves to yellow, whereas RNAi-mediated silence of Ygl7 causes a lethal phenotype of the transgenic plants. This indicates the importance of the gene for rice plant. On the other hand, it corroborates that ygl7 is a non-null mutants. The content of photosynthetic pigment is lower in Ygl7 than the wild type, but its light efficiency was comparatively high. All these results indicated that the mutational YGL7 protein does not cause a complete loss of original function but instead acts as a new protein performing a new function. This new function partially includes its preceding function and possesses an additional feature to promote photosynthesis. Chl1, Ygl98, and Ygl3 are three alleles of the OsChlD gene that have been documented previously. However, mutational sites of OsChlD mutant gene and their encoded protein products were different in the three mutants. The three mutants have suppressed grain output. In our experiment, plant materials of three mutants (ygl7, chl1, and ygl98) all exhibited mutational leaf-color during the whole growth period. This result was somewhat different from previous studies. We used ygl7 as female crossed with chl1 and ygl98, respectively. Both the F1 and F2 generation display yellow-green leaf phenotype with their chlorophyll and carotenoid content falling between the values of their parents. Moreover, we noted an important phenomenon: ygl7-NIL's leaf-color is yellow, not yellowy-green, and this is also true of all back-crossed offspring with ygl7. PMID:24932524

Mapped clone and functional analysis of leaf-color gene Ygl7 in a rice hybrid (Oryza sativa L. ssp. indica).

PubMed

Deng, Xiao-juan; Zhang, Hai-qing; Wang, Yue; He, Feng; Liu, Jin-ling; Xiao, Xiao; Shu, Zhi-feng; Li, Wei; Wang, Guo-huai; Wang, Guo-liang

2014-01-01

Leaf-color is an effective marker to identify the hybridization of rice. Leaf-color related genes function in chloroplast development and the photosynthetic pigment biosynthesis of higher plants. The ygl7 (yellow-green leaf 7) is a mutant with spontaneous yellow-green leaf phenotype across the whole lifespan but with no change to its yield traits. We cloned gene Ygl7 (Os03g59640) which encodes a magnesium-chelatase ChlD protein. Expression of ygl7 turns green-leaves to yellow, whereas RNAi-mediated silence of Ygl7 causes a lethal phenotype of the transgenic plants. This indicates the importance of the gene for rice plant. On the other hand, it corroborates that ygl7 is a non-null mutants. The content of photosynthetic pigment is lower in Ygl7 than the wild type, but its light efficiency was comparatively high. All these results indicated that the mutational YGL7 protein does not cause a complete loss of original function but instead acts as a new protein performing a new function. This new function partially includes its preceding function and possesses an additional feature to promote photosynthesis. Chl1, Ygl98, and Ygl3 are three alleles of the OsChlD gene that have been documented previously. However, mutational sites of OsChlD mutant gene and their encoded protein products were different in the three mutants. The three mutants have suppressed grain output. In our experiment, plant materials of three mutants (ygl7, chl1, and ygl98) all exhibited mutational leaf-color during the whole growth period. This result was somewhat different from previous studies. We used ygl7 as female crossed with chl1 and ygl98, respectively. Both the F1 and F2 generation display yellow-green leaf phenotype with their chlorophyll and carotenoid content falling between the values of their parents. Moreover, we noted an important phenomenon: ygl7-NIL's leaf-color is yellow, not yellowy-green, and this is also true of all back-crossed offspring with ygl7.

Bacterial Leaf Scorch of Amenity Trees a Wide-Spread Problem of Economic Significance to the Urban Forest

Treesearch

James Lashomb; Alan Iskra; Ann Brooks Gould; George Hamilton

2003-01-01

Bacterial leaf scorch (BLS) of amenity trees is caused by the bacterium Xylella fastidiosa, a xylem-limited pathogen that causes water stress resulting in leaf scorch, decline, and eventual death of affected trees. Recent surveys indicate that BLS is widespread throughout the eastern half of the United States. In New Jersey, BLS primarily affects red and pin oaks...

Interactions between senescence and leaf orientation determine in situ patterns of photosynthesis and photoinhibition in field-grown rice

PubMed

Murchie; Chen; Hubbart; Peng; Horton

1999-02-01

Photosynthesis and photoinhibition in field-grown rice (Oryza sativa L.) were examined in relation to leaf age and orientation. Two varieties (IR72 and IR65598-112-2 [BSI206]) were grown in the field in the Philippines during the dry season under highly irrigated, well-fertilized conditions. Flag leaves were examined 60 and 100 d after transplanting. Because of the upright nature of 60-d-old rice leaves, patterns of photosynthesis were determined by solar movements: light falling on the exposed surface in the morning, a low incident angle of irradiance at midday, and light striking the opposite side of the leaf blade in the afternoon. There was an early morning burst of CO2 assimilation and high levels of saturation of photosystem II electron transfer as incident irradiance reached a maximum level. However, by midday the photochemical efficiency increased again almost to maximum. Leaves that were 100 d old possessed a more horizontal orientation and were found to suffer greater levels of photoinhibition than younger leaves, and this was accompanied by increases in the de-epoxidation state of the xanthophyll cycle. Older leaves had significantly lower chlorophyll content but only slightly diminished photosynthesis capacity.

Development of breeding lines with three pyramided resistance genes that confer broad-spectrum bacterial blight resistance and their molecular analysis in rice.

PubMed

Suh, Jung-Pil; Jeung, Ji-Ung; Noh, Tae-Hwan; Cho, Young-Chan; Park, So-Hyun; Park, Hyun-Su; Shin, Mun-Sik; Kim, Chung-Kon; Jena, Kshirod K

2013-02-08

The development of resistant cultivars has been the most effective and economical strategy to control bacterial leaf blight (BB) disease of rice caused by Xanthomonas oryzae pv. oryzae (Xoo). Molecular markers have made it possible to identify and pyramid valuable genes of agronomic importance in resistance rice breeding. In this study, three resistance genes (Xa4 + xa5 + Xa21) were transferred from an indica donor (IRBB57), using a marker-assisted backcrossing (MAB) breeding strategy, into a BB-susceptible elite japonica rice cultivar, Mangeumbyeo, which is high yielding with good grain quality. Our analysis led to the development of three elite advanced backcross breeding lines (ABL) with three resistance genes by foreground and phenotypic selection in a japonica genetic background without linkage drag. The background genome recovery of the ABL expressed more than 92.1% using genome-wide SSR marker analysis. The pathogenicity assays of three resistance-gene-derived ABL were conducted under glasshouse conditions with the 18 isolates of Xoo prevalent in Korea. The ABL exhibited very small lesion lengths, indicating a hypersensitive reaction to all 18 isolates of Xoo, with agronomic and grain quality traits similar to those of the recurrent parent. Pyramiding the resistance genes Xa4, xa5 and Xa21 provided a higher resistance to Xoo than the introduction of the individual resistance genes. Additionally, the combination of two dominant and one recessive BB resistance gene did not express any negative effect on agronomic traits in the ABL. The strategy of simultaneous foreground and phenotypic selection to introduce multiple R genes is very useful to reduce the cost and the time required for the isolation of desirable recombinants with target resistance genes in rice. The resistance-gene-derived ABL have practical breeding value without a yield penalty by providing broad-spectrum resistance against most of the existing isolates of BB in South Korea and will

Sites of action of elevated CO2 on leaf development in rice: discrimination between the effects of elevated CO2 and nitrogen deficiency.

PubMed

Tsutsumi, Koichi; Konno, Masae; Miyazawa, Shin-Ichi; Miyao, Mitsue

2014-02-01

Elevated CO2 concentrations (eCO2) trigger various plant responses. Despite intensive studies of these responses, the underlying mechanisms remain obscure. In this work, we investigated when and how leaf physiology and anatomy are affected by eCO2 in rice plants. We analyzed the most recently fully expanded leaves that developed successively after transfer of the plant to eCO2. To discriminate between the effects of eCO2 and those of nitrogen deficiency, we used three different levels of N application. We found that a decline in the leaf soluble protein content (on a leaf area basis) at eCO2 was only observed under N deficiency. The length and width of the leaf blade were reduced by both eCO2 and N deficiency, whereas the blade thickness was increased by eCO2 but was not affected by N deficiency. The change in length by eCO2 became detectable in the secondly fully expanded leaf, and those in width and thickness in the thirdly fully expanded leaf, which were at the leaf developmental stages P4 and P3, respectively, at the onset of the eCO2 treatment. The decreased blade length at eCO2 was associated with a decrease in the epidermal cell number on the adaxial side and a reduction in cell length on the abaxial side. The decreased width resulted from decreased numbers of small vascular bundles and epidermal cell files. The increased thickness was ascribed mainly to enhanced development of bundle sheath extensions at the ridges of vascular bundles. These observations enable us to identify the sites of action of eCO2 on rice leaf development.

An ATP-binding cassette subfamily G full transporter is essential for the retention of leaf water in both wild barley and rice.

PubMed

Chen, Guoxiong; Komatsuda, Takao; Ma, Jian Feng; Nawrath, Christiane; Pourkheirandish, Mohammad; Tagiri, Akemi; Hu, Yin-Gang; Sameri, Mohammad; Li, Xinrong; Zhao, Xin; Liu, Yubing; Li, Chao; Ma, Xiaoying; Wang, Aidong; Nair, Sudha; Wang, Ning; Miyao, Akio; Sakuma, Shun; Yamaji, Naoki; Zheng, Xiuting; Nevo, Eviatar

2011-07-26

Land plants have developed a cuticle preventing uncontrolled water loss. Here we report that an ATP-binding cassette (ABC) subfamily G (ABCG) full transporter is required for leaf water conservation in both wild barley and rice. A spontaneous mutation, eibi1.b, in wild barley has a low capacity to retain leaf water, a phenotype associated with reduced cutin deposition and a thin cuticle. Map-based cloning revealed that Eibi1 encodes an HvABCG31 full transporter. The gene was highly expressed in the elongation zone of a growing leaf (the site of cutin synthesis), and its gene product also was localized in developing, but not in mature tissue. A de novo wild barley mutant named "eibi1.c," along with two transposon insertion lines of rice mutated in the ortholog of HvABCG31 also were unable to restrict water loss from detached leaves. HvABCG31 is hypothesized to function as a transporter involved in cutin formation. Homologs of HvABCG31 were found in green algae, moss, and lycopods, indicating that this full transporter is highly conserved in the evolution of land plants.

An ATP-binding cassette subfamily G full transporter is essential for the retention of leaf water in both wild barley and rice

PubMed Central

Chen, Guoxiong; Komatsuda, Takao; Ma, Jian Feng; Nawrath, Christiane; Pourkheirandish, Mohammad; Tagiri, Akemi; Hu, Yin-Gang; Sameri, Mohammad; Li, Xinrong; Zhao, Xin; Liu, Yubing; Li, Chao; Ma, Xiaoying; Wang, Aidong; Nair, Sudha; Wang, Ning; Miyao, Akio; Sakuma, Shun; Yamaji, Naoki; Zheng, Xiuting; Nevo, Eviatar

2011-01-01

Land plants have developed a cuticle preventing uncontrolled water loss. Here we report that an ATP-binding cassette (ABC) subfamily G (ABCG) full transporter is required for leaf water conservation in both wild barley and rice. A spontaneous mutation, eibi1.b, in wild barley has a low capacity to retain leaf water, a phenotype associated with reduced cutin deposition and a thin cuticle. Map-based cloning revealed that Eibi1 encodes an HvABCG31 full transporter. The gene was highly expressed in the elongation zone of a growing leaf (the site of cutin synthesis), and its gene product also was localized in developing, but not in mature tissue. A de novo wild barley mutant named “eibi1.c,” along with two transposon insertion lines of rice mutated in the ortholog of HvABCG31 also were unable to restrict water loss from detached leaves. HvABCG31 is hypothesized to function as a transporter involved in cutin formation. Homologs of HvABCG31 were found in green algae, moss, and lycopods, indicating that this full transporter is highly conserved in the evolution of land plants. PMID:21737747

Evaluation of hyperspectral LiDAR for monitoring rice leaf nitrogen by comparison with multispectral LiDAR and passive spectrometer

NASA Astrophysics Data System (ADS)

Sun, Jia; Shi, Shuo; Gong, Wei; Yang, Jian; Du, Lin; Song, Shalei; Chen, Biwu; Zhang, Zhenbing

2017-01-01

Fast and nondestructive assessment of leaf nitrogen concentration (LNC) is critical for crop growth diagnosis and nitrogen management guidance. In the last decade, multispectral LiDAR (MSL) systems have promoted developments in the earth and ecological sciences with the additional spectral information. With more wavelengths than MSL, the hyperspectral LiDAR (HSL) system provides greater possibilities for remote sensing crop physiological conditions. This study compared the performance of ASD FieldSpec Pro FR, MSL, and HSL for estimating rice (Oryza sativa) LNC. Spectral reflectance and biochemical composition were determined in rice leaves of different cultivars (Yongyou 4949 and Yangliangyou 6) throughout two growing seasons (2014-2015). Results demonstrated that HSL provided the best indicator for predicting rice LNC, yielding a coefficient of determination (R2) of 0.74 and a root mean square error of 2.80 mg/g with a support vector machine, similar to the performance of ASD (R2 = 0.73). Estimation of rice LNC could be significantly improved with the finer spectral resolution of HSL compared with MSL (R2 = 0.56).

Pyramiding transgenes for multiple resistance in rice against bacterial blight, yellow stem borer and sheath blight.

PubMed

Datta, K; Baisakh, N; Thet, K Maung; Tu, J; Datta, S K

2002-12-01

Here we describe the development of transgene-pyramided stable elite rice lines resistant to disease and insect pests by conventional crossing of two transgenic parental lines transformed independently with different genes. The Xa21 gene (resistance to bacterial blight), the Bt fusion gene (for insect resistance) and the chitinase gene (for tolerance of sheath blight) were combined in a single rice line by reciprocal crossing of two transgenic homozygous IR72 lines. F4 plant lines carrying all the genes of interest stably were identified using molecular methods. The identified lines, when exposed to infection caused by Xanthomonas oryzae pv oryzae, showed resistance to bacterial blight. Neonate larval mortality rates of yellow stem borer ( Scirpophaga incertulas) in an insect bioassay of the same identified lines were 100%. The identified line pyramided with different genes to protect against yield loss showed high tolerance of sheath blight disease caused by Rhizoctonia solani.

Characterization and comparison of the temporal dynamics of ruminal bacterial microbiota colonizing rice straw and alfalfa hay within ruminants.

PubMed

Liu, Junhua; Zhang, Mengling; Xue, Chunxu; Zhu, Weiyun; Mao, Shengyong

2016-12-01

Three ruminally cannulated Holstein cows were used to characterize the dynamics of bacterial colonization of rice straw and alfalfa hay and to assess the differences in the composition and inferred gene function of the colonized microbiota between these 2 forages. Nonincubated (0h) rice straw and alfalfa hay samples and residues in nylon bags incubated for 0.5, 2, 6, 16, and 48h were analyzed for dry matter and were used for DNA extraction and MiSeq (Illumina Inc., San Diego, CA) sequencing of the 16S rRNA gene. The microbial communities that colonized the air-dried and nonincubated (0h) rice straw and alfalfa hay were both dominated by members of the Proteobacteria (contributing toward 70.47% of the 16S RNA reads generated). In situ incubation of the 2 forages revealed major shifts in the community composition: Proteobacteria were replaced within 30min by members belonging to the Bacteroidetes and Firmicutes, contributing toward 51.9 and 36.6% of the 16S rRNA reads generated, respectively. A second significant shift was observed after 6h of rumen incubation, when members of the Spirochaetes and Fibrobacteria phyla became abundant in the forage-adherent community. During the first 30min of rumen incubation, ~20.7 and 36.1% of the rice straw and alfalfa hay, respectively, were degraded, whereas little biomass degradation occurred between 30min and 2h after the rice straw or alfalfa hay was placed in the rumen. Significant differences were noted in attached bacterial community structure between the 2 forage groups, and the abundances of dominant genera Anaeroplasma, Butyrivibrio, Fibrobacter, and Prevotella were affected by the forage types. Real-time PCR results showed that the 16S rRNA copies of total bacteria attached to these 2 forages were affected by the forage types and incubation time, and higher numbers of attached bacterial 16S rRNA were observed in the alfalfa hay samples than in the rice straw from 0.5 to 16h of incubation. The metagenomes predicted by

Chromosome mapping, molecular cloning and expression analysis of a novel gene response for leaf width in rice.

PubMed

Wu, Yahui; Luo, Lixin; Chen, Likai; Tao, Xingxing; Huang, Ming; Wang, Hui; Chen, Zhiqiang; Xiao, Wuming

2016-11-18

Genetic analysis revealed that narrow leaf, small panicle, thin and slender stems as well as low fertility rate of an Indica rice variety were recessive traits and controlled by a single gene. Applying map-based cloning strategy, a novel narrow leaf gene, which was named nal11 was delimited to an interval of 58.3 kb between the InDel markers N10 and InD5016. There are 9 genes in the mapping interval, and only a heat shock DNAJ protein encode gene (Os07g09450) has a specific G to T SNP, which was occurred at the last base of the second exon of Os07g09450 in ZYX. 5' and 3' RACE result shown that there were two transcripts in NAL11, and the SNP in nal11 leads to a variable shear of mRNA. In addition, this type of mRNA alternative splicing together with a stop codon closely followed the SNP which caused termination of translation destroyed the DNAJ domain of nal11's product. These results suggested that the heat shock DNAJ gene was most likely to be the candidate gene of nal11. The results of RT-PCR and real-time PCR further verified that the SNP in the ZYX-nal11 gene affects mRNA splicing pattern. Phenotype of ZYX may be caused by a statistically significant reduction in the total number of small veins in leaf, size and number of small vascular bundles and cells in stems, similar to several previous reported mutations. The basic molecular information we provide here will be useful for further investigations of the physiological function of the heat shock DNAJ gene, which will be helpful in better understanding the role of the DNAJ family in regulation of plant type traits such as leaf width of rice. Copyright © 2016 Elsevier Inc. All rights reserved.

Dietary Supplementation with Rice Bran or Navy Bean Alters Gut Bacterial Metabolism in Colorectal Cancer Survivors

PubMed Central

Sheflin, Amy M.; Borresen, Erica C.; Kirkwood, Jay S.; Boot, Claudia M.; Whitney, Alyssa K.; Lu, Shen; Brown, Regina J.; Broeckling, Corey D.; Ryan, Elizabeth P.; Weir, Tiffany L.

2016-01-01

Scope Heat-stabilized rice bran and cooked navy bean powder contain a variety of phytochemicals that are fermented by colonic microbiota and may influence intestinal health. Dietary interventions with these foods should be explored for modulating colorectal cancer risk. Methods and results A randomized-controlled pilot clinical trial investigated the effects of eating heat-stabilized rice bran (30g/day) or cooked navy bean powder (35g/day) on gut microbiota and metabolites (NCT01929122). Twenty-nine overweight/obese volunteers with a prior history of colorectal cancer consumed a study-provided meal and snack daily for 28 days. Volunteers receiving rice bran or bean powder showed increased gut bacterial diversity and altered gut microbial composition at 28 days compared to baseline. Supplementation with rice bran or bean powder increased total dietary fiber intake similarly, yet only rice bran intake led to a decreased Firmicutes:Bacteroidetes ratio and increased short chain fatty acids (propionate and acetate) in stool after 14 days but not at 28 days. Conclusion These findings support modulation of gut microbiota and fermentation by-products by heat-stabilized rice bran and suggest that foods with similar ability to increase dietary fiber intake may not have equal effects on gut microbiota and microbial metabolism. PMID:27461523

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

PubMed

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

2011-07-01

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

DgcA, a diguanylate cyclase from Xanthomonas oryzae pv. oryzae regulates bacterial pathogenicity on rice

PubMed Central

Su, Jianmei; Zou, Xia; Huang, Liangbo; Bai, Tenglong; Liu, Shu; Yuan, Meng; Chou, Shan-Ho; He, Ya-Wen; Wang, Haihong; He, Jin

2016-01-01

Xanthomonas oryzae pv. oryzae (Xoo) is the causal agent of rice blight disease as well as a serious phytopathogen worldwide. It is also one of the model organisms for studying bacteria-plant interactions. Current progress in bacterial signal transduction pathways has identified cyclic di-GMP as a major second messenger molecule in controlling Xanthomonas pathogenicity. However, it still remains largely unclear how c-di-GMP regulates the secretion of bacterial virulence factors in Xoo. In this study, we focused on the important roles played by DgcA (XOO3988), one of our previously identified diguanylate cyclases in Xoo, through further investigating the phenotypes of several dgcA-related mutants, namely, the dgcA-knockout mutant ΔdgcA, the dgcA overexpression strain OdgcA, the dgcA complemented strain CdgcA and the wild-type strain. The results showed that dgcA negatively affected virulence, EPS production, bacterial autoaggregation and motility, but positively triggered biofilm formation via modulating the intracellular c-di-GMP levels. RNA-seq data further identified 349 differentially expressed genes controlled by DgcA, providing a foundation for a more solid understanding of the signal transduction pathways in Xoo. Collectively, the present study highlights DgcA as a major regulator of Xoo virulence, and can serve as a potential target for preventing rice blight diseases. PMID:27193392

The effect of silicon on the leaf proteome of rice (Oryza sativa L.) plants under cadmium-stress.

PubMed

Nwugo, Chika C; Huerta, Alfredo J

2011-02-04

The best known silicon (Si)-accumulating plant, rice (Oryza sativa L.), stores most of its Si in leaves, but the importance of Si has been limited to a mechanical role. Our initial studies showed that Si-induced cadmium (Cd) tolerance is mediated by the enhancement of instantaneous water-use-efficiency, carboxylation efficiency of ribulose-1,5-bisphosphate carboxylase oxygenase (RuBisCO), and light-use-efficiency in leaves of rice plants. In this study, we investigated changes in the rice leaf proteome in order to identify molecular mechanisms involved in Si-induced Cd tolerance. Our study identified 60 protein spots that were differentially regulated due to Cd and/or Si treatments. Among them, 50 were significantly regulated by Si, including proteins associated with photosynthesis, redox homeostasis, regulation/protein synthesis, pathogen response and chaperone activity. Interestingly, we observed a Si-induced up-regulation of a class III peroxidase and a thaumatin-like protein irrespective of Cd treatment, in addition to a Cd-induced up-regulation of protein disulfide isomerase, a HSP70 homologue, a NADH-ubiquinone oxidoreductase, and a putative phosphogluconate dehydrogenase, especially in the presence of Si. Taken together, our study sheds light on molecular mechanisms involved in Si-induced Cd tolerance in rice leaves and suggests a more active involvement of Si in plant physiological processes than previously proposed.

Fine Mapping of Carbon Assimilation Rate 8, a Quantitative Trait Locus for Flag Leaf Nitrogen Content, Stomatal Conductance and Photosynthesis in Rice

PubMed Central

Adachi, Shunsuke; Yoshikawa, Kazuaki; Yamanouchi, Utako; Tanabata, Takanari; Sun, Jian; Ookawa, Taiichiro; Yamamoto, Toshio; Sage, Rowan F.; Hirasawa, Tadashi; Yonemaru, Junichi

2017-01-01

Increasing the rate of leaf photosynthesis is one important approach for increasing grain yield in rice (Oryza sativa). Exploiting the natural variation in CO2 assimilation rate (A) between rice cultivars using quantitative genetics is one promising means to identify genes contributing to higher photosynthesis. In this study, we determined precise location of Carbon Assimilation Rate 8 (CAR8) by crossing a high-yielding indica cultivar with a Japanese commercial cultivar. Fine mapping suggested that CAR8 encodes a putative Heme Activator Protein 3 (OsHAP3) subunit of a CCAAT-box-binding transcription factor called OsHAP3H. Sequencing analysis revealed that the indica allele of CAR8 has a 1-bp deletion at 322 bp from the start codon, resulting in a truncated protein of 125 amino acids. In addition, CAR8 is identical to DTH8/Ghd8/LHD1, which was reported to control rice flowering date. The increase of A is largely due to an increase of RuBP regeneration rate via increased leaf nitrogen content, and partially explained by reduced stomatal limitation via increased stomatal conductance relative to A. This allele also increases hydraulic conductivity, which would promote higher stomatal conductance. This indicates that CAR8 affects multiple physiological aspects relating to photosynthesis. The detailed analysis of molecular functions of CAR8 would help to understand the association between photosynthesis and flowering and demonstrate specific genetic mechanisms that can be exploited to improve photosynthesis in rice and potentially other crops. PMID:28197156

Influence of straw incorporation with and without straw decomposer on soil bacterial community structure and function in a rice-wheat cropping system.

PubMed

Zhao, Jun; Ni, Tian; Xun, Weibing; Huang, Xiaolei; Huang, Qiwei; Ran, Wei; Shen, Biao; Zhang, Ruifu; Shen, Qirong

2017-06-01

To study the influence of straw incorporation with and without straw decomposer on bacterial community structure and biological traits, a 3-year field experiments, including four treatments: control without fertilizer (CK), chemical fertilizer (NPK), chemical fertilizer plus 7500 kg ha -1 straw incorporation (NPKS), and chemical fertilizer plus 7500 kg ha -1 straw incorporation and 300 kg ha -1 straw decomposer (NPKSD), were performed in a rice-wheat cropping system in Changshu (CS) and Jintan (JT) city, respectively. Soil samples were taken right after wheat (June) and rice (October) harvest in both sites, respectively. The NPKS and NPKSD treatments consistently increased crop yields, cellulase activity, and bacterial abundance in both sampling times and sites. Moreover, the NPKS and NPKSD treatments altered soil bacterial community structure, particularly in the wheat harvest soils in both sites, separating from the CK and NPK treatments. In the rice harvest soils, both NPKS and NPKSD treatments had no considerable impacts on bacterial communities in CS, whereas the NPKSD treatment significantly shaped bacterial communities compared to the other treatments in JT. These practices also significantly shifted the bacterial composition of unique operational taxonomic units (OTUs) rather than shared OTUs. The relative abundances of copiotrophic bacteria (Proteobacteria, Betaproteobacteria, and Actinobacteria) were positively correlated with soil total N, available N, and available P. Taken together, these results indicate that application of straw incorporation with and without straw decomposer could particularly stimulate the copiotrophic bacteria, enhance the soil biological activity, and thus, contribute to the soil productivity and sustainability in agro-ecosystems.

Indoleacetic acid production and plant growth promoting potential of bacterial endophytes isolated from rice (Oryza sativa L.) seeds.

PubMed

Shahzad, Raheem; Waqas, Muhammad; Khan, Abdul Latif; Al-Hosni, Khadija; Kang, Sang-Mo; Seo, Chang-Woo; Lee, In-Jung

2017-06-01

Bacterial endophytes from the phyllosphere and rhizosphere have been used to produce bioactive metabolites and to promote plant growth. However, little is known about the endophytes residing in seeds. This study aimed to isolate and identify seed-borne bacterial endophytes from rice and elucidate their potential for phytohormone production and growth enhancement. The isolated endophytes included Micrococcus yunnanensis RWL-2, Micrococcus luteus RWL-3, Enterobacter soli RWL-4, Leclercia adecarboxylata RWL-5, Pantoea dispersa RWL-6, and Staphylococcus epidermidis RWL-7, which were identified using 16S rRNA sequencing and phylogenetic analysis. These strains were analyzed for indoleacetic acid (IAA) production by using GC-MS and IAA was found in the range of 11.50 ± 0.77 μg ml -1 to 38.80 ± 1.35 μg ml -1 . We also assessed the strains for plant growth promoting potential because these isolates were able to produce IAA in pure culture. Most of the growth attributes of rice plants (shoot and root length, fresh and dry biomass, and chlorophyll content) were significantly increased by bacterial endophytes compared to the controls. These results show that IAA producing bacterial endophytes can improve hostplant growth traits and can be used as bio-fertilizers.

Silencing of the Rice Gene LRR1 Compromises Rice Xa21 Transcript Accumulation and XA21-Mediated Immunity.

PubMed

Caddell, Daniel F; Park, Chang-Jin; Thomas, Nicholas C; Canlas, Patrick E; Ronald, Pamela C

2017-12-01

The rice immune receptor XA21 confers resistance to Xanthomonas oryzae pv. oryzae (Xoo), the causal agent of bacterial leaf blight. We previously demonstrated that an auxilin-like protein, XA21 BINDING PROTEIN 21 (XB21), positively regulates resistance to Xoo. To further investigate the function of XB21, we performed a yeast two-hybrid screen. We identified 22 unique XB21 interacting proteins, including LEUCINE-RICH REPEAT PROTEIN 1 (LRR1), which we selected for further analysis. Silencing of LRR1 in the XA21 genetic background (XA21-LRR1Ri) compromises resistance to Xoo compared with control XA21 plants. XA21-LRR1Ri plants have reduced Xa21 transcript levels and reduced expression of genes that serve as markers of XA21-mediated activation. Overexpression of LRR1 is insufficient to alter resistance to Xoo in rice lines lacking XA21. Taken together, our results indicate that LRR1 is required for wild-type Xa21 transcript expression and XA21-mediated immunity.

Analyzing the performance of fluorescence parameters in the monitoring of leaf nitrogen content of paddy rice

PubMed Central

Yang, Jian; Gong, Wei; Shi, Shuo; Du, Lin; Sun, Jia; Song, Shalei; Chen, Biwu; Zhang, Zhenbing

2016-01-01

Leaf nitrogen content (LNC) is a significant factor which can be utilized to monitor the status of paddy rice and it requires a reliable approach for fast and precise quantification. This investigation aims to quantitatively analyze the correlation between fluorescence parameters and LNC based on laser-induced fluorescence (LIF) technology. The fluorescence parameters exhibited a consistent positive linear correlation with LNC in different growing years (2014 and 2015) and different rice cultivars. The R2 of the models varied from 0.6978 to 0.9045. Support vector machine (SVM) was then utilized to verify the feasibility of the fluorescence parameters for monitoring LNC. Comparison of the fluorescence parameters indicated that F740 is the most sensitive (the R2 of linear regression analysis of the between predicted and measured values changed from 0.8475 to 0.9226, and REs ranged from 3.52% to 4.83%) to the changes in LNC among all fluorescence parameters. Experimental results demonstrated that fluorescence parameters based on LIF technology combined with SVM is a potential method for realizing real-time, non-destructive monitoring of paddy rice LNC, which can provide guidance for the decision-making of farmers in their N fertilization strategies. PMID:27350029

Influence of leaf vein density and thickness on hydraulic conductance and photosynthesis in rice (Oryza sativa L.) during water stress.

PubMed

Tabassum, Muhammad Adnan; Zhu, Guanglong; Hafeez, Abdul; Wahid, Muhammad Atif; Shaban, Muhammad; Li, Yong

2016-11-16

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 (K plant ) 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 (g s ), and K plant 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, g s and K plant were positively correlated with each other, and they were negatively correlated with LVD. A, g s and K plant 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.

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

Inferring Roles in Defense from Metabolic Allocation of Rice Diterpenoids.

PubMed

Lu, Xuan; Zhang, Juan; Brown, Benjamin; Li, Riqing; Rodríguez-Romero, Julio; Berasategui, Aileen; Liu, Bo; Xu, Meimei; Luo, Dangping; Pan, Zhiqiang; Baerson, Scott; Gershenzon, Jonathan; Li, Zhaohu; Sesma, Ane; Yang, Bing; Peters, Reuben J

2018-04-24

Among their responses to microbial infection, plants deploy an arsenal of natural antibiotic products. These historically have been identified on the basis of their antibiotic activity in vitro, which leaves open the question of their relevance to defense in planta. The vast majority of such natural products from the important crop plant rice (Oryza sativa) are diterpenoids whose biosynthesis proceeds via either ent- or syn- copalyl diphosphate (CPP) intermediates, and which were isolated on the basis of their antibiotic activity against the fungal blast pathogen Magnaporthe oryzae. However, rice plants in which the gene for the syn-CPP synthase Os-CPS4 is knocked-out do not exhibit increased susceptibility to M. oryzae. Here we show that knocking-out or knocking-down Os-CPS4 actually decreases susceptibility to the bacterial leaf blight pathogen Xanthomonas oryzae. By contrast, genetic manipulation of the gene for the ent-CPP synthase Os-CPS2 alters susceptibility to both M. oryzae and X. oryzae. Despite the secretion of diterpenoids dependent on Os-CPS2 or Os-CPS4 from roots, neither knock-out exhibited significant changes in the composition of their rhizosphere bacterial communities. Nevertheless, rice plants allocate substantial metabolic resources towards syn- and ent-CPP derived diterpenoids upon infection/induction. Further investigation revealed that Os-CPS4 plays a role in fungal non-host disease resistance. Thus, examination of metabolic allocation provides important clues into physiological function. © 2018 American Society of Plant Biologists. All rights reserved.

Leaf gas exchange, carbon isotope discrimination, and grain yield in contrasting rice genotypes subjected to water deficits during the reproductive stage.

PubMed

Centritto, Mauro; Lauteri, Marco; Monteverdi, Maria Cristina; Serraj, Rachid

2009-01-01

Genotypic variations in leaf gas exchange and yield were analysed in five upland-adapted and three lowland rice cultivars subjected to a differential soil moisture gradient, varying from well-watered to severely water-stressed conditions. A reduction in the amount of water applied resulted in a significant decrease in leaf gas exchange and, subsequently, in above-ground dry mass and grain yield, that varied among genotypes and distance from the line source. The comparison between the variable J and the Delta values in recently synthesized sugars methods, yielded congruent estimations of mesophyll conductance (g(m)), confirming the reliability of these two techniques. Our data demonstrate that g(m) is a major determinant of photosynthesis (A), because rice genotypes with inherently higher g(m) were capable of keeping higher A in stressed conditions. Furthermore, A, g(s), and g(m) of water-stressed genotypes rapidly recovered to the well-watered values upon the relief of water stress, indicating that drought did not cause any lasting metabolic limitation to photosynthesis. The comparisons between the A/C(i) and corresponding A/C(c) curves, measured in the genotypes that showed intrinsically higher and lower instantaneous A, confirmed this finding. Moreover, the effect of drought stress on grain yield was correlated with the effects on both A and total diffusional limitations to photosynthesis. Overall, these data indicate that genotypes which showed higher photosynthesis and conductances were also generally more productive across the entire soil moisture gradient. The analysis of Delta revealed a substantial variation of water use efficiency among the genotypes, both on the long-term (leaf pellet analysis) and short-term scale (leaf soluble sugars analysis).

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

PubMed Central

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

2011-01-01

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

A bacterial-type ABC transporter is involved in aluminum tolerance in rice.

PubMed

Huang, Chao Feng; Yamaji, Naoki; Mitani, Namiki; Yano, Masahiro; Nagamura, Yoshiaki; Ma, Jian Feng

2009-02-01

Aluminum (Al) toxicity is a major factor limiting crop production in acidic soil, but the molecular mechanisms of Al tolerance are poorly understood. Here, we report that two genes, STAR1 (for sensitive to Al rhizotoxicity1) and STAR2, are responsible for Al tolerance in rice. STAR1 encodes a nucleotide binding domain, while STAR2 encodes a transmembrane domain, of a bacterial-type ATP binding cassette (ABC) transporter. Disruption of either gene resulted in hypersensitivity to aluminum toxicity. Both STAR1 and STAR2 are expressed mainly in the roots and are specifically induced by Al exposure. Expression in onion epidermal cells, rice protoplasts, and yeast showed that STAR1 interacts with STAR2 to form a complex that localizes to the vesicle membranes of all root cells, except for those in the epidermal layer of the mature zone. When expressed together in Xenopus laevis oocytes, STAR1/2 shows efflux transport activity specific for UDP-glucose. Furthermore, addition of exogenous UDP-glucose rescued root growth in the star1 mutant exposed to Al. These results indicate that STAR1 and STAR2 form a complex that functions as an ABC transporter, which is required for detoxification of Al in rice. The ABC transporter transports UDP-glucose, which may be used to modify the cell wall.

Coordination of Leaf Photosynthesis, Transpiration, and Structural Traits in Rice and Wild Relatives (Genus Oryza)1[W][OA

PubMed Central

Giuliani, Rita; Koteyeva, Nuria; Voznesenskaya, Elena; Evans, Marc A.; Cousins, Asaph B.; Edwards, Gerald E.

2013-01-01

The genus Oryza, which includes rice (Oryza sativa and Oryza glaberrima) and wild relatives, is a useful genus to study leaf properties in order to identify structural features that control CO2 access to chloroplasts, photosynthesis, water use efficiency, and drought tolerance. Traits, 26 structural and 17 functional, associated with photosynthesis and transpiration were quantified on 24 accessions (representatives of 17 species and eight genomes). Hypotheses of associations within, and between, structure, photosynthesis, and transpiration were tested. Two main clusters of positively interrelated leaf traits were identified: in the first cluster were structural features, leaf thickness (Thickleaf), mesophyll (M) cell surface area exposed to intercellular air space per unit of leaf surface area (Smes), and M cell size; a second group included functional traits, net photosynthetic rate, transpiration rate, M conductance to CO2 diffusion (gm), stomatal conductance to gas diffusion (gs), and the gm/gs ratio. While net photosynthetic rate was positively correlated with gm, neither was significantly linked with any individual structural traits. The results suggest that changes in gm depend on covariations of multiple leaf (Smes) and M cell (including cell wall thickness) structural traits. There was an inverse relationship between Thickleaf and transpiration rate and a significant positive association between Thickleaf and leaf transpiration efficiency. Interestingly, high gm together with high gm/gs and a low Smes/gm ratio (M resistance to CO2 diffusion per unit of cell surface area exposed to intercellular air space) appear to be ideal for supporting leaf photosynthesis while preserving water; in addition, thick M cell walls may be beneficial for plant drought tolerance. PMID:23669746

Bacterial colonization of the phyllosphere of mediterranean perennial species as influenced by leaf structural and chemical features.

PubMed

Yadav, R K P; Karamanoli, K; Vokou, D

2005-08-01

In this study, we assessed various leaf structural and chemical features as possible predictors of the size of the phyllosphere bacterial population in the Mediterranean environment. We examined eight perennial species, naturally occurring and coexisting in the same area, in Halkidiki (northern Greece). They are Arbutus unedo, Quercus coccifera, Pistacia lentiscus, and Myrtus communis (evergreen sclerophyllous species), Lavandula stoechas and Cistus incanus (drought semi-deciduous species), and Calamintha nepeta and Melissa officinalis (non-woody perennial species). M. communis, L. stoechas, C. nepeta, and M. officinalis produce essential oil in substantial quantities. We sampled summer leaves from these species and (1) estimated the size of the bacterial population of their phyllosphere, (2) estimated the concentration of different leaf constituents, and (3) studied leaf morphological and anatomical features and expressed them in a quantitative way. The aromatic plants are on average more highly colonized than the other species, whereas the non-woody perennials are more highly colonized than the woody species. The population size of epiphytic bacteria is positively correlated with glandular and non-glandular trichome densities, and with water and phosphorus contents; it is negatively correlated with total phenolics content and the thickness of the leaf, of the mesophyll, and of the abaxial epidermis. No correlation was found with the density of stomata, the nitrogen, and the soluble sugar contents. By regression tree analysis, we found that the leaf-microbe system can be effectively described by three leaf attributes with leaf water content being the primary explanatory attribute. Leaves with water content >73% are the most highly colonized. For leaves with water content <73%, the phosphorus content, with a critical value of 1.34 mg g(-1) d.w., is the next explanatory leaf attribute, followed by the thickness of the adaxial epidermis. Leaves higher in phosphorus

Grazing of leaf-associated Cercomonads (Protists: Rhizaria: Cercozoa) structures bacterial community composition and function.

PubMed

Flues, Sebastian; Bass, David; Bonkowski, Michael

2017-08-01

Preferential food selection in protists is well documented, but we still lack basic understanding on how protist predation modifies the taxonomic and functional composition of bacterial communities. We conducted feeding trials using leaf-associated cercomonad Cercozoa by incubating them on a standardized, diverse bacterial community washed from plant leaves. We used a shotgun metagenomics approach to investigate the taxonomic and functional changes of the bacterial community after five days protist predation on bacteria. Predation-induced shifts in bacterial community composition could be linked to phenotypic protist traits. Protist reproduction rate, morphological plasticity and cell speed were most important in determining bacterial community composition. Analyses of co-occurrence patterns showed less complex correlations between bacterial taxa in the protist-grazed treatments with a higher proportion of positive correlations than in non-grazed controls, suggesting that predation reduced the influence of strong competitors. Protist predation influenced 14 metabolic core functions including membrane transport from which type VI secretion systems were in particular upregulated. In view of the functional importance of bacterial communities in the phyllosphere and rhizosphere of plants, a more detailed understanding of predator-prey interactions, changes in microbial composition and function, and subsequent repercussions on plant performance are clearly required. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

[Tasseled cap triangle (TCT)-leaf area index (LAI)model of rice fields based on PROSAIL model and its application].

PubMed

Li, Ya Ni; Lu, Lei; Liu, Yong

2017-12-01

The tasseled cap triangle (TCT)-leaf area index (LAI) isoline is a model that reflects the distribution of LAI isoline in the spectral space constituted by reflectance of red and near-infrared (NIR) bands, and the LAI retrieval model developed on the basis of this is more accurate than the commonly used statistical relationship models. This study used ground-based measurements of the rice field, validated the applicability of PROSAIL model in simulating canopy reflectance of rice field, and calibrated the input parameters of the model. The ranges of values of PROSAIL input parameters for simulating rice canopy reflectance were determined. Based on this, the TCT-LAI isoline model of rice field was established, and a look-up table (LUT) required in remote sensing retrieval of LAI was developed. Then, the LUT was used for Landsat 8 and WorldView 3 data to retrieve LAI of rice field, respectively. The results showed that the LAI retrieved using the LUT developed from TCT-LAI isoline model had a good linear relationship with the measured LAI R 2 =0.76, RMSE=0.47. Compared with the LAI retrieved from Landsat 8, LAI values retrieved from WorldView 3 va-ried with wider range, and data distribution was more scattered. Resampling the Landsat 8 and WorldView 3 reflectance data to 1 km to retrieve LAI, the result of MODIS LAI product was significantly underestimated compared to that of retrieved LAI.

Physiological and morphological responses of Ischaemum rugosum Salisb. (wrinkled grass) to different nitrogen rates and rice seeding rates.

PubMed

Awan, Tahir Hussain; Chauhan, Bhagirath Singh; Cruz, Pompe C Sta

2014-01-01

Ischaemum rugosum is a competitive weed in direct-seeded rice systems. Developing integrated weed management strategies that promote the suppression of weeds by crop density, cultivar selection, and nutrition requires better understanding of the extent to which rice interferes with the growth of this weed and how it responds to resource limitation due to rice interference. The growth of I. rugosum was studied when grown with four rice seeding rates (0, 25, 50, and 100 kg ha(-1)) and four nitrogen (N) rates (0, 50, 100, and 150 kg ha(-1)). Compared to the weed plants grown alone, weed tiller number was reduced by 63-80%, leaf number by 68-77%, leaf area by 69-77%, leaf biomass by 72-84%, and inflorescence biomass by 81-93% at the rice seeding rates of 25-100 kg ha(-1). All these parameters increased with increasing rates of N from 0 to 150 kg ha(-1). At weed maturity, I. rugosum plants were 100% taller than rice at 0 kg N ha(-1), whereas, with added N, the weeds were only 50% taller than rice. Weed biomass increased by 82-160%, whereas rice biomass increased by 92-229%, with the application of 50-150 kg N ha(-1). Added N favored rice biomass production more than it did the weed. Rice interference reduced the height and biomass of I. rugosum, but did not suppress its growth completely. I. rugosum showed the ability to reduce the effects of rice interference by increasing leaf area, leaf weight ratio, and specific leaf area, and by decreasing the root-shoot weight ratio in comparison to the weed plants grown alone. The results suggest that rice crop interference alone may reduce I. rugosum growth but may not provide complete control of this weed. The need for integrated weed management practices to effectively control this weed species is highlighted.

Effects of Insect-Proof Net Cultivation, Rice-Duck Farming, and Organic Matter Return on Rice Dry Matter Accumulation and Nitrogen Utilization

PubMed Central

Liu, Xin; Xu, Guochun; Wang, Qiangsheng; Hang, Yuhao

2017-01-01

Insect-proof net cultivation (IPN), rice-duck farming (RD), and organic matter return (OM) are important methods to realize sustainable development of rice production. A split-plot field experiment was performed to study the effects of IPN, RD, and OM on the rice yield, dry matter accumulation and N utilization. Results showed that compared to inorganic N fertilizer (IN), wheat straw return, and biogas residue return increased the rice yield by 2.11–4.28 and 4.78–7.67%, respectively, and also improved dry matter and N accumulation after the elongation stage (EG), dry matter and N translocation, and N recovery efficiency (NRE). These results attributed to an increase in leaf SPAD values and net photosynthetic rate (Pn) after the EG. Compared to conventional rice farming (CR), RD promoted the rice yield by 1.52–3.74%, and contributed to higher the leaf photosynthesis, dry matter and N accumulation, dry matter and N translocation, and NRE. IPN decreased the intensity of sun radiation in the nets due to the coverage of the insect-proof nets, which declined the leaf Pn, dry matter accumulation and translocation, N absorption and translocation, and NRE compared to open field cultivation (OFC). The rice yield of IPN were 2.48–4.98% lower than that of OFC. Compared to the interaction between CR and IN, the interaction between RD and OM improved the rice yield by 5.26–9.33%, and increased dry matter and N accumulation after the EG, dry matter and N translocation, and NRE. These results indicated that OM, RD and the interaction between RD and OM could promote dry matter accumulation and N utilization, which was beneficial to improve the rice yield. PMID:28174589

Transcriptome and Gene Expression Analysis of the Rice Leaf Folder, Cnaphalocrosis medinalis

PubMed Central

Li, Shang-Wei; Yang, Hong; Liu, Yue-Feng; Liao, Qi-Rong; Du, Juan; Jin, Dao-Chao

2012-01-01

Background The rice leaf folder (RLF), Cnaphalocrocis medinalis (Guenee) (Lepidoptera: Pyralidae), is one of the most destructive pests affecting rice in Asia. Although several studies have been performed on the ecological and physiological aspects of this species, the molecular mechanisms underlying its developmental regulation, behavior, and insecticide resistance remain largely unknown. Presently, there is a lack of genomic information for RLF; therefore, studies aimed at profiling the RLF transcriptome expression would provide a better understanding of its biological function at the molecular level. Principal Findings De novo assembly of the RLF transcriptome was performed via the short read sequencing technology (Illumina). In a single run, we produced more than 23 million sequencing reads that were assembled into 44,941 unigenes (mean size = 474 bp) by Trinity. Through a similarity search, 25,281 (56.82%) unigenes matched known proteins in the NCBI Nr protein database. The transcriptome sequences were annotated with gene ontology (GO), cluster of orthologous groups of proteins (COG), and KEGG orthology (KO). Additionally, we profiled gene expression during RLF development using a tag-based digital gene expression (DGE) system. Five DGE libraries were constructed, and variations in gene expression were compared between collected samples: eggs vs. 3rd instar larvae, 3rd instar larvae vs. pupae, pupae vs. adults. The results demonstrated that thousands of genes were significantly differentially expressed during various developmental stages. A number of the differentially expressed genes were confirmed by quantitative real-time PCR (qRT-PCR). Conclusions The RLF transcriptome and DGE data provide a comprehensive and global gene expression profile that would further promote our understanding of the molecular mechanisms underlying various biological characteristics, including development, elevated fecundity, flight, sex differentiation, olfactory behavior, and

The pepper Bs4C proteins are localized to the endoplasmic reticulum (ER) membrane and confer disease resistance to bacterial blight in transgenic rice.

PubMed

Wang, Jun; Zeng, Xuan; Tian, Dongsheng; Yang, Xiaobei; Wang, Lanlan; Yin, Zhongchao

2018-03-30

Transcription activator-like effector (TALE)-dependent dominant disease resistance (R) genes in plants, also referred to as executor R genes, are induced on infection by phytopathogenic bacteria of the genus Xanthomonas harbouring the corresponding TALE genes. Unlike the traditional R proteins, the executor R proteins do not determine the resistance specificity and may function broadly in different plant species. The executor R gene Bs4C-R in the resistant genotype PI 235047 of the pepper species Capsicum pubescens (CpBs4C-R) confers disease resistance to Xanthomonas campestris pv. vesicatoria (Xcv) harbouring the TALE genes avrBsP/avrBs4. In this study, the synthetic genes of CpBs4C-R and two other Bs4C-like genes, the susceptible allele in the genotype PI585270 of C. pubescens (CpBs4C-S) and the CaBs4C-R homologue gene in the cultivar 'CM334' of Capsicum annum (CaBs4C), were characterized in tobacco (Nicotiana benthamiana) and rice (Oryza sativa). The Bs4C genes induced cell death in N. benthamiana. The functional Bs4C-eCFP fusion proteins were localized to the endoplasmic reticulum (ER) membrane in the leaf epidermal cells of N. benthamiana. The Xa10 promoter-Bs4C fusion genes in transgenic rice conferred strain-specific disease resistance to Xanthomonas oryzae pv. oryzae (Xoo), the causal agent of bacterial blight in rice, and were specifically induced by the Xa10-incompatible Xoo strain PXO99 A (pHM1avrXa10). The results indicate that the Bs4C proteins from pepper species function broadly in rice and the Bs4C protein-mediated cell death from the ER is conserved between dicotyledonous and monocotyledonous plants, which can be utilized to engineer novel and enhanced disease resistance in heterologous plants. © 2018 TEMASEK LIFE SCIENCES LABORATORY. MOLECULAR PLANT PATHOLOGY © 2018 JOHN WILEY & SONS LTD.

Estimating the leaf nitrogen content of paddy rice by using the combined reflectance and laser-induced fluorescence spectra.

PubMed

Yang, Jian; Du, Lin; Sun, Jia; Zhang, Zhenbing; Chen, Biwu; Shi, Shuo; Gong, Wei; Song, Shalei

2016-08-22

Paddy rice is one of the most important crops in China, and leaf nitrogen content (LNC) serves as a significant indictor for monitoring crop status. A reliable method is needed for precise and fast quantification of LNC. Laser-induced fluorescence (LIF) technology and reflectance spectra of crops are widely used to monitor leaf biochemical content. However, comparison between the fluorescence and reflectance spectra has been rarely investigated in the monitoring of LNC. In this study, the performance of the fluorescence and reflectance spectra for LNC estimation was discussed based on principal component analysis (PCA) and back-propagation neural network (BPNN). The combination of fluorescence and reflectance spectra was also proposed to monitor paddy rice LNC. The fluorescence and reflectance spectra exhibited a high degree of multi-collinearity. About 95.38%, and 97.76% of the total variance included in the spectra were efficiently extracted by using the first three PCs in PCA. The BPNN was implemented for LNC prediction based on new variables calculated using PCA. The experimental results demonstrated that the fluorescence spectra (R² = 0.810, 0.804 for 2014 and 2015, respectively) are superior to the reflectance spectra (R² = 0.721, 0.671 for 2014 and 2015, respectively) for estimating LNC based on the PCA-BPNN model. The proposed combination of fluorescence and reflectance spectra can greatly improve the accuracy of LNC estimation (R² = 0.912, 0.890 for 2014 and 2015, respectively).

Gene silencing using the recessive rice bacterial blight resistance gene xa13 as a new paradigm in plant breeding.

PubMed

Li, Changyan; Wei, Jing; Lin, Yongjun; Chen, Hao

2012-05-01

Resistant germplasm resources are valuable for developing resistant varieties in agricultural production. However, recessive resistance genes are usually overlooked in hybrid breeding. Compared with dominant traits, however, they may confer resistance to different pathogenic races or pest biotypes with different mechanisms of action. The recessive rice bacterial blight resistance gene xa13, also involved in pollen development, has been cloned and its resistance mechanism has been recently characterized. This report describes the conversion of bacterial blight resistance mediated by the recessive xa13 gene into a dominant trait to facilitate its use in a breeding program. This was achieved by knockdown of the corresponding dominant allele Xa13 in transgenic rice using recently developed artificial microRNA technology. Tissue-specific promoters were used to exclude most of the expression of artificial microRNA in the anther to ensure that Xa13 functioned normally during pollen development. A battery of highly bacterial blight resistant transgenic plants with normal seed setting rates were acquired, indicating that highly specific gene silencing had been achieved. Our success with xa13 provides a paradigm that can be adapted to other recessive resistance genes.

Compositional shifts in root-associated bacterial and archaeal microbiota track the plant life cycle in field-grown rice

PubMed Central

Edwards, Joseph A.; Santos-Medellín, Christian M.; Liechty, Zachary S.; Nguyen, Bao; Lurie, Eugene; Eason, Shane; Phillips, Gregory

2018-01-01

Bacterial communities associated with roots impact the health and nutrition of the host plant. The dynamics of these microbial assemblies over the plant life cycle are, however, not well understood. Here, we use dense temporal sampling of 1,510 samples from root spatial compartments to characterize the bacterial and archaeal components of the root-associated microbiota of field grown rice (Oryza sativa) over the course of 3 consecutive growing seasons, as well as 2 sites in diverse geographic regions. The root microbiota was found to be highly dynamic during the vegetative phase of plant growth and then stabilized compositionally for the remainder of the life cycle. Bacterial and archaeal taxa conserved between field sites were defined as predictive features of rice plant age by modeling using a random forest approach. The age-prediction models revealed that drought-stressed plants have developmentally immature microbiota compared to unstressed plants. Further, by using genotypes with varying developmental rates, we show that shifts in the microbiome are correlated with rates of developmental transitions rather than age alone, such that different microbiota compositions reflect juvenile and adult life stages. These results suggest a model for successional dynamics of the root-associated microbiota over the plant life cycle. PMID:29474469

Compositional shifts in root-associated bacterial and archaeal microbiota track the plant life cycle in field-grown rice.

PubMed

Edwards, Joseph A; Santos-Medellín, Christian M; Liechty, Zachary S; Nguyen, Bao; Lurie, Eugene; Eason, Shane; Phillips, Gregory; Sundaresan, Venkatesan

2018-02-01

Bacterial communities associated with roots impact the health and nutrition of the host plant. The dynamics of these microbial assemblies over the plant life cycle are, however, not well understood. Here, we use dense temporal sampling of 1,510 samples from root spatial compartments to characterize the bacterial and archaeal components of the root-associated microbiota of field grown rice (Oryza sativa) over the course of 3 consecutive growing seasons, as well as 2 sites in diverse geographic regions. The root microbiota was found to be highly dynamic during the vegetative phase of plant growth and then stabilized compositionally for the remainder of the life cycle. Bacterial and archaeal taxa conserved between field sites were defined as predictive features of rice plant age by modeling using a random forest approach. The age-prediction models revealed that drought-stressed plants have developmentally immature microbiota compared to unstressed plants. Further, by using genotypes with varying developmental rates, we show that shifts in the microbiome are correlated with rates of developmental transitions rather than age alone, such that different microbiota compositions reflect juvenile and adult life stages. These results suggest a model for successional dynamics of the root-associated microbiota over the plant life cycle.

Transgenic rice expressing Allium sativum leaf lectin with enhanced resistance against sap-sucking insect pests.

PubMed

Saha, Prasenjit; Majumder, Pralay; Dutta, Indrajit; Ray, Tui; Roy, S C; Das, Sampa

2006-05-01

Mannose binding Allium sativum leaf agglutinin (ASAL) has been shown to be antifeedant and insecticidal against sap-sucking insects. In the present investigation, ASAL coding sequence was expressed under the control of CaMV35S promoter in a chimeric gene cassette containing plant selection marker, hpt and gusA reporter gene of pCAMBIA1301 binary vector in an elite indica rice cv. IR64. Many fertile transgenic plants were generated using scutellar calli as initial explants through Agrobacterium-mediated transformation technology. GUS activity was observed in selected calli and in mature plants. Transformation frequency was calculated to be approximately 12.1%+/-0.351 (mean +/- SE). Southern blot analyses revealed the integration of ASAL gene into rice genome with a predominant single copy insertion. Transgene localization was detected on chromosomes of transformed plants using PRINS and C-PRINS techniques. Northern and western blot analyses determined the expression of transgene in transformed lines. ELISA analyses estimated ASAL expression up to 0.72 and 0.67% of total soluble protein in T0 and T1 plants, respectively. Survival and fecundity of brown planthopper and green leafhopper were reduced to 36% (P < 0.01), 32% (P < 0.05) and 40.5, 29.5% (P < 0.001), respectively, when tested on selected plants in comparison to control plants. Specific binding of expressed ASAL to receptor proteins of insect gut was analysed. Analysis of T1 progenies confirmed the inheritance of the transgenes. Thus, ASAL promises to be a potential component in insect resistance rice breeding programme.

Overexpression of miR169o, an Overlapping microRNA in Response to Both Nitrogen Limitation and Bacterial Infection, Promotes Nitrogen Use Efficiency and Susceptibility to Bacterial Blight in Rice.

PubMed

Chao, Yu; Chen, Yutong; Cao, Yaqian; Chen, Huamin; Wang, Jichun; Bi, Yong-Mei; Tian, Fang; Yang, Fenghuan; Rothstein, Steven J; Zhou, Xueping; He, Chenyang

2018-03-15

Limiting nitrogen (N) supply contributes to improved resistance to bacterial blight (BB) caused by Xanthomonas oryzae pv. oryzae (Xoo) in susceptible rice (Oryza sativa). To understand the regulatory roles of microRNAs in this phenomenon, sixty-three differentially-expressed overlapping miRNAs in response to Xoo infection and N-limitation stress in rice were identified through deep RNA-sequence and stem loop qRT-PCR. Among these, miR169o was further assessed as a typical overlapping miRNA through the overexpression of the miR169o primary gene. Osa-miR169o-OX plants were taller, and had more biomass accumulation with significantly increased nitrate and total amino acid contents in roots than wild type (WT). Transcript level assays showed that under different N supply conditions miR169o opposite regulated NRT2 which is reduced under normal N supply condition but remarkably induced under N limiting stress. On the other hand, osa-miR169o-OX plants also displayed increased disease lesion lengths and reduced transcriptional levels of defense gene (PR1b, PR10a, PR10b and PAL) compared with WT after inoculation with Xoo. In addition, miR169o impeded Xoo-mediated NRT transcription. Therefore, the overlapping miR169o contributes to increase N use efficiency and negatively regulates the resistance to bacterial blight in rice. Consistently, transient expression of NF-YAs in rice protoplast promoted the transcripts of PR genes and NRT2 genes, while reduced the transcripts of NRT1 genes. Our results provide novel and additional insights into the coordinated regulatory mechanisms of crosstalk between Xoo infection and N-deficiency responses in rice.

Effects of transgenic Bt rice on growth, reproduction, and superoxide dismutase activity of Folsomia candida (Collembola: Isotomidae) in laboratory studies.

PubMed

Bai, Yaoyu; Yan, Ruihong; Ke, Xin; Ye, Gongyin; Huang, Fangneng; Luo, Yongming; Cheng, Jiaan

2011-12-01

Transgenic rice expressing Bacillus thuringiensis (Bt) CrylAb protein is expected to be commercialized in China in the near future. The use of Bt rice for controlling insect pests sparks intensive debates regarding its biosafety. Folsomia candida is an euedaphic species and is often used as a "standard" test organism in assessing effects of environmental pollutants on soil organisms. In this study, growth, development, reproduction, and superoxide dismutase activity (SOD) of F. candida were investigated in the laboratory for populations reared on leaf tissue or leaf-soil mixtures of two CrylAb rice lines and a non-Bt rice isoline. Two independent tests were performed: 1) a 35-d test using petri dishes containing yeast diet (positive control) or fresh rice leaf tissue, and 2) a 28-d test in soil-litter microcosms containing yeast or a mixture of soil and rice leaf tissue. Biological parameters measured in both tests were number of progeny production, population growth rate, and SOD activity. For the petri dish test, data measured also included insect body length and number of exuviation. There were no significant differences between the populations reared on Bt and non-Bt rice leaf tissue in all measured parameters in both tests and for both Bt rice lines, suggesting no significant effects of the CrylAb protein in Bt rice on F. candida in the laboratory studies. Results of this study should add additional biosafety proofs for use of Bt rice to manage rice pests in China.

Assessing the Effect of Litter Species on the Dynamic of Bacterial and Fungal Communities during Leaf Decomposition in Microcosm by Molecular Techniques

PubMed Central

Xu, Wenjing; Shi, Lingling; Chan, Onchim; Li, Jiao; Casper, Peter; Zou, Xiaoming

2013-01-01

Although bacteria and fungi are well-known to be decomposers of leaf litter, few studies have examined their compositions and diversities during the decomposition process in tropical stream water. Xishuangbanna is a tropical region preserving one of the highest floristic diversity areas in China. In this study, leaf litter of four dominant plant species in Xishuangbanna was incubated in stream water for 42 days during which samples were taken regularly. Following DNA extraction, PCR-DGGE (denaturing gradient gel electrophoresis) and clone-sequencing analyses were performed using bacterial and fungal specific primers. Leaf species have slightly influences on bacterial community rather than fungal community. The richness and diversity of bacteria was higher than that of fungi, which increased towards the end of the 42-day-incubation. The bacterial community was initially more specific upon the type of leaves and gradually became similar at the later stage of decomposition with alpha-proteobacteria as major component. Sequences affiliated to methanotrophs were obtained that indicates potentially occurrence of methane oxidation and methanogenesis. For the fungal community, sequences affiliated to Aspergillus were predominant at the beginning and then shifted to Pleosporales. Our results suggest that the microorganisms colonizing leaf biofilm in tropical stream water were mostly generalists that could exploit the resources of leaves of various species equally well. PMID:24367682

Increasing rice plant growth by Trichoderma sp.

NASA Astrophysics Data System (ADS)

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

2016-11-01

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

Physiological and Morphological Responses of Ischaemum rugosum Salisb. (Wrinkled Grass) to Different Nitrogen Rates and Rice Seeding Rates

PubMed Central

Awan, Tahir Hussain; Chauhan, Bhagirath Singh; Cruz, Pompe C. Sta.

2014-01-01

Ischaemum rugosum is a competitive weed in direct-seeded rice systems. Developing integrated weed management strategies that promote the suppression of weeds by crop density, cultivar selection, and nutrition requires better understanding of the extent to which rice interferes with the growth of this weed and how it responds to resource limitation due to rice interference. The growth of I. rugosum was studied when grown with four rice seeding rates (0, 25, 50, and 100 kg ha−1) and four nitrogen (N) rates (0, 50, 100, and 150 kg ha−1). Compared to the weed plants grown alone, weed tiller number was reduced by 63–80%, leaf number by 68–77%, leaf area by 69–77%, leaf biomass by 72–84%, and inflorescence biomass by 81–93% at the rice seeding rates of 25–100 kg ha−1. All these parameters increased with increasing rates of N from 0 to 150 kg ha−1. At weed maturity, I. rugosum plants were 100% taller than rice at 0 kg N ha−1, whereas, with added N, the weeds were only 50% taller than rice. Weed biomass increased by 82–160%, whereas rice biomass increased by 92–229%, with the application of 50–150 kg N ha−1. Added N favored rice biomass production more than it did the weed. Rice interference reduced the height and biomass of I. rugosum, but did not suppress its growth completely. I. rugosum showed the ability to reduce the effects of rice interference by increasing leaf area, leaf weight ratio, and specific leaf area, and by decreasing the root-shoot weight ratio in comparison to the weed plants grown alone. The results suggest that rice crop interference alone may reduce I. rugosum growth but may not provide complete control of this weed. The need for integrated weed management practices to effectively control this weed species is highlighted. PMID:24910995

Evaluation of assembling methods on determination of whole genome sequence of Xylella fastidiosa blueberry bacterial leaf scorch strain

USDA-ARS?s Scientific Manuscript database

Blueberry bacterial leaf scorch (BBLS) disease, a threat to blueberry production in the Southern USA and potentially elsewhere, is caused by Xylella fastidiosa. Efficient control of BBLS requires knowledge of the pathogen. However, this is challenging because Xylella fastidiosa is difficult to cultu...

Show us your spots! Researchers need samples of bacterial leaf spots on celery, cilantro, parsley, and other crops.

USDA-ARS?s Scientific Manuscript database

Since 2002, a severe leaf spot disease on parsley has occurred throughout central coastal California and particularly in Monterey County. Three different bacterial pathogens (Pseudomonas syringae pv. apii, P. syringae pv. coriandricola and an organism very closely related to P. viridiflava) have bee...

Mapping of Biophysical Parameters of Rice Agriculture System from Hyperspectral Imagery

NASA Astrophysics Data System (ADS)

Moharana, Shreedevi; Duta, Subashisa

2017-04-01

Chlorophyll, nitrogen and leaf water content are the most essential parameters for paddy crop growth. Ground hyperspectral observations were collected at canopy level during critical growth period of rice by using hand held Spectroradiometer. Chemical analysis was carried out to quantify the total chlorophyll, nitrogen and leaf water content. By exploiting the in-situ hyperspectral measurements, regression models were established between each of the crop growth parameters and the spectral indices specifically designed for chlorophyll, nitrogen and water stress. Narrow band vegetation index models were developed for mapping these parameters from Hyperion imagery in an agriculture system. It was inferred that the modified simple ratio (SR) and leaf nitrogen concentration (LNC) predictive index models, which followed a linear and nonlinear relationship respectively, produced satisfactory results in predicting rice nitrogen content from hyperspectral imagery. The presently developed model was compared with other models proposed by researchers. It was ascertained that, nitrogen content varied widely from 1-4 percentage and only 2-3 percentage for paddy crop using present modified index models and well-known predicted Tian et al. (2011) model respectively. The modified present LNC index model performed better than the established Tian et al. (2011) model as far as the estimated nitrogen content from Hyperion imagery was concerned. Moreover, within the observed chlorophyll range attained from the rice genotypes cultivated in the studied rice agriculture system, the index models (LNC, OASVI, Gitelson, mSR and MTCI) accomplished satisfactory results in the spatial distribution of rice chlorophyll content from Hyperion imagery. Spatial distribution of total chlorophyll content widely varied from 1.77-5.81 mg/g (LNC), 3.0-13 mg/g (OASVI) and 2.90-5.40 mg/g (MTCI). Following the similar guideline, it was found that normalized difference water index (NDWI) and normalized

Response of rice genotypes to weed competition in dry direct-seeded rice in India.

PubMed

Mahajan, Gulshan; Ramesha, Mugalodi S; Chauhan, Bhagirath S

2014-01-01

The differential weed-competitive abilities of eight rice genotypes and the traits that may confer such attributes were investigated under partial weedy and weed-free conditions in naturally occurring weed flora in dry direct-seeded rice during the rainy seasons of 2011 and 2012 at Ludhiana, Punjab, India. The results showed genotypic differences in competitiveness against weeds. In weed-free plots, grain yield varied from 6.6 to 8.9 t ha(-1) across different genotypes; it was lowest for PR-115 and highest for the hybrid H-97158. In partial weedy plots, grain yield and weed biomass at flowering varied from 3.6 to 6.7 t ha(-1) and from 174 to 419 g m(-2), respectively. In partial weedy plots, grain yield was lowest for PR-115 and highest for PR-120. Average yield loss due to weed competition ranged from 21 to 46% in different rice genotypes. The study showed that early canopy closure, high leaf area index at early stage, and high root biomass and volume correlated positively with competitiveness. This study suggests that some traits (root biomass, leaf area index, and shoot biomass at the early stage) could play an important role in conferring weed competitiveness and these traits can be explored for dry-seeded rice.

Do the rich always become richer? Characterizing the leaf physiological response of the high-yielding rice cultivar Takanari to free-air CO2 enrichment.

PubMed

Chen, Charles P; Sakai, Hidemitsu; Tokida, Takeshi; Usui, Yasuhiro; Nakamura, Hirofumi; Hasegawa, Toshihiro

2014-02-01

The development of crops which are well suited to growth under future environmental conditions such as higher atmospheric CO2 concentrations ([CO2]) is essential to meeting the challenge of ensuring food security in the face of the growing human population and changing climate. A high-yielding indica rice variety (Oryza sativa L. cv. Takanari) has been recently identified as a potential candidate for such breeding, due to its high productivity in present [CO2]. To test if it could further increase its productivity under elevated [CO2] (eCO2), Takanari was grown in the paddy field under season-long free-air CO2 enrichment (FACE, approximately 200 µmol mol(-1) above ambient [CO2]) and its leaf physiology was compared with the representative japonica variety 'Koshihikari'. Takanari showed consistently higher midday photosynthesis and stomatal conductance than Koshihikari under both ambient and FACE growth conditions over 2 years. Maximum ribulose-1,5-bisphosphate carboxylation and electron transport rates were higher for Takanari at the mid-grain filling stage in both years. Mesophyll conductance was higher in Takanari than in Koshihikari at the late grain-filling stage. In contrast to Koshihikari, Takanari grown under FACE conditions showed no decrease in total leaf nitrogen on an area basis relative to ambient-grown plants. Chl content was higher in Takanari than in Koshihikari at the same leaf nitrogen level. These results indicate that Takanari maintains its superiority over Koshihikari in regards to its leaf-level productivity when grown in elevated [CO2] and it may be a valuable resource for rice breeding programs which seek to increase crop productivity under current and future [CO2].

Do the Rich Always Become Richer? Characterizing the Leaf Physiological Response of the High-Yielding Rice Cultivar Takanari to Free-Air CO2 Enrichment

PubMed Central

Chen, Charles P.; Sakai, Hidemitsu; Tokida, Takeshi; Usui, Yasuhiro; Nakamura, Hirofumi; Hasegawa, Toshihiro

2014-01-01

The development of crops which are well suited to growth under future environmental conditions such as higher atmospheric CO2 concentrations ([CO2]) is essential to meeting the challenge of ensuring food security in the face of the growing human population and changing climate. A high-yielding indica rice variety (Oryza sativa L. cv. Takanari) has been recently identified as a potential candidate for such breeding, due to its high productivity in present [CO2]. To test if it could further increase its productivity under elevated [CO2] (eCO2), Takanari was grown in the paddy field under season-long free-air CO2 enrichment (FACE, approximately 200 µmol mol−1 above ambient [CO2]) and its leaf physiology was compared with the representative japonica variety ‘Koshihikari’. Takanari showed consistently higher midday photosynthesis and stomatal conductance than Koshihikari under both ambient and FACE growth conditions over 2 years. Maximum ribulose-1,5-bisphosphate carboxylation and electron transport rates were higher for Takanari at the mid-grain filling stage in both years. Mesophyll conductance was higher in Takanari than in Koshihikari at the late grain-filling stage. In contrast to Koshihikari, Takanari grown under FACE conditions showed no decrease in total leaf nitrogen on an area basis relative to ambient-grown plants. Chl content was higher in Takanari than in Koshihikari at the same leaf nitrogen level. These results indicate that Takanari maintains its superiority over Koshihikari in regards to its leaf-level productivity when grown in elevated [CO2] and it may be a valuable resource for rice breeding programs which seek to increase crop productivity under current and future [CO2]. PMID:24443497

Map-based cloning and functional analysis of YGL8, which controls leaf colour in rice (Oryza sativa).

PubMed

Zhu, Xiaoyan; Guo, Shuang; Wang, Zhongwei; Du, Qing; Xing, Yadi; Zhang, Tianquan; Shen, Wenqiang; Sang, Xianchun; Ling, Yinghua; He, Guanghua

2016-06-13

As the indispensable part of plant, leaf blade mainly functions as the production workshops where organic substance is produced by photosynthesis. Leaf colour mutation is a genetic phenomenon that has a high frequency and is easily identified. The mutations always exhibit negative impact on the development of plants in any of the different stages of growth. Up to now, numerous genes involved in leaf colour mutations have been cloned. In this study, a yellow-green leaf mutant, yellow-green leaf 8 (ygl8), with stable genetic phenotype, has been screened out in the progeny of an excellent indica restorer line Jinhui 10 with seeds treated by EMS. The levels of Chl a, Chl b and total chlorophyll were significantly lower in ygl8 than those in the WT throughout the whole growth period, while no clear change was noted in the Chl a/b ratio. Transmission electron microscopy demonstrated that the lamellae were clearly intumescent and intricately stacked in ygl8. Furthermore, compared with those of the WT, the stomatal conductance, intercellular CO2 concentration, photosynthetic rate and transpiration rate of ylg8 were all significantly lower. Map-based cloning results showed that Loc_Os01g73450, encoding a chloroplast-targeted UMP kinase, corresponded to Ygl8 and played an important role in regulating leaf colour in rice (Oryza sativa). Complementation of ygl8 with the WT DNA sequence of Loc_Os01g73450 led to restoration of the normal phenotype, and transgenic RNA interference plants showed a yellow-green colour. Analysis of the spatial and temporal expression of Ygl8 indicated that it was highly expressed in leaf blades and weakly expressed in other tissues. qRT-PCR also showed that the expression levels of the major Photosystem I core subunits plastome-encoded PsaA, PsaB and PsbC were significantly reduced in ygl8. The expression levels of nuclear-encoded gene involved in Chl biosynthesis HEMC, HEME, and PORA were also decreased when compared with the wild-type. Independent

Quantification of rice brown leaf spot through Taqman real-time PCR specific to the unigene encoding Cochliobolus miyabeanus SCYTALONE DEHYDRATASE1 involved in fungal melanin biosynthesis.

PubMed

Su'udi, Mukhamad; Park, Jong-Mi; Kang, Woo-Ri; Park, Sang-Ryeol; Hwang, Duk-Ju; Ahn, Il-Pyung

2012-12-01

Rice brown leaf spot is a major disease in the rice paddy field. The causal agent Cochliobolus miyabeanus is an ascomycete fungus and a representative necrotrophic pathogen in the investigation of rice-microbe interactions. The aims of this research were to identify a quantitative evaluation method to determine the amount of C. miyabeanus proliferation in planta and determine the method's sensitivity. Real-time polymerase chain reaction (PCR) was employed in combination with the primer pair and Taqman probe specific to CmSCD1, a C. miyabeanus unigene encoding SCYTALONE DEHYDRATASE, which is involved in fungal melanin biosynthesis. Comparative analysis of the nucleotide sequences of CmSCD1 from Korean strains with those from the Japanese and Taiwanese strains revealed some sequence differences. Based on the crossing point (CP) values from Taqman real-time PCR containing a series of increasing concentrations of cloned amplicon or fungal genomic DNA, linear regressions with a high level of reliability (R(2)>0.997) were constructed. This system was able to estimate fungal genomic DNA at the picogram level. The reliability of this equation was further confirmed using DNA samples from both resistant and susceptible cultivars infected with C. miyabeanus. In summary, our quantitative system is a powerful alternative in brown leaf spot forecasting and in the consistent evaluation of disease progression.

Tillage practices and straw-returning methods affect topsoil bacterial community and organic C under a rice-wheat cropping system in central China

NASA Astrophysics Data System (ADS)

Guo, Lijin; Zheng, Shixue; Cao, Cougui; Li, Chengfang

2016-09-01

The objective of this study was to investigate how the relationships between bacterial communities and organic C (SOC) in topsoil (0-5 cm) are affected by tillage practices [conventional intensive tillage (CT) or no-tillage (NT)] and straw-returning methods [crop straw returning (S) or removal (NS)] under a rice-wheat rotation in central China. Soil bacterial communities were determined by high-throughput sequencing technology. After two cycles of annual rice-wheat rotation, compared with CT treatments, NT treatments generally had significantly more bacterial genera and monounsaturated fatty acids/saturated fatty acids (MUFA/STFA), but a decreased gram-positive bacteria/gram-negative bacteria ratio (G+/G-). S treatments had significantly more bacterial genera and MUFA/STFA, but had decreased G+/G- compared with NS treatments. Multivariate analysis revealed that Gemmatimonas, Rudaea, Spingomonas, Pseudomonas, Dyella, Burkholderia, Clostridium, Pseudolabrys, Arcicella and Bacillus were correlated with SOC, and cellulolytic bacteria (Burkholderia, Pseudomonas, Clostridium, Rudaea and Bacillus) and Gemmationas explained 55.3% and 12.4% of the variance in SOC, respectively. Structural equation modeling further indicated that tillage and residue managements affected SOC directly and indirectly through these cellulolytic bacteria and Gemmationas. Our results suggest that Burkholderia, Pseudomonas, Clostridium, Rudaea, Bacillus and Gemmationas help to regulate SOC sequestration in topsoil under tillage and residue systems.

Hydraulic properties of rice and the response of gas exchange to water stress.

PubMed

Stiller, Volker; Lafitte, H Renee; Sperry, John S

2003-07-01

We investigated the role of xylem cavitation, plant hydraulic conductance, and root pressure in the response of rice (Oryza sativa) gas exchange to water stress. In the field (Philippines), the percentage loss of xylem conductivity (PLC) from cavitation exceeded 60% in leaves even in watered controls. The PLC versus leaf water potential relationship indicated diurnal refilling of cavitated xylem. The leaf water potential causing 50 PLC (P(50)) was -1.6 MPa and did not differ between upland versus lowland rice varieties. Greenhouse-grown varieties (Utah) were more resistant to cavitation with a 50 PLC of -1.9 MPa but also showed no difference between varieties. Six-day droughts caused concomitant reductions in leaf-specific photosynthetic rate, leaf diffusive conductance, and soil-leaf hydraulic conductance that were associated with cavitation-inducing water potentials and the disappearance of nightly root pressure. The return of root pressure after drought was associated with the complete recovery of leaf diffusive conductance, leaf-specific photosynthetic rate, and soil-leaf hydraulic conductance. Root pressure after the 6-d drought (61.2 +/- 8.8 kPa) was stimulated 7-fold compared with well-watered plants before drought (8.5 +/- 3.8 kPa). The results indicate: (a) that xylem cavitation plays a major role in the reduction of plant hydraulic conductance during drought, and (b) that rice can readily reverse cavitation, possibly aided by nocturnal root pressure.

Antagonism of rice phylloplane fungi against Cercospora oryzae

NASA Astrophysics Data System (ADS)

Mardani, A.; Hadiwiyono

2018-03-01

Narrow brown leaf spot (NBLS) caused by Cercospora oryzae Miyake is one of the important obstacle in rice cultivation that can decrease the productivity up to 40%. It has been known well that some phylloplane fungi are antagonistic to some leaf diseases. Phylloplane fungi of rice however haven’t been studied much and poorly understood as biological control agent of rice pathogen such C. oryzae. The research aimed to study the antagonism of some phylloplane fungi of rice against C. oryzae. At least 14 isolates of phylloplane fungi were collected which consisted of six pathogenic and eight nonpathogenic variants. All of nonpathogenic isolates were antagonistic against C. oryzae both in vitro and only one isolate could not inhibit the infection of the pathogen in vivo. Some isolates were identified as Aspergillus, Mucor, Penicillium, Fusarium, and Trichoderma. The isolate of Mucor and Fusarium could inhibit the highest growth of pathogen on potato dextrose medium that were at 36.0% and 35.5% respectively. Whereas on artificial inoculation on rice, some isolates such Penicillium and Fusarium could inhibit most effectively and were significantly different to Mencozeb application with dosage 5g L-1.

Soil water availability and capacity of nitrogen accumulation influence variations of intrinsic water use efficiency in rice.

PubMed

Xue, Wei; Nay-Htoon, Bhone; Lindner, Steve; Dubbert, Maren; Otieno, Dennis; Ko, Jonghan; Werner, Christiane; Tenhunen, John

2016-04-01

Leaf intrinsic water use efficiency (WUEi) coupling maximum assimilation rate (Amax) and transpirable water lost via stomatal conductance (gsc) has been gaining increasing concern in sustainable crop production. Factors that influence leaf Amax and WUEi in rice (Oryza sativa L. cv Unkang) at flooding and rainfed conditions were evaluated. Positive correlations for leaf nitrogen content (Nm) and maximum carboxylation rate (Vcmax), for nitrogen allocation in Rubisco enzymes and mesophyll conductance (gm) were evident independent of cropping cultures. Rainfed rice exhibited enriched canopy leaf average Nm resulting in higher Amax, partially supporting improved leaf WUEi. Maximum WUEi (up to 0.14 μmol mmol(-1)) recorded in rainfed rice under drought conditions resulted from increasing gm/gsc ratio while at cost of significant decline in Amax due to hydraulically constrained gsc. Amax sensitivity related to gsc which was regulated by plant hydraulic conductance. WUEi was tightly correlated to Vcmax/gsc and gm/gsc ratios across the paddy and rainfed not to light environment, morphological and physiological traits, highlighting enhance capacity of Nm accumulation in rainfed rice with gsc at moderately high level similar to paddy rice facilitate optimization in Amax and WUEi while, is challenged by drought-vulnerable plant hydraulic conductance. Copyright © 2016 Elsevier GmbH. All rights reserved.

WHITE STRIPE LEAF4 Encodes a Novel P-Type PPR Protein Required for Chloroplast Biogenesis during Early Leaf Development

PubMed Central

Wang, Ying; Ren, Yulong; Zhou, Kunneng; Liu, Linglong; Wang, Jiulin; Xu, Yang; Zhang, Huan; Zhang, Long; Feng, Zhiming; Wang, Liwei; Ma, Weiwei; Wang, Yunlong; Guo, Xiuping; Zhang, Xin; Lei, Cailin; Cheng, Zhijun; Wan, Jianmin

2017-01-01

Pentatricopeptide repeat (PPR) proteins comprise a large family in higher plants and perform diverse functions in organellar RNA metabolism. Despite the rice genome encodes 477 PRR proteins, the regulatory effects of PRR proteins on chloroplast development remains unknown. In this study, we report the functional characterization of the rice white stripe leaf4 (wsl4) mutant. The wsl4 mutant develops white-striped leaves during early leaf development, characterized by decreased chlorophyll content and malformed chloroplasts. Positional cloning of the WSL4 gene, together with complementation and RNA-interference tests, reveal that it encodes a novel P-family PPR protein with 12 PPR motifs, and is localized to chloroplast nucleoids. Quantitative RT-PCR analyses demonstrate that WSL4 is a low temperature response gene abundantly expressed in young leaves. Further expression analyses show that many nuclear- and plastid-encoded genes in the wsl4 mutant are significantly affected at the RNA and protein levels. Notably, the wsl4 mutant causes defects in the splicing of atpF, ndhA, rpl2, and rps12. Our findings identify WSL4 as a novel P-family PPR protein essential for chloroplast RNA group II intron splicing during early leaf development in rice. PMID:28694820

Gibberellin biosynthesis and signal transduction is essential for internode elongation in deepwater rice.

PubMed

Ayano, Madoka; Kani, Takahiro; Kojima, Mikiko; Sakakibara, Hitoshi; Kitaoka, Takuya; Kuroha, Takeshi; Angeles-Shim, Rosalyn B; Kitano, Hidemi; Nagai, Keisuke; Ashikari, Motoyuki

2014-10-01

Under flooded conditions, the leaves and internodes of deepwater rice can elongate above the water surface to capture oxygen and prevent drowning. Our previous studies showed that three major quantitative trait loci (QTL) regulate deepwater-dependent internode elongation in deepwater rice. In this study, we investigated the age-dependent internode elongation in deepwater rice. We also investigated the relationship between deepwater-dependent internode elongation and the phytohormone gibberellin (GA) by physiological and genetic approach using a QTL pyramiding line (NIL-1 + 3 + 12). Deepwater rice did not show internode elongation before the sixth leaf stage under deepwater condition. Additionally, deepwater-dependent internode elongation occurred on the sixth and seventh internodes during the sixth leaf stage. These results indicate that deepwater rice could not start internode elongation until the sixth leaf stage. Ultra-performance liquid chromatography tandem mass-spectrometry (UPLC-MS/MS) method for the phytohormone contents showed a deepwater-dependent GA1 and GA4 accumulation in deepwater rice. Additionally, a GA inhibitor abolished deepwater-dependent internode elongation in deepwater rice. On the contrary, GA feeding mimicked internode elongation under ordinary growth conditions. However, mutations in GA biosynthesis and signal transduction genes blocked deepwater-dependent internode elongation. These data suggested that GA biosynthesis and signal transduction are essential for deepwater-dependent internode elongation in deepwater rice. © 2014 The Authors. Plant, Cell & Environment published by John Wiley & Sons Ltd.

Response of Rice Genotypes to Weed Competition in Dry Direct-Seeded Rice in India

PubMed Central

Mahajan, Gulshan; Ramesha, Mugalodi S.; Chauhan, Bhagirath S.

2014-01-01

The differential weed-competitive abilities of eight rice genotypes and the traits that may confer such attributes were investigated under partial weedy and weed-free conditions in naturally occurring weed flora in dry direct-seeded rice during the rainy seasons of 2011 and 2012 at Ludhiana, Punjab, India. The results showed genotypic differences in competitiveness against weeds. In weed-free plots, grain yield varied from 6.6 to 8.9 t ha−1 across different genotypes; it was lowest for PR-115 and highest for the hybrid H-97158. In partial weedy plots, grain yield and weed biomass at flowering varied from 3.6 to 6.7 t ha−1 and from 174 to 419 g m−2, respectively. In partial weedy plots, grain yield was lowest for PR-115 and highest for PR-120. Average yield loss due to weed competition ranged from 21 to 46% in different rice genotypes. The study showed that early canopy closure, high leaf area index at early stage, and high root biomass and volume correlated positively with competitiveness. This study suggests that some traits (root biomass, leaf area index, and shoot biomass at the early stage) could play an important role in conferring weed competitiveness and these traits can be explored for dry-seeded rice. PMID:25093205

Gibberellin biosynthesis and signal transduction is essential for internode elongation in deepwater rice

PubMed Central

Ayano, Madoka; Kani, Takahiro; Kojima, Mikiko; Sakakibara, Hitoshi; Kitaoka, Takuya; Kuroha, Takeshi; Angeles-Shim, Rosalyn B; Kitano, Hidemi; Nagai, Keisuke; Ashikari, Motoyuki

2014-01-01

Under flooded conditions, the leaves and internodes of deepwater rice can elongate above the water surface to capture oxygen and prevent drowning. Our previous studies showed that three major quantitative trait loci (QTL) regulate deepwater-dependent internode elongation in deepwater rice. In this study, we investigated the age-dependent internode elongation in deepwater rice. We also investigated the relationship between deepwater-dependent internode elongation and the phytohormone gibberellin (GA) by physiological and genetic approach using a QTL pyramiding line (NIL-1 + 3 + 12). Deepwater rice did not show internode elongation before the sixth leaf stage under deepwater condition. Additionally, deepwater-dependent internode elongation occurred on the sixth and seventh internodes during the sixth leaf stage. These results indicate that deepwater rice could not start internode elongation until the sixth leaf stage. Ultra-performance liquid chromatography tandem mass-spectrometry (UPLC-MS/MS) method for the phytohormone contents showed a deepwater-dependent GA1 and GA4 accumulation in deepwater rice. Additionally, a GA inhibitor abolished deepwater-dependent internode elongation in deepwater rice. On the contrary, GA feeding mimicked internode elongation under ordinary growth conditions. However, mutations in GA biosynthesis and signal transduction genes blocked deepwater-dependent internode elongation. These data suggested that GA biosynthesis and signal transduction are essential for deepwater-dependent internode elongation in deepwater rice. Deepwater rice obtained the ability for rapid internode elongation to avoid drowning and adapt to flooded condition. How does it regulate internode elongation? Using both physiological and genetic approach, this paper shows that the plant hormone, gibberellin (GA) regulates internode elongation. PMID:24891164

Rice PLASTOCHRON genes regulate leaf maturation downstream of the gibberellin signal transduction pathway.

PubMed

Mimura, Manaki; Nagato, Yasuo; Itoh, Jun-Ichi

2012-05-01

Rice PLASTOCHRON 1 (PLA1) and PLA2 genes regulate leaf maturation and plastochron, and their loss-of-function mutants exhibit small organs and rapid leaf emergence. They encode a cytochrome P450 protein CYP78A11 and an RNA-binding protein, respectively. Their homologs in Arabidopsis and maize are also associated with plant development/organ size. Despite the importance of PLA genes in plant development, their molecular functions remain unknown. Here, we investigated how PLA1 and PLA2 genes are related to phytohormones. We found that gibberellin (GA) is the major phytohormone that promotes PLA1 and PLA2 expression. GA induced PLA1 and PLA2 expression, and conversely the GA-inhibitor uniconazole suppressed PLA1 and PLA2 expression. In pla1-4 and pla2-1 seedlings, expression levels of GA biosynthesis genes and the signal transduction gene were similar to those in wild-type seedlings. GA treatment slightly down-regulated the GA biosynthesis gene GA20ox2 and up-regulated the GA-catabolizing gene GA2ox4, whereas the GA biosynthesis inhibitor uniconazole up-regulated GA20ox2 and down-regulated GA2ox4 both in wild-type and pla mutants, suggesting that the GA feedback mechanism is not impaired in pla1 and pla2. To reveal how GA signal transduction affects the expression of PLA1 and PLA2, PLA expression in GA-signaling mutants was examined. In GA-insensitive mutant, gid1 and less-sensitive mutant, Slr1-d1, PLA1 and PLA2 expression was down-regulated. On the other hand, the expression levels of PLA1 and PLA2 were highly enhanced in a GA-constitutive-active mutant, slr1-1, causing ectopic overexpression. These results indicate that both PLA1 and PLA2 act downstream of the GA signal transduction pathway to regulate leaf development.

Characterization of functional trait diversity among Indian cultivated and weedy rice populations

PubMed Central

Rathore, M.; Singh, Raghwendra; Kumar, B.; Chauhan, B. S.

2016-01-01

Weedy rice, a menace in rice growing areas globally, is biosimilar having attributes similar to cultivated and wild rice, and therefore is difficult to manage. A study was initiated to characterize the functional traits of 76 weedy rice populations and commonly grown rice cultivars from different agro-climatic zones for nine morphological, five physiological, and three phenological parameters in a field experiment under an augmented block design. Comparison between weedy and cultivated rice revealed a difference in duration (days) from panicle emergence to heading as the most variable trait and awn length as the least variable one, as evidenced from their coefficients of variation. The results of principal component analysis revealed the first three principal components to represent 47.3% of the total variation, which indicates an important role of transpiration, conductance, leaf-air temperature difference, days to panicle emergence, days to heading, flag leaf length, SPAD (soil-plant analysis development), grain weight, plant height, and panicle length to the diversity in weedy rice populations. The variations existing in weedy rice population are a major reason for its wider adaptability to varied environmental conditions and also a problem while trying to manage it. PMID:27072282

Morphological characterization of several strains of the rice-pathogenic bacterium Burkholderia glumae in North Sumatra

NASA Astrophysics Data System (ADS)

Hasibuan, M.; Safni, I.; Lisnawita; Lubis, K.

2018-02-01

Burkholderia glumae is a quarantine seed-borne bacterial pathogen causing panicle blight disease on rice. This pathogen has been detected in some locations in Java, and recently, farmers in North Sumatra have reported rice yield loss with symptoms similar with those on rice infeced by the rice-pathogenic bacterium B. glumae. This research was aimed to isolate several bacterial strains from several rice varieties in various locations in North Sumatra and characterize the morphology of the strains to detect and identify the unknown bacterial strains presumably B. glumae. Several rice seed varieties were collected from Medan and Deli Serdang Districts. The seed samples were extracted, isolated and purified, then grown in semi-selective media PPGA. The morphological characteristics of the bacterial strains were determined including Gram staining, bacterial colony’s and bacterial cell’s morphology. The results showed that of eleven strains isolated, two strains were Gram negative and nine strains were Gram positive. On the basis of colony morphology, all strains had circular form, flat elevation and cream colour while the colony margin varied, i.e. entire and undulate. Most strains had bacillus/rod shape (8 strains) and only 3 strains were coccus.

A technique system for the measurement, reconstruction and character extraction of rice plant architecture

PubMed Central

Li, Xumeng; Wang, Xiaohui; Wei, Hailin; Zhu, Xinguang; Peng, Yulin; Li, Ming; Li, Tao; Huang, Huang

2017-01-01

This study developed a technique system for the measurement, reconstruction, and trait extraction of rice canopy architectures, which have challenged functional–structural plant modeling for decades and have become the foundation of the design of ideo-plant architectures. The system uses the location-separation-measurement method (LSMM) for the collection of data on the canopy architecture and the analytic geometry method for the reconstruction and visualization of the three-dimensional (3D) digital architecture of the rice plant. It also uses the virtual clipping method for extracting the key traits of the canopy architecture such as the leaf area, inclination, and azimuth distribution in spatial coordinates. To establish the technique system, we developed (i) simple tools to measure the spatial position of the stem axis and azimuth of the leaf midrib and to capture images of tillers and leaves; (ii) computer software programs for extracting data on stem diameter, leaf nodes, and leaf midrib curves from the tiller images and data on leaf length, width, and shape from the leaf images; (iii) a database of digital architectures that stores the measured data and facilitates the reconstruction of the 3D visual architecture and the extraction of architectural traits; and (iv) computation algorithms for virtual clipping to stratify the rice canopy, to extend the stratified surface from the horizontal plane to a general curved surface (including a cylindrical surface), and to implement in silico. Each component of the technique system was quantitatively validated and visually compared to images, and the sensitivity of the virtual clipping algorithms was analyzed. This technique is inexpensive and accurate and provides high throughput for the measurement, reconstruction, and trait extraction of rice canopy architectures. The technique provides a more practical method of data collection to serve functional–structural plant models of rice and for the optimization of rice

Autoregulation of Nodulation Interferes with Impacts of Nitrogen Fertilization Levels on the Leaf-Associated Bacterial Community in Soybeans ▿ †

PubMed Central

Ikeda, Seishi; Anda, Mizue; Inaba, Shoko; Eda, Shima; Sato, Shusei; Sasaki, Kazuhiro; Tabata, Satoshi; Mitsui, Hisayuki; Sato, Tadashi; Shinano, Takuro; Minamisawa, Kiwamu

2011-01-01

The diversities leaf-associated bacteria on nonnodulated (Nod−), wild-type nodulated (Nod+), and hypernodulated (Nod++) soybeans were evaluated by clone library analyses of the 16S rRNA gene. To analyze the impact of nitrogen fertilization on the bacterial leaf community, soybeans were treated with standard nitrogen (SN) (15 kg N ha−1) or heavy nitrogen (HN) (615 kg N ha−1) fertilization. Under SN fertilization, the relative abundance of Alphaproteobacteria was significantly higher in Nod− and Nod++ soybeans (82% to 96%) than in Nod+ soybeans (54%). The community structure of leaf-associated bacteria in Nod+ soybeans was almost unaffected by the levels of nitrogen fertilization. However, differences were visible in Nod− and Nod++ soybeans. HN fertilization drastically decreased the relative abundance of Alphaproteobacteria in Nod− and Nod++ soybeans (46% to 76%) and, conversely, increased those of Gammaproteobacteria and Firmicutes in these mutant soybeans. In the Alphaproteobacteria, cluster analyses identified two operational taxonomic units (OTUs) (Aurantimonas sp. and Methylobacterium sp.) that were especially sensitive to nodulation phenotypes under SN fertilization and to nitrogen fertilization levels. Arbuscular mycorrhizal infection was not observed on the root tissues examined, presumably due to the rotation of paddy and upland fields. These results suggest that a subpopulation of leaf-associated bacteria in wild-type Nod+ soybeans is controlled in similar ways through the systemic regulation of autoregulation of nodulation, which interferes with the impacts of N levels on the bacterial community of soybean leaves. PMID:21239540

Development of disease-resistant rice using regulatory components of induced disease resistance

PubMed Central

Takatsuji, Hiroshi

2014-01-01

Infectious diseases cause huge crop losses annually. In response to pathogen attacks, plants activate defense systems that are mediated through various signaling pathways. The salicylic acid (SA) signaling pathway is the most powerful of these pathways. Several regulatory components of the SA signaling pathway have been identified, and are potential targets for genetic manipulation of plants’ disease resistance. However, the resistance associated with these regulatory components is often accompanied by fitness costs; that is, negative effects on plant growth and crop yield. Chemical defense inducers, such as benzothiadiazole and probenazole, act on the SA pathway and induce strong resistance to various pathogens without major fitness costs, owing to their ‘priming effect.’ Studies on how benzothiadiazole induces disease resistance in rice have identified WRKY45, a key transcription factor in the branched SA pathway, and OsNPR1/NH1. Rice plants overexpressing WRKY45 were extremely resistant to rice blast disease caused by the fungus Magnaporthe oryzae and bacterial leaf blight disease caused by Xanthomonas oryzae pv. oryzae (Xoo), the two major rice diseases. Disease resistance is often accompanied by fitness costs; however, WRKY45 overexpression imposed relatively small fitness costs on rice because of its priming effect. This priming effect was similar to that of chemical defense inducers, although the fitness costs were amplified by some environmental factors. WRKY45 is degraded by the ubiquitin–proteasome system, and the dual role of this degradation partly explains the priming effect. The synergistic interaction between SA and cytokinin signaling that activates WRKY45 also likely contributes to the priming effect. With a main focus on these studies, I review the current knowledge of SA-pathway-dependent defense in rice by comparing it with that in Arabidopsis, and discuss potential strategies to develop disease-resistant rice using signaling components

Incorporation of Bacterial Blight Resistance Genes Into Lowland Rice Cultivar Through Marker-Assisted Backcross Breeding.

PubMed

Pradhan, Sharat Kumar; Nayak, Deepak Kumar; Pandit, Elssa; Behera, Lambodar; Anandan, Annamalai; Mukherjee, Arup Kumar; Lenka, Srikanta; Barik, Durga Prasad

2016-07-01

Bacterial blight (BB) of rice caused by Xanthomonas oryzae pv. oryzae is a major disease of rice in many rice growing countries. Pyramided lines carrying two BB resistance gene combinations (Xa21+xa13 and Xa21+xa5) were developed in a lowland cultivar Jalmagna background through backcross breeding by integrating molecular markers. In each backcross generation, markers closely linked to the disease resistance genes were used to select plants possessing the target genes. Background selection was continued in those plants carrying resistant genes until BC(3) generation. Plants having the maximum contribution from the recurrent parent genome were selected in each generation and hybridized with the recipient parent. The BB-pyramided line having the maximum recipient parent genome recovery of 95% was selected among BC3F1 plants and selfed to isolate homozygous BC(3)F(2) plants with different combinations of BB resistance genes. Twenty pyramided lines with two resistance gene combinations exhibited high levels of tolerance against the BB pathogen. In order to confirm the resistance, the pyramided lines were inoculated with different X. oryzae pv. oryzae strains of Odisha for bioassay. The genotypes with combination of two BB resistance genes conferred high levels of resistance to the predominant X. oryzae pv. oryzae isolates prevalent in the region. The pyramided lines showed similarity with the recipient parent with respect to major agro-morphologic traits.

Hpa1 harpin needs nitroxyl terminus to promote vegetative growth and leaf photosynthesis in Arabidopsis.

PubMed

Li, Xiaojie; Han, Liping; Zhao, Yanying; You, Zhenzhen; Dong, Hansong; Zhang, Chunling

2014-03-01

Hpa1 is a harpin protein produced by Xanthomonas oryzae, an important bacterial pathogen of rice, and has the growth-promoting activity in plants. To understand the molecular basis for the function of Hpa1, we generated an inactive variant protein, Hpa1 delta NT, by deleting the nitroxyl-terminal region of the Hpa1 sequence and compared Hpa1 delta NT with the full-length protein in terms of the effects on vegetative growth and related physiological responses in Arabidopsis. When Hpa1 was applied to plants, it acted to enhance the vegetative growth but did not affect the floral development. Enhanced plant growth was accompanied by induced expression of growth-promoting genes in plant leaves. The growth-promoting activity of Hpa1 was further correlated with a physiological consequence shown as promoted leaf photosynthesis as a result of facilitated CO2 conduction through leaf stomata and mesophyll cells. On the contrary, plant growth, growth-promoting gene expression, and the physiological consequence changed little in response to the Hpa1 delta NT treatment. These analyses suggest that Hpa1 requires the nitroxyl-terminus to facilitate CO2 transport inside leaf cells and promote leaf photosynthesis and vegetative growth of the plant.

A detailed analysis of the leaf rolling mutant sll2 reveals complex nature in regulation of bulliform cell development in rice (Oryza sativa L.).

PubMed

Zhang, J-J; Wu, S-Y; Jiang, L; Wang, J-L; Zhang, X; Guo, X-P; Wu, C-Y; Wan, J-M

2015-03-01

Bulliform cells are large, thin-walled and highly vacuolated cells, and play an important role in controlling leaf rolling in response to drought and high temperature. However, the molecular mechanisms regulating bulliform cell development have not been well documented. Here, we report isolation and characterisation of a rice leaf-rolling mutant, named shallot-like 2 (sll2). The sll2 plants exhibit adaxially rolled leaves, starting from the sixth leaf stage, accompanied by increased photosynthesis and reduced plant height and tiller number. Histological analyses showed shrinkage of bulliform cells, resulting in inward-curved leaves. The mutant is recessive and revertible at a rate of 9%. The leaf rolling is caused by a T-DNA insertion. Cloning of the insertion using TAIL-PCR revealed that the T-DNA was inserted in the promoter region of LOC_Os07 g38664. Unexpectedly, the enhanced expression of LOC_Os07 g38664 by the 35S enhancer in the T-DNA is not responsible for the leaf rolling phenotype. Further, the enhancer also exerted a long-distance effect, including up-regulation of several bulliform cell-related genes. sll2 suppressed the outward leaf rolling of oul1 in the sll2oul1 double mutant. We conclude that leaf rolling in sll2 could be a result of the combined effect of multi-genes, implying a complex network in regulation of bulliform cell development. © 2014 German Botanical Society and The Royal Botanical Society of the Netherlands.

Cadmium remobilization from shoot to grain is related to pH of vascular bundle in rice.

PubMed

Zhang, Bing-Lin; Ouyang, You-Nan; Xu, Jun-Ying; Liu, Ke

2018-01-01

The remobilization of cadmium (Cd) from shoots to grain is the key process to determine the Cd accumulation in grain. The apoplastic pH of plants is an important factor and signal in influencing on plant responding to environmental variation and inorganic elements uptake. It is proposed that pH of rice plants responds and influences on Cd remobilization from shoots to grain when rice is exposed to Cd stress. The results of hydroponic experiment showed that: pH of the rice leaf vascular bundles among 3 cultivars was almost increased, pH value of 1 cultivar was slightly increasing when rice plants were treated with Cd. The decrease degree of H + concentration in leaf vascular bundles was different among cultivars. The cultivar with higher decreasing in H + concentration, showed higher Cd transfer efficiency from shoots to grain. The H + concentration of leaf vascular bundles under normal condition was negatively correlated to cadmium accumulation in leaf. Moreover, pH change was related to Cd accumulation in shots and remobilization from shoots to grain. Uncovering the role of pH response is a key component for the understanding Cd uptake and remobilization mechanism for rice production. Copyright © 2017 Elsevier Inc. All rights reserved.

Root morphology, hydraulic conductivity and plant water relations of high-yielding rice grown under aerobic conditions.

PubMed

Kato, Yoichiro; Okami, Midori

2011-09-01

Increasing physical water scarcity is a major constraint for irrigated rice (Oryza sativa) production. 'Aerobic rice culture' aims to maximize yield per unit water input by growing plants in aerobic soil without flooding or puddling. The objective was to determine (a) the effect of water management on root morphology and hydraulic conductance, and (b) their roles in plant-water relationships and stomatal conductance in aerobic culture. Root system development, stomatal conductance (g(s)) and leaf water potential (Ψ(leaf)) were monitored in a high-yielding rice cultivar ('Takanari') under flooded and aerobic conditions at two soil moisture levels [nearly saturated (> -10 kPa) and mildly dry (> -30 kPa)] over 2 years. In an ancillary pot experiment, whole-plant hydraulic conductivity (soil-leaf hydraulic conductance; K(pa)) was measured under flooded and aerobic conditions. Adventitious root emergence and lateral root proliferation were restricted even under nearly saturated conditions, resulting in a 72-85 % reduction in total root length under aerobic culture conditions. Because of their reduced rooting size, plants grown under aerobic conditions tended to have lower K(pa) than plants grown under flooded conditions. Ψ(leaf) was always significantly lower in aerobic culture than in flooded culture, while g(s) was unchanged when the soil moisture was at around field capacity. g(s) was inevitably reduced when the soil water potential at 20-cm depth reached -20 kPa. Unstable performance of rice in water-saving cultivations is often associated with reduction in Ψ(leaf). Ψ(leaf) may reduce even if K(pa) is not significantly changed, but the lower Ψ(leaf) would certainly occur in case K(pa) reduces as a result of lower water-uptake capacity under aerobic conditions. Rice performance in aerobic culture might be improved through genetic manipulation that promotes lateral root branching and rhizogenesis as well as deep rooting.

Mechanism study of sulfur fertilization mediating copper translocation and biotransformation in rice (Oryza sativa L.) plants.

PubMed

Sun, Lijuan; Yang, Jianjun; Fang, Huaxiang; Xu, Chen; Peng, Cheng; Huang, Haomin; Lu, Lingli; Duan, Dechao; Zhang, Xiangzhi; Shi, Jiyan

2017-07-01

Metabolism of sulfur (S) is suggested to be an important factor for the homeostasis and detoxification of Cu in plants. We investigated the effects of S fertilizers (S 0 , Na 2 SO 4 ) on Cu translocation and biotransformation in rice plants by using multiple synchrotron-based techniques. Fertilization of S increased the biomass and yield of rice plants, as well as the translocation factor of Cu from root to shoot and shoot to grain, resulting in enhanced Cu in grain. Sulfur K-edge X-ray near edge structure (XANES) analysis showed that fertilization of S increased the concentration of glutathione in different rice tissues, especially in rice stem and leaf. Copper K-edge XANES results indicated that a much higher proportion of Cu (I) species existed in rice grain than husk and leaf, which was further confirmed by soft X-ray scanning transmission microscopy results. Sulfur increased the proportion of Cu (I) species in rice grain, husk and leaf, suggesting the inducing of Cu (II) reduction in rice tissues by S fertilization. These results suggested that fertilization of S in paddy soils increased the accumulation of Cu in rice grain, possibly due to the reduction of Cu (II) to Cu (I) by enhancing glutathione synthesis and increasing the translocation of Cu from shoot to grain. Copyright © 2017 Elsevier Ltd. All rights reserved.

Innate immunity in rice

PubMed Central

Chen, Xuewei; Ronald, Pamela C.

2011-01-01

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

A consortium of rhizobacterial strains and biochemical growth elicitors improve cold and drought stress tolerance in rice (Oryza sativa L.).

PubMed

Kakar, K U; Ren, X-L; Nawaz, Z; Cui, Z-Q; Li, B; Xie, G-L; Hassan, M A; Ali, E; Sun, G-C

2016-05-01

In the present study, a consortium of two rhizobacteria Bacillus amyloliquefaciens Bk7 and Brevibacillus laterosporus B4, termed 'BB', biochemical elicitors salicylic acid and β-aminobutyric acid (SB) and their mixture (BBSB) were investigated for cold and drought stress tolerance in rice plants. After withholding water for 16 days, rice plants treated with BBSB showed 100% survival, improved seedling height (35.4 cm), shoot number (6.12), and showed minimum symptoms of chlorosis (19%), wilting (4%), necrosis (6%) and rolling of leaves. Similarly, BB inoculation enhanced plant growth and reduced overall symptoms in rice seedlings subjected to 0 ± 5 °C for 24 h. Our results imply several mechanisms underlying BB- and BBSB-elicited stress tolerance. In contrast to the control, both treatments significantly decreased leaf monodehydroascorbate (MDA) content and electrolyte leakage, and increased leaf proline and cholorophyll content. Moreover, activities of antioxidant enzymes, superoxide dismutase (SOD) and catalase (CAT) increased 3.0- and 3.6-fold, respectively. Moreover, expression of OsMYB3R-2, OsDIL, OsDREB1A and OsCDPK13 genes was significantly up-regulated, suggesting that these genes play important roles in abiotic stress tolerance of rice. In addition, bacterial strains Bk7 and B4 were able to produce high amounts of IAA and siderophores, and colonise the plant roots, while only strain Bk7 exhibited the capability to form biofilms and solubilise inorganic phosphate. This study indicates that the BB and BBSB bio-formulations can be used to confer induced systematic tolerance and improve the health of rice plants subject to chilling and drought stress. © 2016 German Botanical Society and The Royal Botanical Society of the Netherlands.

The inheritance of resistance to bacterial leaf spot of lettuce caused by Xanthomonas campestris pv. vitians in three lettuce cultivars

USDA-ARS?s Scientific Manuscript database

Lettuce yields can be reduced by the disease bacterial leaf spot (BLS) caused by the pathogen Xanthomonas campestris pv. vitians (Xcv) and host resistance is the most feasible method to reduce disease losses. The cultivars La Brillante, Pavane, and Little Gem express an incompatible host-pathogen in...

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

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

Chou, Hong L.; Dai, Ziyu; Hsieh, Chia W.

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

Accumulation and Transfer of Cadmium, by Indica Rice Cultivars Fujian Province of China

NASA Astrophysics Data System (ADS)

James, B.; Wang, G.

2016-12-01

This study was designed to evaluate the accumulating ability of cadmium (Cd) by different Indica rice varieties and to understand the differences in transfer factor in the soil-to-rice grain. A total of 189 crop samples and 189 corresponding soil samples were collected for treatment and chemical analysis. Sixteen (16) Indica rice varieties were selected for this study. Our preliminary results showed that there exist significant differences (p<0.05) in the grain Cd concentrations of the variety studied. A regression method was adopted to calculate the representative soil-to-grain (TF0.1) of each cultivar. The accumulating ability of cadmium of the 16 cultivars varied greatly.Yi-xiang 2292 had the highest TFsoil-grain (2.91), which was 22 times higher than the lowest cultivar Pei- za-tai- fen (0.13). However, no significant difference in TFsoil-grain was observed between conventional and hybrid cultivars. A further study was carried out to understand the transfer characteristics and accumulating ability of cadmium using four (4) selected cultivars (both of hybrid and conventional indica rice cultivars).The TFstem-grain among the variety revealed that significant differences (p<0.05) exist in the stem of the selected variety in the translocation of Cd among indica rice variety and cadmium decreases in the pattern: root>stem>leaf>grain in the four cultivars except Te -you 009 that showed similar cadmium content in root and stem. Among the hybrid cultivars Yi -you 673 accumulated the most Cadmium in root, stem, leaf and grain, while Te- you 009 accumulated the least Cadmium in root, whereas the conventional cultivar Jia-fu-zhan accumulated the lowest Cadmium in leaf and grain. Our findings also revealed that the Cadmium concentrations in rice grains were more significantly correlated with the Cadmium in stem, followed by leaf, which reveals that the transfer from stem and leaf to grain may be the determinant steps for Cadmium accumulation in the grains.

Increased leaf angle1, a Raf-like MAPKKK that interacts with a nuclear protein family, regulates mechanical tissue formation in the Lamina joint of rice.

PubMed

Ning, Jing; Zhang, Baocai; Wang, Nili; Zhou, Yihua; Xiong, Lizhong

2011-12-01

Mitogen-activated protein kinase kinase kinases (MAPKKKs), which function at the top level of mitogen-activated protein kinase cascades, are clustered into three groups. However, no Group C Raf-like MAPKKKs have yet been functionally identified. We report here the characterization of a rice (Oryza sativa) mutant, increased leaf angle1 (ila1), resulting from a T-DNA insertion in a Group C MAPKKK gene. The increased leaf angle in ila1 is caused by abnormal vascular bundle formation and cell wall composition in the leaf lamina joint, as distinct from the mechanism observed in brassinosteroid-related mutants. Phosphorylation assays revealed that ILA1 is a functional kinase with Ser/Thr kinase activity. ILA1 is predominantly resident in the nucleus and expressed in the vascular bundles of leaf lamina joints. Yeast two-hybrid screening identified six closely related ILA1 interacting proteins (IIPs) of unknown function. Using representative IIPs, the interaction of ILA1 and IIPs was confirmed in vivo. IIPs were localized in the nucleus and showed transactivation activity. Furthermore, ILA1 could phosphorylate IIP4, indicating that IIPs may be the downstream substrates of ILA1. Microarray analyses of leaf lamina joints provided additional evidence for alterations in mechanical strength in ila1. ILA1 is thus a key factor regulating mechanical tissue formation at the leaf lamina joint.

Acidovorax anthurii sp. nov., a new phytopathogenic bacterium which causes bacterial leaf-spot of anthurium.

PubMed

Gardan, L; Dauga, C; Prior, P; Gillis, M; Saddler, G S

2000-01-01

The bacterial leaf-spot of anthurium emerged during the 1980s, in the French West Indies and Trinidad. This new bacterial disease is presently wide spread and constitutes a serious limiting factor for commercial anthurium production. Twenty-nine strains isolated from leaf-spots of naturally infected anthurium were characterized and compared with reference strains belonging to the Comamonadaceae family, the genera Ralstonia and Burkholderia, and representative fluorescent pseudomonads. From artificial inoculations 25 out of 29 strains were pathogenic on anthurium. Biochemical and physiological tests, fatty acid analysis, DNA-DNA hybridization, 16S rRNA gene sequence analysis, DNA-16S RNA hybridization were performed. The 25 pathogenic strains on anthurium were clustered in one phenon closely related to phytopathogenic strains of the genus Acidovorax. Anthurium strains were 79-99% (deltaTm range 0.2-1.6) related to the strain CFBP 3232 and constituted a discrete DNA homology group indicating that they belong to the same species. DNA-rRNA hybridization, 16S rRNA sequence and fatty acid analysis confirmed that this new species belongs to the beta-subclass of Proteobacteria and to rRNA superfamily III, to the family of Comamonadaceae and to the genus Acidovorax. The name Acidovorax anthurii is proposed for this new phytopathogenic bacterium. The type strain has been deposited in the Collection Française des Bactéries Phytopathogènes as CFBP 3232T.

Effect of Vaccinium bracteatum Thunb. leaf pigment on the thermal, pasting, and textural properties and microstructure characterization of rice starch.

PubMed

Xu, Yuan; Fan, Mingcong; Zhou, Sumei; Wang, Li; Qian, Haifeng; Zhang, Hui; Qi, Xiguang

2017-08-01

In this study, the thermal, pasting and gel textural properties of japonica rice starch (JRS) and glutinous rice starch (GRS) fortified with Vaccinium bracteatum Thunb. leaf pigment (VBTLP) were investigated. The results showed that VBTLP facilitated the gelatinization of JRS and GRS with earlier onsets of onset temperature (T o ), peak temperature (T p ), conclusion temperature (T c ), and lower values of gelatinization enthalpy (ΔH g ), and retrogradation enthalpy (ΔH r ), as the VBTLP level increased. For JRS, VBTLP increased the peak viscosity and breakdown, reduced the final viscosity and setback, but for GRS it increased the peak viscosity, final viscosity, breakdown and setback. VBTLP also reduced the hardness and adhesiveness of the JRS gel. The values of lightness (L ∗ ) for JRS and GRS with VBTLP decreased by 47.60 and 49.56%, respectively. Scanning electron microscopy (SEM) revealed that VBTLP caused looser matrices in dried JRS and GRS gels which had lower crystallinities compared with the control. Copyright © 2017 Elsevier Ltd. All rights reserved.

Soil and water warming accelerates phenology and down-regulation of leaf photosynthesis of rice plants grown under free-air CO2 enrichment (FACE).

PubMed

Adachi, Minaco; Hasegawa, Toshihiro; Fukayama, Hiroshi; Tokida, Takeshi; Sakai, Hidemitsu; Matsunami, Toshinori; Nakamura, Hirofumi; Sameshima, Ryoji; Okada, Masumi

2014-02-01

To enable prediction of future rice production in a changing climate, we need to understand the interactive effects of temperature and elevated [CO2] (E[CO2]). We therefore examined if the effect of E[CO2] on the light-saturated leaf photosynthetic rate (Asat) was affected by soil and water temperature (NT, normal; ET, elevated) under open-field conditions at the rice free-air CO2 enrichment (FACE) facility in Shizukuishi, Japan, in 2007 and 2008. Season-long E[CO2] (+200 µmol mol(-1)) increased Asat by 26%, when averaged over two years, temperature regimes and growth stages. The effect of ET (+2°C) on Asat was not significant at active tillering and heading, but became negative and significant at mid-grain filling; Asat in E[CO2]-ET was higher than in ambient [CO2] (A[CO2])-NT by only 4%. Photosynthetic down-regulation at E[CO2] also became apparent at mid-grain filling; Asat compared at the same [CO2] in the leaf cuvette was significantly lower in plants grown in E[CO2] than in those grown in A[CO2]. The additive effects of E[CO2] and ET decreased Asat by 23% compared with that of A[CO2]-NT plants. Although total crop nitrogen (N) uptake was increased by ET, N allocation to the leaves and to Rubisco was reduced under ET and E[CO2] at mid-grain filling, which resulted in a significant decrease (32%) in the maximum rate of ribulose-1,5-bisphosphate carboxylation on a leaf area basis. Because the change in N allocation was associated with the accelerated phenology in E[CO2]-ET plants, we conclude that soil and water warming accelerates photosynthetic down-regulation at E[CO2].

Dose-dependent response of Trichoderma harzianum in improving drought tolerance in rice genotypes.

PubMed

Pandey, Veena; Ansari, Mohammad W; Tula, Suresh; Yadav, Sandep; Sahoo, Ranjan K; Shukla, Nandini; Bains, Gurdeep; Badal, Shail; Chandra, Subhash; Gaur, A K; Kumar, Atul; Shukla, Alok; Kumar, J; Tuteja, Narendra

2016-05-01

This study demonstrates a dose-dependent response of Trichoderma harzianum Th-56 in improving drought tolerance in rice by modulating proline, SOD, lipid peroxidation product and DHN / AQU transcript level, and the growth attributes. In the present study, the effect of colonization of different doses of T. harzianum Th-56 strain in rice genotypes were evaluated under drought stress. The rice genotypes treated with increasing dose of T. harzianum strain Th-56 showed better drought tolerance as compared with untreated control plant. There was significant change in malondialdehyde, proline, higher superoxide dismutase level, plant height, total dry matter, relative chlorophyll content, leaf rolling, leaf tip burn, and the number of scorched/senesced leaves in T. harzianum Th-56 treated rice genotypes under drought stress. This was corroborated with altered expression of aquaporin and dehydrin genes in T. harzianum Th-56 treated rice genotypes. The present findings suggest that a dose of 30 g/L was the most effective in improving drought tolerance in rice, and its potential exploitation will contribute to the advancement of rice genotypes to sustain crop productivity under drought stress. Interaction studies of T. harzianum with three aromatic rice genotypes suggested that PSD-17 was highly benefitted from T. harzianum colonization under drought stress.

Bioefficacy of larvicdial and pupicidal properties of Carica papaya (Caricaceae) leaf extract and bacterial insecticide, spinosad, against chikungunya vector, Aedes aegypti (Diptera: Culicidae).

PubMed

Kovendan, Kalimuthu; Murugan, Kadarkarai; Naresh Kumar, Arjunan; Vincent, Savariar; Hwang, Jiang-Shiou

2012-02-01

The present study was carried out to establish the properties of Carica papaya leaf extract and bacterial insecticide, spinosad on larvicidal and pupicidal activity against the chikungunya vector, Aedes aegypti. The medicinal plants were collected from the area around Bharathiar University, Coimbatore, India. C. papaya leaf was washed with tap water and shade-dried at room temperature. An electrical blender powdered the dried plant materials (leaves). The powder (500 g) of the leaf was extracted with 1.5 l of organic solvents of methanol for 8 h using a Soxhlet apparatus and then filtered. The crude leaf extracts were evaporated to dryness in a rotary vacuum evaporator. The plant extract showed larvicidal and pupicidal effects after 24 h of exposure; however, the highest larval and pupal mortality was found in the leaf extract of methanol C. papaya against the first- to fourth-instar larvae and pupae of values LC(50) = I instar was 51.76 ppm, II instar was 61.87 ppm, III instar was 74.07 ppm, and IV instar was 82.18 ppm, and pupae was 440.65 ppm, respectively, and bacterial insecticide, spinosad against the first to fourth instar larvae and pupae of values LC(50) = I instar was 51.76 ppm, II instar was 61.87 ppm, III instar was 74.07 ppm, and IV instar was 82.18 ppm, and pupae was 93.44 ppm, respectively. Moreover, combined treatment of values of LC(50) = I instar was 55.77 ppm, II instar was 65.77 ppm, III instar was 76.36 ppm, and IV instar was 92.78 ppm, and pupae was 107.62 ppm, respectively. No mortality was observed in the control. The results that the leaves extract of C. papaya and bacterial insecticide, Spinosad is promising as good larvicidal and pupicidal properties of against chikungunya vector, A. aegypti. This is an ideal eco-friendly approach for the control of chikungunya vector, A. aegypti as target species of vector control programs.

Association analysis of bacterial leaf spot resistance and SNP markers derived from expressed sequence tags (ESTs) in lettuce (Lactuca sativa L.)

USDA-ARS?s Scientific Manuscript database

Bacterial leaf spot of lettuce, caused by Xanthomonas campestris pv. vitians, is a devastating disease of lettuce worldwide. Since there are no chemicals available for effective control of the disease, host-plant resistance is highly desirable to protect lettuce production. A total of 179 lettuce ge...

Organic rice disease management using genetic resistance, cover crop and organic fertilizer

USDA-ARS?s Scientific Manuscript database

The strong market demand for organic rice has driven the continued increase of organic rice production in the US. However, growers still lack effective tools to manage narrow brown leaf spot (NBLS) caused by Cercospora janseana and brown spot caused by Cochliobolus miyabeanus, two common diseases af...

Evaluation of Mercury Uptake and Distribution in Rice (Oryza sativa L.).

PubMed

Hang, Xiaoshuai; Gan, Fangqun; Chen, Yudong; Chen, Xiaoqin; Wang, Huoyan; Du, Changwen; Zhou, Jianmin

2018-03-01

Mercury (Hg) contamination in soil-rice systems from industry, mining and agriculture has received increasing attention recently in China. Pot experiments were conducted to research the Hg accumulation capacity of rice under exogenous Hg in the soil and study the major soil factors affecting translocation of Hg from soil to plant. Soil treated with 2 mg kg -1 Hg decreased rice grain yield and inhibited the growth of rice plants. With increased Hg contamination of the rice, the enrichment rate of Hg was significantly higher in the rice grain than that in the stalk and leaf. Soil pH and cation exchange capacity are the key factors controlling Hg bioavailability in soils.

Effects of drought stress on global gene expression profile in leaf and root samples of Dongxiang wild rice (Oryza rufipogon).

PubMed

Zhang, Fantao; Zhou, Yi; Zhang, Meng; Luo, Xiangdong; Xie, Jiankun

2017-06-30

Drought is a serious constraint to rice production throughout the world, and although Dongxiang wild rice ( Oryza rufipogon , DXWR) possesses a high degree of drought resistance, the underlying mechanisms of this trait remains unclear. In the present study, cDNA libraries were constructed from the leaf and root tissues of drought-stressed and untreated DXWR seedlings, and transcriptome sequencing was performed with the goal of elucidating the molecular mechanisms involved in drought-stress response. The results indicated that 11231 transcripts were differentially expressed in the leaves (4040 up-regulated and 7191 down-regulated) and 7025 transcripts were differentially expressed in the roots (3097 up-regulated and 3928 down-regulated). Among these differentially expressed genes (DEGs), the detection of many transcriptional factors and functional genes demonstrated that multiple regulatory pathways were involved in drought resistance. Meanwhile, the DEGs were also annotated with gene ontology (GO) terms and key pathways via functional classification and Kyoto Encyclopedia of Gene and Genomes (KEGG) pathway mapping, respectively. A set of the most interesting candidate genes was then identified by combining the DEGs with previously identified drought-resistant quantitative trait loci (QTL). The present work provides abundant genomic information for functional dissection of the drought resistance of DXWR, and findings will further help the current understanding of the biological regulatory mechanisms of drought resistance in plants and facilitate the breeding of new drought-resistant rice cultivars. © 2017 The Author(s).

RNA-Seq analysis reveals insight into enhanced rice Xa7-mediated bacterial blight resistance at high temperature.

PubMed

Cohen, Stephen P; Liu, Hongxia; Argueso, Cristiana T; Pereira, Andy; Vera Cruz, Casiana; Verdier, Valerie; Leach, Jan E

2017-01-01

Plant disease is a major challenge to agriculture worldwide, and it is exacerbated by abiotic environmental factors. During some plant-pathogen interactions, heat stress allows pathogens to overcome host resistance, a phenomenon which could severely impact crop productivity considering the global warming trends associated with climate change. Despite the importance of this phenomenon, little is known about the underlying molecular mechanisms. To better understand host plant responses during simultaneous heat and pathogen stress, we conducted a transcriptomics experiment for rice plants (cultivar IRBB61) containing Xa7, a bacterial blight disease resistance (R) gene, that were infected with Xanthomonas oryzae, the bacterial blight pathogen of rice, during high temperature stress. Xa7-mediated resistance is unusual relative to resistance mediated by other R genes in that it functions better at high temperatures. Using RNA-Seq technology, we identified 8,499 differentially expressed genes as temperature responsive in rice cultivar IRBB61 experiencing susceptible and resistant interactions across three time points. Notably, genes in the plant hormone abscisic acid biosynthesis and response pathways were up-regulated by high temperature in both mock-treated plants and plants experiencing a susceptible interaction and were suppressed by high temperature in plants exhibiting Xa7-mediated resistance. Genes responsive to salicylic acid, an important plant hormone for disease resistance, were down-regulated by high temperature during both the susceptible and resistant interactions, suggesting that enhanced Xa7-mediated resistance at high temperature is not dependent on salicylic acid signaling. A DNA sequence motif similar to known abscisic acid-responsive cis-regulatory elements was identified in the promoter region upstream of genes up-regulated in susceptible but down-regulated in resistant interactions. The results of our study suggest that the plant hormone abscisic

RNA-Seq analysis reveals insight into enhanced rice Xa7-mediated bacterial blight resistance at high temperature

PubMed Central

Argueso, Cristiana T.; Pereira, Andy; Vera Cruz, Casiana; Verdier, Valerie

2017-01-01

Plant disease is a major challenge to agriculture worldwide, and it is exacerbated by abiotic environmental factors. During some plant-pathogen interactions, heat stress allows pathogens to overcome host resistance, a phenomenon which could severely impact crop productivity considering the global warming trends associated with climate change. Despite the importance of this phenomenon, little is known about the underlying molecular mechanisms. To better understand host plant responses during simultaneous heat and pathogen stress, we conducted a transcriptomics experiment for rice plants (cultivar IRBB61) containing Xa7, a bacterial blight disease resistance (R) gene, that were infected with Xanthomonas oryzae, the bacterial blight pathogen of rice, during high temperature stress. Xa7-mediated resistance is unusual relative to resistance mediated by other R genes in that it functions better at high temperatures. Using RNA-Seq technology, we identified 8,499 differentially expressed genes as temperature responsive in rice cultivar IRBB61 experiencing susceptible and resistant interactions across three time points. Notably, genes in the plant hormone abscisic acid biosynthesis and response pathways were up-regulated by high temperature in both mock-treated plants and plants experiencing a susceptible interaction and were suppressed by high temperature in plants exhibiting Xa7-mediated resistance. Genes responsive to salicylic acid, an important plant hormone for disease resistance, were down-regulated by high temperature during both the susceptible and resistant interactions, suggesting that enhanced Xa7-mediated resistance at high temperature is not dependent on salicylic acid signaling. A DNA sequence motif similar to known abscisic acid-responsive cis-regulatory elements was identified in the promoter region upstream of genes up-regulated in susceptible but down-regulated in resistant interactions. The results of our study suggest that the plant hormone abscisic

Development of transgenic finger millet (Eleusine coracana (L.) Gaertn.) resistant to leaf blast disease.

PubMed

Ignacimuthu, S; Ceasar, S Antony

2012-03-01

Finger millet plants conferring resistance to leaf blast disease have been developed by inserting a rice chitinase (chi11) gene through Agrobacterium-mediated transformation. Plasmid pHyg-Chi.11 harbouring the rice chitinase gene under the control of maize ubiquitin promoter was introduced into finger millet using Agrobacterium strain LBA4404 (pSB1). Transformed plants were selected and regenerated on hygromycin-supplemented medium. Transient expression of transgene was confirmed by GUS histochemical staining. The incorporation of rice chitinase gene in R0 and R1 progenies was confirmed by PCR and Southern blot analyses. Expression of chitinase gene in finger millet was confirmed by Western blot analysis with a barley chitinase antibody. A leaf blast assay was also performed by challenging the transgenic plants with spores of Pyricularia grisea. The frequency of transient expression was 16.3% to 19.3%. Stable frequency was 3.5% to 3.9%. Southern blot analysis confirmed the integration of 3.1 kb chitinase gene. Western blot analysis detected the presence of 35 kDa chitinase enzyme. Chitinase activity ranged from 19.4 to 24.8. In segregation analysis, the transgenic R1 lines produced three resistant and one sensitive for hygromycin, confirming the normal Mendelian pattern of transgene segregation. Transgenic plants showed high level of resistance to leaf blast disease compared to control plants. This is the first study reporting the introduction of rice chitinase gene into finger millet for leaf blast resistance.

Unusual small subunit that is not expressed in photosynthetic cells alters the catalytic properties of rubisco in rice.

PubMed

Morita, Koichi; Hatanaka, Tomoko; Misoo, Shuji; Fukayama, Hiroshi

2014-01-01

Rubisco small subunits (RbcSs) are encoded by a nuclear multigene family in plants. Five RbcS genes, OsRbcS1, OsRbcS2, OsRbcS3, OsRbcS4, and OsRbcS5, have been identified in rice (Oryza sativa). Among them, the amino acid sequence of OsRbcS1 differs notably from those of other rice RbcSs. Phylogenetic analysis showed that OsRbcS1 is genetically distant from other rice RbcS genes and more closely related to RbcS from a fern and two woody plants. Reverse transcription-PCR and promoter β-glucuronidase analyses revealed that OsRbcS1 was not expressed in leaf blade, a major photosynthetic organ in rice, but was expressed in leaf sheath, culm, anther, and root central cylinder. In leaf blade of transgenic rice overexpressing OsRbcS1 and leaf sheath of nontransgenic rice, OsRbcS1 was incorporated into the Rubisco holoenzyme. Incorporation of OsRbcS1 into Rubisco increased the catalytic turnover rate and Km for CO2 of the enzyme and slightly decreased the specificity for CO2, indicating that the catalytic properties were shifted to those of a high-activity type Rubisco. The CO2 assimilation rate at low CO2 partial pressure was decreased in overexpression lines but was not changed under ambient and high CO2 partial pressure compared with nontransgenic rice. Although the Rubisco content was increased, Rubisco activation state was decreased in overexpression lines. These results indicate that the catalytic properties of Rubisco can be altered by ectopic expression of OsRbcS1, with substantial effects on photosynthetic performance in rice. We believe this is the first demonstration of organ-specific expression of individual members of the RbcS gene family resulting in marked effects on Rubisco catalytic activity.

Metagenomic and metaproteomic insights into bacterial communities in leaf-cutter ant fungus gardens.

PubMed

Aylward, Frank O; Burnum, Kristin E; Scott, Jarrod J; Suen, Garret; Tringe, Susannah G; Adams, Sandra M; Barry, Kerrie W; Nicora, Carrie D; Piehowski, Paul D; Purvine, Samuel O; Starrett, Gabriel J; Goodwin, Lynne A; Smith, Richard D; Lipton, Mary S; Currie, Cameron R

2012-09-01

Herbivores gain access to nutrients stored in plant biomass largely by harnessing the metabolic activities of microbes. Leaf-cutter ants of the genus Atta are a hallmark example; these dominant neotropical herbivores cultivate symbiotic fungus gardens on large quantities of fresh plant forage. As the external digestive system of the ants, fungus gardens facilitate the production and sustenance of millions of workers. Using metagenomic and metaproteomic techniques, we characterize the bacterial diversity and physiological potential of fungus gardens from two species of Atta. Our analysis of over 1.2 Gbp of community metagenomic sequence and three 16S pyrotag libraries reveals that in addition to harboring the dominant fungal crop, these ecosystems contain abundant populations of Enterobacteriaceae, including the genera Enterobacter, Pantoea, Klebsiella, Citrobacter and Escherichia. We show that these bacterial communities possess genes associated with lignocellulose degradation and diverse biosynthetic pathways, suggesting that they play a role in nutrient cycling by converting the nitrogen-poor forage of the ants into B-vitamins, amino acids and other cellular components. Our metaproteomic analysis confirms that bacterial glycosyl hydrolases and proteins with putative biosynthetic functions are produced in both field-collected and laboratory-reared colonies. These results are consistent with the hypothesis that fungus gardens are specialized fungus-bacteria communities that convert plant material into energy for their ant hosts. Together with recent investigations into the microbial symbionts of vertebrates, our work underscores the importance of microbial communities in the ecology and evolution of herbivorous metazoans.

Metagenomic and metaproteomic insights into bacterial communities in leaf-cutter ant fungus gardens

PubMed Central

Aylward, Frank O; Burnum, Kristin E; Scott, Jarrod J; Suen, Garret; Tringe, Susannah G; Adams, Sandra M; Barry, Kerrie W; Nicora, Carrie D; Piehowski, Paul D; Purvine, Samuel O; Starrett, Gabriel J; Goodwin, Lynne A; Smith, Richard D; Lipton, Mary S; Currie, Cameron R

2012-01-01

Herbivores gain access to nutrients stored in plant biomass largely by harnessing the metabolic activities of microbes. Leaf-cutter ants of the genus Atta are a hallmark example; these dominant neotropical herbivores cultivate symbiotic fungus gardens on large quantities of fresh plant forage. As the external digestive system of the ants, fungus gardens facilitate the production and sustenance of millions of workers. Using metagenomic and metaproteomic techniques, we characterize the bacterial diversity and physiological potential of fungus gardens from two species of Atta. Our analysis of over 1.2 Gbp of community metagenomic sequence and three 16S pyrotag libraries reveals that in addition to harboring the dominant fungal crop, these ecosystems contain abundant populations of Enterobacteriaceae, including the genera Enterobacter, Pantoea, Klebsiella, Citrobacter and Escherichia. We show that these bacterial communities possess genes associated with lignocellulose degradation and diverse biosynthetic pathways, suggesting that they play a role in nutrient cycling by converting the nitrogen-poor forage of the ants into B-vitamins, amino acids and other cellular components. Our metaproteomic analysis confirms that bacterial glycosyl hydrolases and proteins with putative biosynthetic functions are produced in both field-collected and laboratory-reared colonies. These results are consistent with the hypothesis that fungus gardens are specialized fungus–bacteria communities that convert plant material into energy for their ant hosts. Together with recent investigations into the microbial symbionts of vertebrates, our work underscores the importance of microbial communities in the ecology and evolution of herbivorous metazoans. PMID:22378535

Responses of Bacterial Communities in Arable Soils in a Rice-Wheat Cropping System to Different Fertilizer Regimes and Sampling Times

PubMed Central

Zhao, Jun; Ni, Tian; Li, Yong; Xiong, Wu; Ran, Wei; Shen, Biao; Shen, Qirong; Zhang, Ruifu

2014-01-01

Soil physicochemical properties, soil microbial biomass and bacterial community structures in a rice-wheat cropping system subjected to different fertilizer regimes were investigated in two seasons (June and October). All fertilizer regimes increased the soil microbial biomass carbon and nitrogen. Both fertilizer regime and time had a significant effect on soil physicochemical properties and bacterial community structure. The combined application of inorganic fertilizer and manure organic-inorganic fertilizer significantly enhanced the bacterial diversity in both seasons. The bacterial communities across all samples were dominated by Proteobacteria, Acidobacteria and Chloroflexi at the phylum level. Permutational multivariate analysis confirmed that both fertilizer treatment and season were significant factors in the variation of the composition of the bacterial community. Hierarchical cluster analysis based on Bray-Curtis distances further revealed that bacterial communities were separated primarily by season. The effect of fertilizer treatment is significant (P = 0.005) and accounts for 7.43% of the total variation in bacterial community. Soil nutrients (e.g., available K, total N, total P and organic matter) rather than pH showed significant correlation with the majority of abundant taxa. In conclusion, both fertilizer treatment and seasonal changes affect soil properties, microbial biomass and bacterial community structure. The application of NPK plus manure organic-inorganic fertilizer may be a sound fertilizer practice for sustainable food production. PMID:24465530

Season, Irrigation, Leaf Age, and Escherichia coli Inoculation Influence the Bacterial Diversity in the Lettuce Phyllosphere

PubMed Central

Williams, Thomas R.; Moyne, Anne-Laure; Harris, Linda J.; Marco, Maria L.

2013-01-01

The developmental and temporal succession patterns and disturbance responses of phyllosphere bacterial communities are largely unknown. These factors might influence the capacity of human pathogens to persist in association with those communities on agriculturally-relevant plants. In this study, the phyllosphere microbiota was identified for Romaine lettuce plants grown in the Salinas Valley, CA, USA from four plantings performed over 2 years and including two irrigation methods and inoculations with an attenuated strain of Escherichia coli O157:H7. High-throughput DNA pyrosequencing of the V5 to V9 variable regions of bacterial 16S rRNA genes recovered in lettuce leaf washes revealed that the bacterial diversity in the phyllosphere was distinct for each field trial but was also strongly correlated with the season of planting. Firmicutes were generally most abundant in early season (June) plantings and Proteobacteria comprised the majority of bacteria recovered later in the year (August and October). Comparisons within individual field trials showed that bacterial diversity differed between sprinkler (overhead) and drip (surface) irrigated lettuce and increased over time as the plants grew. The microbiota were also distinct between control and E. coli O157:H7-inoculated plants and between E. coli O157:H7-inoculated plants with and without surviving pathogen cells. The bacterial inhabitants of the phyllosphere therefore appear to be affected by seasonal, irrigation, and biological factors in ways that are relevant for assessments of fresh produce food safety. PMID:23844230

GDSL lipases modulate immunity through lipid homeostasis in rice

PubMed Central

Lam, Sin Man; Tong, Xiaohong; Liu, Jiyun; Wang, Xin; Shui, Guanghou

2017-01-01

Lipids and lipid metabolites play important roles in plant-microbe interactions. Despite the extensive studies of lipases in lipid homeostasis and seed oil biosynthesis, the involvement of lipases in plant immunity remains largely unknown. In particular, GDSL esterases/lipases, characterized by the conserved GDSL motif, are a subfamily of lipolytic enzymes with broad substrate specificity. Here, we functionally identified two GDSL lipases, OsGLIP1 and OsGLIP2, in rice immune responses. Expression of OsGLIP1 and OsGLIP2 was suppressed by pathogen infection and salicylic acid (SA) treatment. OsGLIP1 was mainly expressed in leaf and leaf sheath, while OsGLIP2 showed high expression in elongating internodes. Biochemical assay demonstrated that OsGLIP1 and OsGLIP2 are functional lipases that could hydrolyze lipid substrates. Simultaneous down-regulation of OsGLIP1 and OsGLIP2 increased plant resistance to both bacterial and fungal pathogens, whereas disease resistance in OsGLIP1 and OsGLIP2 overexpression plants was significantly compromised, suggesting that both genes act as negative regulators of disease resistance. OsGLIP1 and OsGLIP2 proteins mainly localize to lipid droplets and the endoplasmic reticulum (ER) membrane. The proper cellular localization of OsGLIP proteins is indispensable for their functions in immunity. Comprehensive lipid profiling analysis indicated that the alteration of OsGLIP gene expression was associated with substantial changes of the levels of lipid species including monogalactosyldiacylglycerol (MGDG) and digalactosyldiacylglycerol (DGDG). We show that MGDG and DGDG feeding could attenuate disease resistance. Taken together, our study indicates that OsGLIP1 and OsGLIP2 negatively regulate rice defense by modulating lipid metabolism, thus providing new insights into the function of lipids in plant immunity. PMID:29131851

Evaluation of bacteria isolated from rice for plant growth promotion and biological control of seedling disease of rice.

PubMed

Adhikari, T B; Joseph, C M; Yang, G; Phillips, D A; Nelson, L M

2001-10-01

Of 102 rhizoplane and endophytic bacteria isolated from rice roots and stems in California, 37% significantly (P < or = 0.05) inhibited the growth in vitro of two pathogens, Achlya klebsiana and Pythium spinosum, causing seedling disease of rice. Four endophytic strains were highly effective against seedling disease in growth pouch assays, and these were identified as Pseudomonas fluorescens (S3), Pseudomonas tolaasii (S20), Pseudomonas veronii (S21), and Sphingomonas trueperi (S12) by sequencing of amplified 16S rRNA genes. Strains S12, S20, and S21 contained the nitrogen fixation gene, nifD, but only S12 was able to reduce acetylene in pure culture. The four strains significantly enhanced plant growth in the absence of pathogens, as evidenced by increases in plant height and dry weight of inoculated rice seedlings relative to noninoculated rice. Three bacterial strains (S3, S20, and S21) were evaluated in pot bioassays and reduced disease incidence by 50%-73%. Strain S3 was as effective at suppressing disease at the lowest inoculum density (106 CFU/mL) as at higher density (10(8) CFU/mL or undiluted suspension). This study indicates that selected endophytic bacterial strains have potential for control of seedling disease of rice and for plant growth promotion.

Rice root-associated bacteria – insights in community structures across ten cultivars

PubMed Central

Hardoim, Pablo Rodrigo; Andreote, Fernando Dini; Reinhold-Hurek, Barbara; Sessitsch, Angela; van Overbeek, Leonard Simon; van Elsas, Jan Dirk

2015-01-01

In this study, the effect of plant genotype, soil type and nutrient use efficiency on the composition of different bacterial communities associated with rice roots were investigated. Thus, total bacteria, Alpha- and Beta-proteobacteria, Pseudomonas and Actinobacteria were studied using PCR followed by denaturing gradient gel electrophoresis (PCR-DGGE). Rice genotype determined to a large extent the composition of the different bacterial communities across cultivars. Several cultivars belonging to Oryza sativa subspecies indica tended to select similar bacterial communities, whereas those belonging to subspecies japonica and aromatica selected ones with divergent community structures. An effect of soil type was pronounced for the Actinobacteria communities, while a small effect of ‘improved’ and ‘traditional’ plants was noted for all communities analysed. A few dominant bands in PCR-DGGE, affiliated with Rhizobium radiobacter, Dickeya zeae, Mycobacterium bolletii and with members of the Rhizobiales, Rhodospirillaceae and Paenibacillaceae were spread across cultivars. In contrast, a majority of bands (e.g. affiliated with Enterobacter cloacae or Burkholderia kururiensis) was only present in particular cultivars or was erratically distributed amongst rice replicates. The data suggested that both bacterial adaptation and plant genotype contribute to the shaping of the dynamic bacterial communities associated with roots of rice plants. PMID:21426364

First report of pecan bacterial leaf scorch caused by Xylella fastidiosa in pecan (Carya illinoinensis) in Arizona, New Mexico, California, and Texas

USDA-ARS?s Scientific Manuscript database

Pecan bacterial leaf scorch (PBLS) is a chronic disease that can cause major yield losses in pecan orchards. In the 2015-16 growing seasons, symptoms consistent with PBLS were observed in commercial pecan cultivars in AZ, NM, CA and TX. Symptoms included tan to light brown necrotic lesions, which ...

Impact of solar radiation exposure on phyllosphere bacterial community of red-pigmented baby leaf lettuce.

PubMed

Truchado, Pilar; Gil, M Isabel; Reboleiro, Patricia; Rodelas, Belén; Allende, Ana

2017-09-01

Solar radiation has been identified as a stress factor affecting phyllosphere associated bacteria colonization and survival during primary production. In the present study, the impact of different solar radiation doses on the phyllosphere microbiota of red-pigmented baby leaf lettuce cultivated in open field under commercial conditions was evaluated. Four weeks before harvest, the growing field was divided into four plots; each one was consecutively covered with one-week-interval with a light-excluding plastic to reduce the sunlight exposure. Four different solar radiation treatments were generated and cumulative photosynthetically active radiation (PAR) was used to differentiate treatments as follows: 4889 ± 428 μmol/m 2 /s (uncovered), 4265 ± 356 μmol/m 2 /s (covered for 1 week), 3602 ± 225 μmol/m 2 /s (covered for 2 weeks) and 3115 ± 313 μmol/m 2 /s (covered for 3 weeks). The size and composition of the phyllosphere bacterial community were determined by cultivation-depended (plate count) and independent (qPCR) techniques. Exposure to decreased levels of cumulative PAR did not produce significant differences in total bacterial community size, regardless of the chosen quantification techniques. However, total bacteria size quantified by qPCR was around 3.5 orders of magnitude higher than those obtained by plate count. The observed differences between cultivation-depended and independent techniques could be attributed to the presence of non-viable or viable but non-culturable (VBNC) bacteria. The bacterial community structure was analyzed using temperature gradient gel electrophoresis (TGGE), and significant differences were detected when the four solar treatment were compared. A qPCR approach was applied to the quantification of specific bacterial phyla and classes, previously identified in the phyllosphere of plants available literature, confirming that Proteobacteria, Bacteroidetes, Actinobacterias and Firmicutes were the most abundantly

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

PubMed

Kant, Ravi; Dasgupta, Indranil

2017-07-01

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

The Role of Node Restriction on Cadmium Accumulation in the Brown Rice of 12 Chinese Rice (Oryza sativa L.) Cultivars.

PubMed

Huang, Gaoxiang; Ding, Changfeng; Guo, Fuyu; Li, Xiaogang; Zhou, Zhigao; Zhang, Taolin; Wang, Xingxiang

2017-11-29

For selection or breeding of rice (Oryza sativa L.) cultivars with low Cd affinity, the role of node Cd restriction on Cd accumulation in brown rice was studied. A pot experiment was conducted to investigate the concentration of Cd in different sections of 12 Chinese rice cultivars. The results indicated that the Cd accumulation in the brown rice was mainly dependent on the root or shoot Cd concentration. Among the cultivars with nearly equal shoot Cd concentrations, Cd accumulation in brown rice was mainly dependent on the transport of Cd in the shoot. However, the Cd transport in the shoot was significantly restricted by the nodes, especially by the first node. Furthermore, the area of the diffuse vascular bundle in the junctional region of the flag leaf and the first node was a key contributor to the variations in Cd restriction by the nodes.

Panicle blast and canopy moisture in rice cultivar mixtures.

PubMed

Zhu, You-Yong; Fang, Hui; Wang, Yun-Yue; Fan, Jin Xiang; Yang, Shi-Sheng; Mew, Twng Wah; Mundt, Christopher C

2005-04-01

ABSTRACT Glutinous rice cultivars were sown after every fourth row of a nonglutinous, hybrid cultivar in an additive design. The glutinous cultivars were 35 to 40 cm taller and substantially more susceptible to blast than was the nonglutinous cultivar. Interplanting of glutinous and nonglutinous rice reduced the incidence and severity of panicle blast on the glutinous cultivars by >90%, and on the nonglutinous cultivar by 30 to 40%. Mixing increased the per unit area yield of glutinous rice by 80 to 90% relative to pure stand, whereas yield of the nonglutinous cultivar was essentially unaffected by mixing. To determine whether the different plant heights and canopy structures may contribute to a microclimate that is less favorable to blast infection, we monitored the moisture status of the glutinous cultivars in pure stand and mixture at 0800 h by measuring relative humidity at the height of the glutinous panicles using a swing psychrometer and by visually estimating the percentage of leaf area covered by dew. Averaged over the two seasons, the number of days of 100% humidity at 0800 h was 20.0 and 2.2 for pure stands and mixtures, respectively. The mean percentage of glutinous leaf area covered by dewwas 84 and 36% for the pure stands and mixtures, respectively. Although other mechanisms also were operative, reduced leaf wetness was likely a substantial contributor to panicle blast control in the mixtures.

Salicaceae Endophytes Modulate Stomatal Behavior and Increase Water Use Efficiency in Rice

PubMed Central

Rho, Hyungmin; Van Epps, Victor; Wegley, Nicholas; Doty, Sharon L.; Kim, Soo-Hyung

2018-01-01

Bacterial and yeast endophytes isolated from the Salicaceae family have been shown to promote growth and alleviate stress in plants from different taxa. To determine the physiological pathways through which endophytes affect plant water relations, we investigated leaf water potential, whole-plant water use, and stomatal responses of rice plants to Salicaceae endophyte inoculation under CO2 enrichment and water deficit. Daytime stomatal conductance and stomatal density were lower in inoculated plants compared to controls. Leaf ABA concentrations increased with endophyte inoculation. As a result, transpirational water use decreased significantly with endophyte inoculation while biomass did not change or slightly increased. This response led to a significant increase in cumulative water use efficiency at harvest. Different endophyte strains produced the same results in host plant water relations and stomatal responses. These stomatal responses were also observed under elevated CO2 conditions, and the increase in water use efficiency was more pronounced under water deficit conditions. The effect on water use efficiency was positively correlated with daily light integrals across different experiments. Our results provide insights on the physiological mechanisms of plant-endophyte interactions involving plant water relations and stomatal functions. PMID:29552021

No effect of Bt-transgenic rice litter on the meiobenthos community in field ditches.

PubMed

Liu, Yongbo; Jiang, Wanxiang; Liang, Yuyong; Zhao, Caiyun; Li, Junsheng

2017-06-01

The non-target effect of Bacillus thuringiensis (Bt) toxins in aquatic ecosystems is crucial to improve the present assessment of Bt-transgenic plants, particularly where crops are cultivated near aquatic ecosystems. We conducted decomposition experiments during two growing seasons to determine the effects of Bt-transgenic rice litter with and without insecticide application on the meiobenthos communities in a field ditch. The community composition of meiobenthos colonised on leaf litter was not significantly different between Bt and non-Bt rice. The abundance of meiobenthos colonising leaves differed between insecticide application and control, and this insecticide effect interacted with rice type. No Bt toxin was detected in field ditch water. Leaf decomposition and nutrient content were comparable for both Bt and non-Bt rice with or without insecticide application. Bt-transgenic rice litter had no effect on the meiobenthos community composition in field ditches, but the chronic persistence of transgenic litter in nature needs to be taken into account at large scales in aquatic ecosystems. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

Regulation of glutamine synthetase isoforms in two differentially drought-tolerant rice (Oryza sativa L.) cultivars under water deficit conditions.

PubMed

Singh, Kamal Krishna; Ghosh, Shilpi

2013-02-01

KEY MESSAGE : The regulation of GS isoforms by WD was organ specific. Two GS isoforms i.e. OsGS1;1 and OsGS2 were differentially regulated in IR-64 (drought-sensitive) and Khitish (drought-tolerant) cultivars of rice. Water deficit (WD) has adverse effect on rice (Oryza sativa L.) and acclimation requires essential reactions of primary metabolism to continue. Rice plants utilize ammonium as major nitrogen source, which is assimilated into glutamine by the reaction of Glutamine synthetase (GS, EC 6.3.1.2). Rice plants possess one gene (OsGS2) for chloroplastic GS2 and three genes (OsGS1;1, OsGS1;2 and OsGS1;3) for cytosolic GS1. Here, we report the effect of WD on regulation of GS isoforms in drought-sensitive (cv. IR-64) and drought-tolerant (cv. Khitish) rice cultivars. Under WD, total GS activity in root and leaf decreased significantly in IR-64 seedlings in comparison to Khitish seedlings. The reduced GS activity in IR-64 leaf was mainly due to decrease in GS2 activity, which correlated with decrease in corresponding transcript and polypeptide contents. GS1 transcript and polypeptide accumulated in leaf during WD, however, GS1 activity was maintained at a constant level. Total GS activity in stem of both the varieties was insensitive to WD. Among GS1 genes, OsGS1;1 expression was differently regulated by WD in the two rice varieties. Its transcript accumulated more abundantly in IR-64 leaf than in Khitish leaf. Following WD, OsGS1;1 mRNA level in stem and root tissues declined in IR-64 and enhanced in Khitish. A steady OsGS1;2 expression patterns were noted in leaf, stem and root of both the cultivars. Results suggest that OsGS2 and OsGS1;1 expression may contribute to drought tolerance of Khitish cultivar under WD conditions.

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

PubMed Central

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

2012-01-01

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

Subcellular Localization of Rice Leaf Aryl Acylamidase Activity 1

PubMed Central

Gaynor, John J.; Still, Cecil C.

1983-01-01

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

Dietary supplementation with rice bran or navy bean alters gut bacterial metabolism in colorectal cancer survivors.

PubMed

Sheflin, Amy M; Borresen, Erica C; Kirkwood, Jay S; Boot, Claudia M; Whitney, Alyssa K; Lu, Shen; Brown, Regina J; Broeckling, Corey D; Ryan, Elizabeth P; Weir, Tiffany L

2017-01-01

Heat-stabilized rice bran (SRB) and cooked navy bean powder (NBP) contain a variety of phytochemicals that are fermented by colonic microbiota and may influence intestinal health. Dietary interventions with these foods should be explored for modulating colorectal cancer risk. A randomized-controlled pilot clinical trial investigated the effects of eating SRB (30 g/day) or cooked navy bean powder (35 g/day) on gut microbiota and metabolites (NCT01929122). Twenty-nine overweight/obese volunteers with a prior history of colorectal cancer consumed a study-provided meal and snack daily for 28 days. Volunteers receiving SRB or NBP showed increased gut bacterial diversity and altered gut microbial composition at 28 days compared to baseline. Supplementation with SRB or NBP increased total dietary fiber intake similarly, yet only rice bran intake led to a decreased Firmicutes:Bacteroidetes ratio and increased SCFA (propionate and acetate) in stool after 14 days but not at 28 days. These findings support modulation of gut microbiota and fermentation byproducts by SRB and suggest that foods with similar ability to increase dietary fiber intake may not have equal effects on gut microbiota and microbial metabolism. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Comparison of leaf color chart observations with digital photographs and spectral measurements for estimating maize leaf chlorophyll content

USDA-ARS?s Scientific Manuscript database

Crop nitrogen management is important world-wide, as much for small fields as it is for large operations. Developed as a non-destructive aid for estimating nitrogen content in rice crops, leaf color charts (LCC) are a numbered series of plastic panels that range from yellowgreen to dark green. By vi...

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

PubMed

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

2007-04-01

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

Code-assisted discovery of TAL effector targets in bacterial leaf streak of rice reveals contrast with bacterial blight and a novel susceptibility gene

USDA-ARS?s Scientific Manuscript database

Transcription activator-like (TAL) effectors found in Xanthomonas spp. promote bacterial growth and plant susceptibility by binding specific DNA sequences or, effector-binding elements (EBEs), and inducing host gene expression. In this study, we have found substantially different transcriptional pro...

Effect of depth of flooding on the rice water weevil, Lissorhoptrus oryzophilus, and yield of rice.

PubMed

Tindall, Kelly V; Bernhardt, John L; Stout, Michael J; Beighley, Donn H

2013-01-01

The rice water weevil, Lissorhoptrus oryzophilus (Kuschel) (Coleoptera: Curculionidae), is a semi-aquatic pest of rice and is the most destructive insect pest of rice in the United States. Adults oviposit after floods are established, and greenhouse studies have shown that plants exposed to deep floods have more eggs oviposited in leaf sheaths than plants exposed to a shallow flood. Experiments were conducted in three mid-southern states in the USA to determine if the depth of flooding would impact numbers of L. oryzophilus on rice plants under field conditions. Rice was flooded at depths of approximately 5 or 10 cm in Arkansas in 2007 and 2008 and Louisiana in 2008, and at depths between 0-20 cm in Missouri in 2008. Plants were sampled three and four weeks after floods were established in all locations, and also two weeks after flood in Missouri. On all sampling dates in four experiments over two years and at three field sites, fewer L. oryzophilus larvae were collected from rice in shallow-flooded plots than from deep-flooded plots. The number of L. oryzophilus was reduced by as much as 27% in shallow-flooded plots. However, the reduction in insect numbers did not translate to a significant increase in rice yield. We discuss how shallow floods could be used as a component of an integrated pest management program for L. oryzophilus.

Effect of Depth of Flooding on the Rice Water Weevil, Lissorhoptrus oryzophilus, and Yield of Rice

PubMed Central

Tindall, Kelly V.; Bernhardt, John L.; Stout, Michael J.; Beighley, Donn H.

2013-01-01

The rice water weevil, Lissorhoptrus oryzophilus (Kuschel) (Coleoptera: Curculionidae), is a semi-aquatic pest of rice and is the most destructive insect pest of rice in the United States. Adults oviposit after floods are established, and greenhouse studies have shown that plants exposed to deep floods have more eggs oviposited in leaf sheaths than plants exposed to a shallow flood. Experiments were conducted in three mid-southern states in the USA to determine if the depth of flooding would impact numbers of L. oryzophilus on rice plants under field conditions. Rice was flooded at depths of approximately 5 or 10 cm in Arkansas in 2007 and 2008 and Louisiana in 2008, and at depths between 0–20 cm in Missouri in 2008. Plants were sampled three and four weeks after floods were established in all locations, and also two weeks after flood in Missouri. On all sampling dates in four experiments over two years and at three field sites, fewer L. oryzophilus larvae were collected from rice in shallow-flooded plots than from deep-flooded plots. The number of L. oryzophilus was reduced by as much as 27% in shallow-flooded plots. However, the reduction in insect numbers did not translate to a significant increase in rice yield. We discuss how shallow floods could be used as a component of an integrated pest management program for L. oryzophilus. PMID:23906324

Temporal interactions of plant - insect - predator after infection of bacterial pathogen on rice plants.

PubMed

Sun, Ze; Liu, Zhuang; Zhou, Wen; Jin, Huanan; Liu, Hao; Zhou, Aiming; Zhang, Aijun; Wang, Man-Qun

2016-05-17

Pathogenic infection on plants may affect interactions of host-plants with their herbivores, as well as the herbivores with their predators. In this study, the effects of infection by pathogenic bacterium Xanthomonas oryzae pv. oryzae (Xoo), which causes a vascular disease in rice, on rice plants and consequent interactions with a rice herbivore, brown rice planthopper (BPH) Nilaparvata lugens, and its major predator, Cyrtorhinus lividipennis, were investigated. The results showed that the rice plants exhibited increased resistance to BPH only at 3 d post-inoculation of Xoo, while the Xoo infection did not affect the development and fecundity of BPH. BPH exhibited a higher preference to Xoo infected rice plants, whereas C. lividipennis preferred the Xoo infected rice plants after BPH fed, but preferred healthy rice plants without BPH fed. Volatile organic compounds emitted from Xoo rice were significantly higher than those from healthy rice plants, Xoo infection on BPH fed plants caused rice plants to emit more the herbivore-induced plant volatiles, while all of these changes correlated to the temporal dimension. These results demonstrated that Xoo infection significantly influenced the interactions of rice plants with two non-vectors, BPH and its predator, although these effects exhibited in a temporal pattern after infection.

Determination of the Water Potential Threshold at Which Rice Growth Is Impacted.

PubMed

Dos Santos, Caio Luiz; de Borja Reis, André Froes; Mazzafera, Paulo; Favarin, José Laércio

2018-06-22

Rice feeds 50% of the world’s population. Flooding is the most common irrigation system used for growing rice, a practice responsible for a large amount of water loss. Climate changes may affect water availability in irrigated agriculture, and it will be necessary to develop more sustainable irrigation practices. The aim of this work was to determine, in controlled conditions, the threshold when water potential begins to decrease plant growth. Two independent greenhouse experiments were conducted during middle summer and fall, in order to validate the results for high and low evapotranspiration conditions. Rice plants were grown in hydroponics and the water potential was adjusted with polyethylene glycol 6000, varying from −0.04 MPa (control) to −0.19 MPa. Leaf water potential, water use efficiency, leaf area, and root and shoot biomass were evaluated. All assayed parameters decreased as the water potential was decreased. The water potential threshold which starts to negatively affect rice growth was between −0.046 and −0.056 MPa, which are values close to those observed in the field in previous research. The definition of a critical value may help to improve water management in rice cultivation and to maintain productivity.

Influence of fertilization on the capability of rice resistance to diseases

NASA Astrophysics Data System (ADS)

Hu, Xue-Feng; Chang, Yue-Ya; Jiang, Ying; Yan, Xiao-Juan; Luo, Fan

2013-04-01

Organic cultivation of rice requires no use of any agricultural chemicals during the entire period of growth, and so the rice's self-prevention of diseases and pests is vitally important. A field experiment was carried out to study the possible influence of different fertilization on the capability of rice resistance to diseases and pests. A rice variety used for this experiment is Jia-He 218. Four treatments (A, B, C and D) were designed: A is a control, without using any fertilizers; B, after manuring of green azolla, 0.67 kg/m2; C, after manuring of rapeseed cake, 0.30 kg/m2; D, after fertilizing of ammonium bicarbonate, 0.025 kg/m2, and urea, 0.025 kg/m2. The experiment plot is 66.7 m2, with three replicates. The results indicated that the fertilization patterns significantly influence the growth of rice seedlings: The heights by A, B, C and D are 37 cm, 40 cm , 42 cm and 45 cm on average, respectively; the spike numbers, 45, 65, 73 and 75, respectively; chlorophyll contents in leaves, 1.84 mg/g, 2.42 mg/g, 3.02 mg/g and 3.97 mg/g, respectively. The rice with the different fertilization also varies in nutrient concentration in leaves: NH4-N concentration in leaves by A, B, C and D is 47.5 mg/kg, 61.1 mg/kg, 74.7 mg/kg and 135.8 mg/kg on average, respectively; NO3-N in leaves, 138.9 mg/kg, 185.2 mg/kg, 154.3 mg/kg and 293.2 mg/kg, respectively. The fertilization patterns, moreover, show a significant influence on the incidence of diseases and pests to rice seedlings: The incidence of rice cnaphalocrocis medinalis by A, B, C and D is 1.33 %, 1.50 %, 1.75 % and 89.0 % on average, respectively; that of bacterial leaf blight, 0, 1.25 %, 1.75 % and 85.0 %, respectively; number of rice planthopper in each plant, 20, 21, 21 and 30, respectively. As a result, the yield of rice grain by A, B, C and D is 4540 kg/ha, 4606 kg/ha, 4503 kg/ha and 4092 kg/ha on average, respectively. In conclusion, the rice seedlings treated with chemical fertilizers grow large and tender

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

PubMed

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

2016-09-01

The rice pathogens Xanthomonas oryzae pathovar (pv.) oryzae and pv. oryzicola produce numerous transcription activator-like (TAL) effectors that increase bacterial virulence by activating expression of host susceptibility genes. Rice resistance mechanisms against TAL effectors include polymorphisms that prevent effector binding to susceptibility gene promoters, or that allow effector activation of resistance genes. This study identifies, in the heirloom variety Carolina Gold Select, a third mechanism of rice resistance involving TAL effectors. This resistance manifests through strong suppression of disease development in response to diverse TAL effectors from both X. oryzae pathovars. The resistance can be triggered by an effector with only 3.5 central repeats, is independent of the composition of the repeat variable di-residues that determine TAL effector binding specificity, and is independent of the transcriptional activation domain. We determined that the resistance is conferred by a single dominant locus, designated Xo1, that maps to a 1.09 Mbp fragment on chromosome 4. The Xo1 interval also confers complete resistance to the strains in the African clade of X. oryzae pv. oryzicola, representing the first dominant resistance locus against bacterial leaf streak in rice. The strong phenotypic similarity between the TAL effector-triggered resistance conferred by Xo1 and that conferred by the tomato resistance gene Bs4 suggests that monocots and dicots share an ancient or convergently evolved mechanism to recognize analogous TAL effector epitopes. © 2016 The Authors The Plant Journal © 2016 John Wiley & Sons Ltd.

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

PubMed Central

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

2016-01-01

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

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

PubMed

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

2013-01-01

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

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

PubMed Central

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

2013-01-01

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

Unusual Small Subunit That Is Not Expressed in Photosynthetic Cells Alters the Catalytic Properties of Rubisco in Rice1[C][W][OPEN

PubMed Central

Morita, Koichi; Hatanaka, Tomoko; Misoo, Shuji; Fukayama, Hiroshi

2014-01-01

Rubisco small subunits (RbcSs) are encoded by a nuclear multigene family in plants. Five RbcS genes, OsRbcS1, OsRbcS2, OsRbcS3, OsRbcS4, and OsRbcS5, have been identified in rice (Oryza sativa). Among them, the amino acid sequence of OsRbcS1 differs notably from those of other rice RbcSs. Phylogenetic analysis showed that OsRbcS1 is genetically distant from other rice RbcS genes and more closely related to RbcS from a fern and two woody plants. Reverse transcription-PCR and promoter β-glucuronidase analyses revealed that OsRbcS1 was not expressed in leaf blade, a major photosynthetic organ in rice, but was expressed in leaf sheath, culm, anther, and root central cylinder. In leaf blade of transgenic rice overexpressing OsRbcS1 and leaf sheath of nontransgenic rice, OsRbcS1 was incorporated into the Rubisco holoenzyme. Incorporation of OsRbcS1 into Rubisco increased the catalytic turnover rate and Km for CO2 of the enzyme and slightly decreased the specificity for CO2, indicating that the catalytic properties were shifted to those of a high-activity type Rubisco. The CO2 assimilation rate at low CO2 partial pressure was decreased in overexpression lines but was not changed under ambient and high CO2 partial pressure compared with nontransgenic rice. Although the Rubisco content was increased, Rubisco activation state was decreased in overexpression lines. These results indicate that the catalytic properties of Rubisco can be altered by ectopic expression of OsRbcS1, with substantial effects on photosynthetic performance in rice. We believe this is the first demonstration of organ-specific expression of individual members of the RbcS gene family resulting in marked effects on Rubisco catalytic activity. PMID:24254313

Difference in oxidative stress tolerance between rice cultivars estimated with chlorophyll fluorescence analysis.

PubMed

Kasajima, Ichiro

2017-04-26

Oxidative stress is considered to be involved in growth retardation of plants when they are exposed to a variety of biotic and abiotic stresses. Despite its potential importance in improving crop production, comparative studies on oxidative stress tolerance between rice (Oryza sativa L.) cultivars are limited. This work describes the difference in term of oxidative stress tolerance between 72 rice cultivars. 72 rice cultivars grown under naturally lit greenhouse were used in this study. Excised leaf discs were subjected to a low concentration of methyl viologen (paraquat), a chemical reagent known to generate reactive oxygen species in chloroplast. Chlorophyll fluorescence analysis using a two-dimensional fluorescence meter, ion leakage analysis as well as the measurement of chlorophyll contents were used to evaluate the oxidative stress tolerance of leaf discs. Furthermore, fluorescence intensities were finely analyzed based on new fluorescence theories that we have optimized. Treatment of leaf discs with methyl viologen caused differential decrease of maximum quantum yield of photosystem II (Fv/Fm) between cultivars. Decrease of Fv/Fm was also closely correlated with increase of ion leakage and decrease of chlorophyll a/b ratio. Fv/Fm was factorized into photochemical and non-photochemical parameters to classify rice cultivars into sensitive and tolerant ones. Among the 72 compared rice cultivars, the traditional cultivar Co13 was identified as the most tolerant to oxidative stress. Koshihikari, a dominant modern Japonica cultivar in Japan as well as IR58, one of the modern Indica breeding lines exhibited a strong tolerance to oxidative stress. Close correlation between Fv/Fm and chlorophyll a/b ratio provides a simple method to estimate oxidative stress tolerance, without measurement of chlorophyll fluorescence with special equipment. The fact that modern cultivars, especially major cultivars possessed tolerance to oxidative stress suggests that oxidative stress

Growth promotion in plants by rice necrosis mosaic virus.

PubMed

Ghosh, S K

1982-08-01

Ludwigia perennis L. infected with rice necrosis mosaic virus (RNMV) showed an increase in both shoot growth and leaf size, along with characteristic chlorotic lesions on leaves. The promotion of growth over the controls extended over a considerable period of time (70 d). Inoculation with RNMV resulted in increased plant height, leaf size, stem diameter, and number and size of fiber bundles in Corchorus olitorius L., C. capsularis L., Hibiscus sabdariffa L. and H. cannabinus L.

Integrated crop management practices for maximizing grain yield of double-season rice crop.

PubMed

Wang, Depeng; Huang, Jianliang; Nie, Lixiao; Wang, Fei; Ling, Xiaoxia; Cui, Kehui; Li, Yong; Peng, Shaobing

2017-01-12

Information on maximum grain yield and its attributes are limited for double-season rice crop grown under the subtropical environment. This study was conducted to examine key characteristics associated with high yielding double-season rice crop through a comparison between an integrated crop management (ICM) and farmers' practice (FP). Field experiments were conducted in the early and late seasons in the subtropical environment of Wuxue County, Hubei Province, China in 2013 and 2014. On average, grain yield in ICM was 13.5% higher than that in FP. A maximum grain yield of 9.40 and 10.53 t ha -1 was achieved under ICM in the early- and late-season rice, respectively. Yield improvement of double-season rice with ICM was achieved with the combined effects of increased plant density and optimized nutrient management. Yield gain of ICM resulted from a combination of increases in sink size due to more panicle number per unit area and biomass production, further supported by the increased leaf area index, leaf area duration, radiation use efficiency, crop growth rate, and total nitrogen uptake compared with FP. Further enhancement in the yield potential of double-season rice should focus on increasing crop growth rate and biomass production through improved and integrated crop management practices.

Identification and Comparative Expression Profiles of Chemoreception Genes Revealed from Major Chemoreception Organs of the Rice Leaf Folder, Cnaphalocrocis medinalis (Lepidoptera: Pyralidae)

PubMed Central

Zeng, Fang-Fang; Zhao, Zhen-Fei; Yan, Miao-Jun; Zhou, Wen; Zhang, Zan; Zhang, Aijun; Lu, Zhong-Xian; Wang, Man-Qun

2015-01-01

To better understand the olfactory mechanisms in the rice leaf folder, Cnaphalocrocis medinalis (Guenée), a serious pest of rice in Asia, we established six partial transcriptomes from antennae, protarsus, and reproductive organs of male and female adults. A total of 102 transcripts were identified, including 29 odorant receptors (ORs), 15 ionotropic receptors (IRs), 30 odorant-binding proteins (OBPs), 26 chemosensory proteins (CSPs), and 2 sensory neuron membrane proteins (SNMPs). The expression patterns of these genes were calculated by fragments per kilobase of exon per million fragments mapped (FPKM) and validated by real-time quantitative PCR (RT-qPCR). Some transcripts were exclusively expressed in specific organs, such as female protarsus, whereas others were universally expressed, this varied expression profile may provide insights into the specific functions mediated by chemoreception proteins in insects. To the best of our knowledge, among the 102 identified transcripts, 81 are novel and have never been reported before. In addition, it also is the first time that ORs and IRs are identified in C. medinalis. Our findings significantly enhance the currently limited understanding olfactory mechanisms of the olfactory mechanisms underlying the chemoreception system in C. medinalis. PMID:26657286

Systems analysis of cis-regulatory motifs in C4 photosynthesis genes using maize and rice leaf transcriptomic data during a process of de-etiolation

PubMed Central

Xu, Jiajia; Bräutigam, Andrea; Weber, Andreas P. M.; Zhu, Xin-Guang

2016-01-01

Identification of potential cis-regulatory motifs controlling the development of C4 photosynthesis is a major focus of current research. In this study, we used time-series RNA-seq data collected from etiolated maize and rice leaf tissues sampled during a de-etiolation process to systematically characterize the expression patterns of C4-related genes and to further identify potential cis elements in five different genomic regions (i.e. promoter, 5′UTR, 3′UTR, intron, and coding sequence) of C4 orthologous genes. The results demonstrate that although most of the C4 genes show similar expression patterns, a number of them, including chloroplast dicarboxylate transporter 1, aspartate aminotransferase, and triose phosphate transporter, show shifted expression patterns compared with their C3 counterparts. A number of conserved short DNA motifs between maize C4 genes and their rice orthologous genes were identified not only in the promoter, 5′UTR, 3′UTR, and coding sequences, but also in the introns of core C4 genes. We also identified cis-regulatory motifs that exist in maize C4 genes and also in genes showing similar expression patterns as maize C4 genes but that do not exist in rice C3 orthologs, suggesting a possible recruitment of pre-existing cis-elements from genes unrelated to C4 photosynthesis into C4 photosynthesis genes during C4 evolution. PMID:27436282

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. Copyright © 2015 Elsevier Ltd. All rights reserved.

Generation of poly-β-hydroxybutyrate from acetate in higher plants: Detection of acetoacetyl CoA reductase- and PHB synthase- activities in rice.

PubMed

Tsuda, Hirohisa; Shiraki, Mari; Inoue, Eri; Saito, Terumi

2016-08-20

It has been reported that Poly-β-hydroxybutyrate (PHB) is generated from acetate in the rice root. However, no information is available about the biosynthetic pathway of PHB from acetate in plant cells. In the bacterium Ralstonia eutropha H16 (R. eutropha), PHB is synthesized from acetyl CoA by the consecutive reaction of three enzymes: β-ketothiolase (EC: 2.3.1.9), acetoacetyl CoA reductase (EC: 1.1.1.36) and PHB synthase (EC: 2.3.1.-). Thus, in this study, we examined whether the above three enzymatic activities were also detected in rice seedlings. The results clearly showed that the activities of the above three enzymes were all detected in rice. In particular, the PHB synthase activity was detected specifically in the sonicated particulate fractions (2000g 10min precipitate (ppt) and the 8000g 30min ppt) of rice roots and leaves. In addition to these enzyme activities, several new experimental results were obtained on PHB synthesis in higher plants: (a) (14)C-PHB generated from 2-(14)C-acetate was mainly localized in the 2000g 10min ppt and the 8000g 30min ppt of rice root. (b) Addition of acetate (0.1-10mM) to culture medium of rice seedlings did not increase the content of PHB in the rice root or leaf. (c) In addition to C3 plants, PHB was generated from acetate in a C4 plant (corn) and in a CAM plant (Bryophyllum pinnatum). d) Washing with ethylenediaminetetraacetic acid (EDTA) strongly suggested that the PHB synthesized from acetate was of plant origin and was not bacterial contamination. Copyright © 2016 Elsevier GmbH. All rights reserved.

Loss‐of‐function mutation of rice SLAC7 decreases chloroplast stability and induces a photoprotection mechanism in rice

PubMed Central

Fan, Xiaolei; Wu, Jiemin; Chen, Taiyu; Tie, Weiwei; Chen, Hao; Zhou, Fei

2015-01-01

Abstract Plants absorb sunlight to power the photochemical reactions of photosynthesis, which can potentially damage the photosynthetic machinery. However, the mechanism that protects chloroplasts from the damage remains unclear. In this work, we demonstrated that rice (Oryza sativa L.) SLAC7 is a generally expressed membrane protein. Loss‐of‐function of SLAC7 caused continuous damage to the chloroplasts of mutant leaves under normal light conditions. Ion leakage indicators related to leaf damage such as H2O2 and abscisic acid levels were significantly higher in slac7‐1 than in the wild type. Consistently, the photosynthesis efficiency and Fv/Fm ratio of slac7‐1 were significantly decreased (similar to photoinhibition). In response to chloroplast damage, slac7‐1 altered its leaf morphology (curled or fused leaf) by the synergy between plant hormones and transcriptional factors to decrease the absorption of light, suggesting that a photoprotection mechanism for chloroplast damage was activated in slac7‐1. When grown in dark conditions, slac7‐1 displayed a normal phenotype. SLAC7 under the control of the AtSLAC1 promoter could partially complement the phenotypes of Arabidopsis slac1 mutants, indicating a partial conservation of SLAC protein functions. These results suggest that SLAC7 is essential for maintaining the chloroplast stability in rice. PMID:25739330

Hygromycin B-induced cell death is partly mediated by reactive oxygen species in rice (Oryza sativa L.).

PubMed

Oung, Hui-Min; Lin, Ke-Chun; Wu, Tsung-Meng; Chandrika, Nulu Naga Prafulla; Hong, Chwan-Yang

2015-12-01

The aminoglycoside antibiotic hygromycin B (Hyg) inhibits prokaryotic, chloroplast and mitochondrial protein synthesis. Because of the toxic effect of Hyg on plant cells, the HPT gene, encoding hygromycin phosphotransferase, has become one of the most widely used selectable markers in plant transformation. Yet the mechanism behind Hyg-induced cell lethality in plants is not clearly understood. In this study, we aimed to decipher this mechanism. With Hyg treatment, rice calli exhibited cell death, and rice seedlings showed severe growth defects, leaf chlorosis and leaf shrinkage. Rice seedlings also exhibited severe lipid peroxidation and protein carbonylation, for oxidative stress damage at the cellular level. The production of reactive oxygen species such as O2(·-), H2O2 and OH(·) was greatly induced in rice seedlings under Hyg stress, and pre-treatment with ascorbate increased resistance to Hyg-induced toxicity indicating the existence of oxidative stress. Overexpression of mitochondrial Alternative oxidase1a gene without HPT selection marker in rice enhanced tolerance to Hyg and attenuated the degradation of protein content, whereas the rice plastidial glutathione reductase 3 mutant showed increased sensitivity to Hyg. These results demonstrate that Hyg-induced cell lethality in rice is not only due to the inhibition of protein synthesis but also mediated by oxidative stress.

Purple rice extract supplemented diet reduces DMH- induced aberrant crypt foci in the rat colon by inhibition of bacterial β-glucuronidase.

PubMed

Summart, Ratasark; Chewonarin, Teera

2014-01-01

Purple rice has become a natural product of interest which is widely used for health promotion. This study investigated the preventive effect of purple rice extract (PRE) mixed diet on DMH initiation of colon carcinogenesis. Rats were fed with PRE mixed diet one week before injection of DMH (40 mg/kg of body weight once a week for 2 weeks). They were killed 12 hrs after a second DMH injection to measure the level of O6-methylguanine and xenobiotic metabolizing enzyme activities. In rats that received PRE, guanine methylation was reduced in the colonic mucosa, but not in the liver, whereas PRE did not affect xenobiotic conjugation, with reference to glutathione-S-transferase or UDP-glucuronyl transferase. After 5 weeks, rats that received PRE with DMH injection had fewer ACF in the colon than those treated with DMH alone. Interestingly, a PRE mixed diet inhibited the activity of bacterial β-glucuronidase in rat feces, a critical enzyme for free methylazoxymethanol (MAM) release in the rat colon. These results indicated that purple rice extract inhibited β-glucuronidase activity in the colonic lumen, causing a reduction of MAM-induced colonic mucosa DNA methylation, leaded to decelerated formation of aberrant crypt foci in the rat colon. The supplemented purple rice extract might thus prevent colon carcinogenesis by the alteration of the colonic environment, and thus could be further developed for neutraceutical products for colon cancer prevention.

Response of rice cultivars to rates of nitrogen and potassium application in field and pot conditions.

PubMed

Bahmaniar, M A; Ranjbar, G A

2007-05-01

Nitrogen and potassium are the yield-limiting nutrients in rice production regions of Iran. Use of N and K efficient cultivars is an important complementary strategy in improving rice yield, increasing the quality properties of rice grains and reducing cost of production. In order to consider the effects of different amounts of N and K application on rice (Oryza sativa L.) yield and yield components in pot and field conditions these experiments were undertaken in 2004 at Sari Agricultural Station, Iran. Four levels of N (0, 50, 100 and 150 Kg N ha(-1) in field and 0, 0.6, 1.2 and 1.8 g N pot(-1) in pot) corresponding with four levels of K (0, 75, 150 and 225 kg K2O ha(-1) in field and 0, 0.5, 1 and 1.5 g K2O pot(-1) in pot) were applied in a split-factorial plot design with three replications in both pot and field experiments, variously. Grain yield, number of grain per panicle, number of tiller, plant height, length of flag leaf, total and shoot dry matter, 1000 grain weight and harvest index have been increased by N application in field conditions. However, in pot conditions grain yield, number of grain per panicle, number of tiller, plant height, width of flag leaf, total and shoot dry matter, leaf nitrogen contents and harvest index have significantly been increased (p < or = 0.05). Potassium application in field conditions has significantly affected on all characteristics but 1000 grain weight and leaf N and K contents. Simultaneous application of N and K have increasingly affected on grain yield, plant height, shoot dry matter and harvest index in field conditions and on plant height, length of flag leaf and shoot dry matter in pot conditions (p < or = 0.05).

Morphology, production, and chemical content performance of black rice Matesih accession with several comparisons

NASA Astrophysics Data System (ADS)

Nandariyah; Purwanto, E.; Meidini, A. N.

2018-03-01

Rice (Oryza sativa L.) is an important food crop in Indonesia. In Matesih area, Karanganyar, recently found new varieties of black rice cultured by local farmers which morphology and chemical content have not yet identified. The purpose of this research was to obtain information of morphology, production, and chemical content of black rice matesih accession and to compare the appearance in order to detect the superiority of black rice matesih accession with the comparison of other accession of black rice. There were four accessions of black rice tested, namely Matesih Accession, Klaten Accession, Toraja, and Cempo. Research data were divided into qualitative data which processed by scoring, and quantitative data are processed with simple descriptive statistic. The kinship test was done by using NTSYSpc program with SIMQual and SIMInt function. The observation of qualitative properties indicates that accession matesih has a form that is relatively similar to other accessions. Qualitatively, accession matesih superior at leaf length, leaf width, plant height and culm diameter. Klaten accession has higher production than accession matesih. Matesih accession has the advantage of having shorter period on heading time and harvest time than other accessions. Matesih accession has the highest amylose content, lower protein content than klaten accession and lower content of anthocyanin than toraja accession. The kinship analysis showed that matesih accession and klaten accession has close kinship.

Localization of cells containing sedimented amyloplasts in the shoots of normal and lazy rice seedlings.

PubMed

Abe, K; Takahashi, H; Suge, H

1994-12-01

We have examined the localization of the cells containing sedimented amyloplasts (putative statocytes) and its relation to the graviresponding sites in the shoots of normal and lazy rice seedlings. All graviresponsive organs of the shoots of normal rice seedlings, the mesocotyl, the coleoptile and the leaf-sheath base, were found to possess the statocytes. This is the first indication that mesocotyl senses gravity by its own cells in inducing gravitropic bending in rice seedlings. In lazy-Kamenoo, although the shoots lost their gravitropic response with the advance of age, sedimentation of amyloplasts itself might not be attributable to the agravitropic growth of the shoots, because, including those of the leaf-sheath bases that had lost their response to gravity, sedimented amyloplasts appeared to be identical to those of normal Kamenoo and of younger seedlings of lazy-Kamenoo whose gravitropism is still apparent.

Four rice seed cDNA clones belonging to the alpha-amylase/trypsin inhibitor gene family encode potential rice allergens.

PubMed

Alvarez, A M; Fukuhara, E; Nakase, M; Adachi, T; Aoki, N; Nakamura, R; Matsuda, T

1995-07-01

Four rice seed proteins encoded by cDNAs belonging to the alpha-amylase/trypsin inhibitor gene family were overexpressed as TrpE-fusion proteins in E. coli. The expressed rice proteins were detected by SDS-PAGE as major proteins in bacterial cell lysates. Western blot analyses showed that all the recombinant proteins were immunologically reactive to rabbit polyclonal antibodies and to a mouse monoclonal antibody (25B9) specific for a previously isolated rice allergen of 16 kDa. Some truncated proteins from deletion mutants of the cDNAs retained their reactivity to the specific antibodies. These results suggest that the cDNAs encode potential rice allergens and that some epitopes of the recombinant proteins are still immunoreactive when they are expressed as their fragments.

Differences and similarities in the photoregulation of gibberellin metabolism between rice and dicots.

PubMed

Hirose, Fumiaki; Inagaki, Noritoshi; Takano, Makoto

2013-03-01

In rice seedlings, elongation of leaf sheaths is suppressed by light stimuli. The response is mediated by two classes of photoreceptors, phytochromes and cryptochromes. However, it remains unclear how these photoreceptors interact in the process. Our recent study using phytochrome mutants and novel cryptochrome RNAi lines revealed that cryptochromes and phytochromes function cooperatively, but independently to reduce active GA contents in seedlings in visible light. Blue light captured by cryptochrome 1 (cry1a and cry1b) induces robust expression of GA 2-oxidase genes (OsGA2ox4-7). In parallel, phytochrome B with auxiliary action of phytochrome A mediates repression of GA 20-oxidase genes (OsGA20ox2 and OsGA20ox4). The independent effects cumulatively reduce active GA contents, leading to a suppression of leaf sheath elongation. These regulatory mechanisms are distinct from phytochrome B function in dicots. We discuss reasons why the distinct system appeared in rice, and advantages of the rice system in early photomorphogenesis.

Study of arsenic accumulation in rice and evaluation of protective effects of Chorchorus olitorius leaves against arsenic contaminated rice induced toxicities in Wistar albino rats.

PubMed

Hosen, Saeed Mohammed Imran; Das, Dipesh; Kobi, Rupkanowar; Chowdhury, Dil Umme Salma; Alam, Md Jibran; Rudra, Bashudev; Bakar, Muhammad Abu; Islam, Saiful; Rahman, Zillur; Al-Forkan, Mohammad

2016-10-14

In the present study, we investigated the arsenic accumulation in different parts of rice irrigated with arsenic contaminated water. Besides, we also evaluated the protective effects of Corchorus olitorius leaves against arsenic contaminated rice induced toxicities in animal model. A pot experiment was conducted with arsenic amended irrigation water (0.0, 25.0, 50.0 and 75.0 mg/L As) to investigate the arsenic accumulation in different parts of rice. In order to evaluate the protective effects of Corchorus olitorius leaves, twenty Wistar albino rats were divided into four different groups. The control group (Group-I) was supplied with normal laboratory pellets while groups II, III, and IV received normal laboratory pellets supplemented with arsenic contaminated rice, C. olitorius leaf powder (4 %), arsenic contaminated rice plus C. olitorius leaf powder (4 %) respectively. Different haematological parameters and serum indices were analyzed to evaluate the protective effects of Corchorus olitorius leaves against arsenic intoxication. To gather more supportive evidences of Corchorus olitorius potentiality against arsenic intoxication, histopathological analysis of liver, kidney, spleen and heart tissues was also performed. From the pot experiment, we have found a significant (p ≤ 0.05) increase of arsenic accumulation in different parts of rice with the increase of arsenic concentrations in irrigation water and the trend of accumulation was found as root > straw > husk > grain. Another part of the experiment revealed that supplementation of C. olitorius leaves with arsenic contaminated rice significantly (p < 0.05) restored the altered haematological parameters and other serum indices towards the normal values. Arsenic deposition pattern on different organs and histological studies on the ultrastructural changes of liver, kidneys, spleen and heart also supported the protective roles of Corchorus olitorius leaves against arsenic contaminated

Transgenic Bt Rice Does Not Challenge Host Preference of the Target Pest of Rice Leaffolder, Cnaphalocrocis medinalis (Lepidoptera: Pyralidae)

PubMed Central

Sun, Xiao; Zhou, Wen; Liu, Hao; Zhang, Aijun; Ai, Chao-Ren; Zhou, Shuang-Shuang; Zhou, Chang-Xiang; Wang, Man-Qun

2013-01-01

Background Transgenic Bt rice line T2A-1 expresses a synthesized cry2A gene that shows high resistance to Lepidoptera pests, including Cnaphalocrocis medinalis (Guenée) (Lepidoptera: Pyralidae). Plant volatile orientation cues and the physical characteristics of the leaf surface play key roles in host location or host-plant acceptance of phytophagous insects. These volatile compounds and physical traits may become altered in Bt rice and it is not known whether this influences the behavior of C. medinalis when searching for oviposition sites. Results The results of electronic nose analysis showed that the Radar map of Bt rice cultivars was analogous to the non- Bt rice cultivars at each growing stage. PCA analysis was able to partly discriminate between some of the Bt vs. non-Bt rice sensors, but could not to separate Bt cultivars from non-Bt cultivars. The total ion chromatogram between Bt and non-Bt rice cultivars at the seedling, booting and tillering stages were similar and 25 main compounds were identified by GC-MS. For most compounds, there was no significant difference in compound quantities between Bt and non-Bt rice cultivars at equivalent growth stages. The densities of the tubercle papicles and the trichomes on the upper and lower surfaces were statistically equal in Bt and non-Bt rice. The target pest, C. medinalis, was attracted to host rice plants, but it could not distinguish between the transgenic and the isogenic rice lines. Conclusions There were no significant differences between the Bt rice line, T2A-1 and the non-Bt rice for volatiles produced or in its physical characteristics and there were no negative impacts on C. medinalis oviposition behavior. These results add to the mounting evidence that Bt rice has no negative impact on the target insect oviposition behavior. PMID:24244410

Diffusional conductance to CO2 is the key limitation to photosynthesis in salt-stressed leaves of rice (Oryza sativa).

PubMed

Wang, Xiaoxiao; Wang, Wencheng; Huang, Jianliang; Peng, Shaobing; Xiong, Dongliang

2018-05-01

Salinity significantly limits leaf photosynthesis but the factors causing the limitation in salt-stressed leaves remain unclear. In the present work, photosynthetic and biochemical traits were investigated in four rice genotypes under two NaCl concentration (0 and 150 mM) to assess the stomatal, mesophyll and biochemical contributions to reduced photosynthetic rate (A) in salt-stressed leaves. Our results indicated that salinity led to a decrease in A, leaf osmotic potential, electron transport rate and CO 2 concentrations in the chloroplasts (C c ) of rice leaves. Decreased A in salt-stressed leaves was mainly attributable to low C c , which was determined by stomatal and mesophyll conductance. The increased stomatal limitation was mainly related to the low leaf osmotic potential caused by soil salinity. However, the increased mesophyll limitation in salt-stressed leaves was related to both osmotic stress and ion stress. These findings highlight the importance of considering mesophyll conductance when developing salinity-tolerant rice cultivars. © 2017 Scandinavian Plant Physiology Society.

Wettability and impact dynamics of water droplets on rice ( Oryza sativa L.) leaves

NASA Astrophysics Data System (ADS)

Kwon, Dae Hee; Huh, Hyung Kyu; Lee, Sang Joon

2014-03-01

We investigated the wettability and impact dynamics of water droplets on rice leaves at various leaf inclination angles and orientations. Contact angle, contact angle hysteresis (CAH), and roll-off angle ( α roll) of water droplets were measured quantitatively. Results showed that droplet motion exhibited less resistance along the longitudinal direction. Impact dynamic parameters, such as impact behaviors, maximum spreading factor, contact distance, and contact time were also investigated. Three different impact behaviors were categorized based on the normal component of Weber number irrespective of the inclination angle of the rice leaf. The asymmetric impact behavior induced by the tangential Weber number was also identified. Variation in the maximum spreading factor according to the normal Weber number was measured and compared with theoretical value obtained according to scaling law to show the wettability of the rice leaves. The contact distance of the impacting droplets depended on the inclination angle of the leaves. Along the longitudinal direction of rice leaves, contact distance was farther than that along the transverse direction. This result is consistent with the smaller values of CAH and α roll along the longitudinal direction.

Evaluating leaf and canopy reflectance of stressed rice plants to monitor arsenic contamination

USDA-ARS?s Scientific Manuscript database

Arsenic contamination is a serious problem in rice cultivated soils of many developing countries. Hence, it is critical to monitor and control arsenic uptake in rice plants to avoid adverse effects on human health. This study evaluated the feasibility of using reflectance spectroscopy to monitor ars...

Bioaccumulation and translocation of polyhalogenated compounds in rice (Oryza sativa L.) planted in paddy soil collected from an electronic waste recycling site, South China.

PubMed

Zhang, Yun; Luo, Xiao-Jun; Mo, Ling; Wu, Jiang-Ping; Mai, Bi-Xian; Peng, Yong-Hong

2015-10-01

The bioaccumulation and translocation of polyhalogenated compounds (PHCs) in rice planted in the paddy soils of an electronic waste (e-waste) recycling site were investigated, along with the effect of contaminated soils on rice growth. The PHCs included polychlorinated biphenyls (PCBs), polybrominated diphenyl ethers (PBDEs), decabromodiphenyl ethane (DBDPE), 1,2-bis(2,4,6-tribromophenoxy) ethane (BTBPE), and dechlorane plus (DPs). The morphological development and all measured physiological parameters of rice plants except for peroxidase were significantly inhibited by e-waste contaminated soils. Specifically, soil-root bioaccumulation factors (RCFs) increased with increasing logarithm of octanol-water partition coefficient (logKow) for PCBs, but decreased for PBDEs. During translocation from root to stem, translocation factors (TFs) and logKow were positively correlated. However, the accumulation mechanism in the leaf was concentration-dependent. In the high concentration exposure group, translocation play more important role in determination PHCs burden in leaf than atmospheric uptake, with logTF (from stem to leaf) being positively correlated with logKow. In contrast, in the low exposure and control groups, logTF (from stem to leaf) was negatively correlated with logKow. In addition, Syn-DP was selectively accumulated in plant tissues. In conclusion, this study demonstrates that e-waste contaminated soils affect rice growth, revealed the rule of the bioaccumulation and translocation of PHCs in rice plants. Copyright © 2015 Elsevier Ltd. All rights reserved.

PGL, encoding chlorophyllide a oxygenase 1, impacts leaf senescence and indirectly affects grain yield and quality in rice.

PubMed

Yang, Yaolong; Xu, Jie; Huang, Lichao; Leng, Yujia; Dai, Liping; Rao, Yuchun; Chen, Long; Wang, Yuqiong; Tu, Zhengjun; Hu, Jiang; Ren, Deyong; Zhang, Guangheng; Zhu, Li; Guo, Longbiao; Qian, Qian; Zeng, Dali

2016-03-01

Chlorophyll (Chl) b is a ubiquitous accessory pigment in land plants, green algae, and prochlorophytes. This pigment is synthesized from Chl a by chlorophyllide a oxygenase and plays a key role in adaptation to various environments. This study characterizes a rice mutant, pale green leaf (pgl), and isolates the gene PGL by using a map-based cloning approach. PGL, encoding chlorophyllide a oxygenase 1, is mainly expressed in the chlorenchyma and activated in the light-dependent Chl synthesis process. Compared with wild-type plants, pgl exhibits a lower Chl content with a reduced and disorderly thylakoid ultrastructure, which decreases the photosynthesis rate and results in reduced grain yield and quality. In addition, pgl exhibits premature senescence in both natural and dark-induced conditions and more severe Chl degradation and reactive oxygen species accumulation than does the wild-type. Moreover, pgl is sensitive to heat stress. © The Author 2015. Published by Oxford University Press on behalf of the Society for Experimental Biology.

Selectable antibiotic resistance marker gene-free transgenic rice harbouring the garlic leaf lectin gene exhibits resistance to sap-sucking planthoppers.

PubMed

Sengupta, Subhadipa; Chakraborti, Dipankar; Mondal, Hossain A; Das, Sampa

2010-03-01

Rice, the major food crop of world is severely affected by homopteran sucking pests. We introduced coding sequence of Allium sativum leaf agglutinin, ASAL, in rice cultivar IR64 to develop sustainable resistance against sap-sucking planthoppers as well as eliminated the selectable antibiotic-resistant marker gene hygromycin phosphotransferase (hpt) exploiting cre/lox site-specific recombination system. An expression vector was constructed containing the coding sequence of ASAL, a potent controlling agent against green leafhoppers (GLH, Nephotettix virescens) and brown planthopper (BPH, Nilaparvata lugens). The selectable marker (hpt) gene cassette was cloned within two lox sites of the same vector. Alongside, another vector was developed with chimeric cre recombinase gene cassette. Reciprocal crosses were performed between three single-copy T(0) plants with ASAL- lox-hpt-lox T-DNA and three single-copy T(0) plants with cre-bar T-DNA. Marker gene excisions were detected in T(1) hybrids through hygromycin sensitivity assay. Molecular analysis of T(1) plants exhibited 27.4% recombination efficiency. T(2) progenies of L03C04(1) hybrid parent showed 25% cre negative ASAL-expressing plants. Northern blot, western blot and ELISA showed significant level of ASAL expression in five marker-free T(2) progeny plants. In planta bioassay of GLH and BPH performed on these T(2) progenies exhibited radical reduction in survivability and fecundity compared with the untransformed control plants.

Describing the physiological responses of different rice genotypes to salt stress using sigmoid and piecewise linear functions.

PubMed

Radanielson, Ando M; Angeles, Olivyn; Li, Tao; Ismail, Abdelbagi M; Gaydon, Donald S

2018-05-01

Rice is the staple food for almost half of the world population. In South and South East Asia, about 40% of rice production is from deltaic regions that are vulnerable to salt stress. A quantitative approach was developed for characterizing genotypic variability in biomass production, leaf transpiration rate and leaf net photosynthesis responses to salinity during the vegetative stage, with the aim of developing efficient screening protocols to accelerate breeding varieties adapted to salt-affected areas. Three varieties were evaluated in pots under greenhouse conditions and in the field, with average soil salinity ranging from 2 to 12 dS m -1 . Plant biomass, net photosynthesis rate, leaf transpiration rate and leaf conductance were measured at regular intervals. Crop responses were fitted using a logistic function with three parameters: 1) maximum rate under control conditions (Y max ), 2) salinity level for 50% of reduction (b), and 3) rate of reduction ( a) . Variation in the three parameters correlated significantly with variation in plant biomass production under increasing salinity. Salt stress levels that caused 50% reduction in net leaf photosynthesis and transpiration rates were higher in the tolerant genotype BRRI Dhan47 (16.5 dS m -1 and 14.3 dS m -1 , respectively) than the sensitive genotype IR29 (11.1 dS m -1 and 6.8 dS m -1 ). In BRRI Dhan47, the threshold beyond which growth was significantly reduced was above 5 dS m -1 and the rate of growth reduction beyond this threshold was as low as 4% per unit increase in salinity. This quantitative approach to screening for salinity tolerance in rice offers a means to better understand rice growth under salt stress and, using simulation modelling, can provide an improved tool for varietal characterization.

Genome Sequence of the Rice-Pathogenic Bacterium Acidovorax avenae subsp. avenae RS-1 ▿

PubMed Central

Xie, Guan-Lin; Zhang, Guo-Qing; Liu, He; Lou, Miao-Miao; Tian, Wen-Xiao; Li, Bin; Zhou, Xue-Ping; Zhu, Bo; Jin, Gu-Lei

2011-01-01

Acidovorax avenae subsp. avenae is a phytobacterium which is the causative agent of several plant diseases with economic significance. Here, we present the draft genome sequence of strain RS-1, which was isolated from rice shoots in a rice field in China. This strain can cause bacterial stripe of rice. PMID:21742879

Dynamic Cytology and Transcriptional Regulation of Rice Lamina Joint Development.

PubMed

Zhou, Li-Juan; Xiao, Lang-Tao; Xue, Hong-Wei

2017-07-01

Rice ( Oryza sativa ) leaf angle is determined by lamina joint and is an important agricultural trait determining leaf erectness and, hence, the photosynthesis efficiency and grain yield. Genetic studies reveal a complex regulatory network of lamina joint development; however, the morphological changes, cytological transitions, and underlying transcriptional programming remain to be elucidated. A systemic morphological and cytological study reveals a dynamic developmental process and suggests a common but distinct regulation of the lamina joint. Successive and sequential cell division and expansion, cell wall thickening, and programmed cell death at the adaxial or abaxial sides form the cytological basis of the lamina joint, and the increased leaf angle results from the asymmetric cell proliferation and elongation. Analysis of the gene expression profiles at four distinct developmental stages ranging from initiation to senescence showed that genes related to cell division and growth, hormone synthesis and signaling, transcription (transcription factors), and protein phosphorylation (protein kinases) exhibit distinct spatiotemporal patterns during lamina joint development. Phytohormones play crucial roles by promoting cell differentiation and growth at early stages or regulating the maturation and senescence at later stages, which is consistent with the quantitative analysis of hormones at different stages. Further comparison with the gene expression profile of leaf inclination1 , a mutant with decreased auxin and increased leaf angle, indicates the coordinated effects of hormones in regulating lamina joint. These results reveal a dynamic cytology of rice lamina joint that is fine-regulated by multiple factors, providing informative clues for illustrating the regulatory mechanisms of leaf angle and plant architecture. © 2017 American Society of Plant Biologists. All Rights Reserved.

CatB is Critical for Total Catalase Activity and Reduces Bactericidal Effects of Phenazine-1-Carboxylic Acid on Xanthomonas oryzae pv. oryzae and X. oryzae pv. oryzicola.

PubMed

Pan, Xiayan; Wu, Jian; Xu, Shu; Duan, Yabing; Zhou, Mingguo

2017-02-01

Rice bacterial leaf blight, caused by Xanthomonas oryzae pv. oryzae, and rice bacterial leaf streak, caused by X. oryzae pv. oryzicola, are major diseases of rice. Phenazine-1-carboxylic acid (PCA) is a natural product that is isolated from Pseudomonas spp. and is used to control many important rice diseases in China. We previously reported that PCA disturbs the redox balance, which results in the accumulation of reactive oxygen species in X. oryzae pv. oryzae. In this study, we found that PCA significantly upregulated the transcript levels of catB and katE, which encode catalases, and that PCA sensitivity was reduced when X. oryzae pvs. oryzae and oryzicola were cultured with exogenous catalase. Furthermore, catB deletion mutants of X. oryzae pvs. oryzae and oryzicola showed dramatically decreased total catalase activity, increased sensitivity to PCA, and reduced virulence in rice. In contrast, deletion mutants of srpA and katG, which also encode catalases, exhibited little change in PCA sensitivity. The results indicate that catB in both X. oryzae pvs. oryzae and oryzicola encodes a catalase that helps protect the bacteria against PCA-induced stress.

Systems analysis of cis-regulatory motifs in C4 photosynthesis genes using maize and rice leaf transcriptomic data during a process of de-etiolation.

PubMed

Xu, Jiajia; Bräutigam, Andrea; Weber, Andreas P M; Zhu, Xin-Guang

2016-09-01

Identification of potential cis-regulatory motifs controlling the development of C4 photosynthesis is a major focus of current research. In this study, we used time-series RNA-seq data collected from etiolated maize and rice leaf tissues sampled during a de-etiolation process to systematically characterize the expression patterns of C4-related genes and to further identify potential cis elements in five different genomic regions (i.e. promoter, 5'UTR, 3'UTR, intron, and coding sequence) of C4 orthologous genes. The results demonstrate that although most of the C4 genes show similar expression patterns, a number of them, including chloroplast dicarboxylate transporter 1, aspartate aminotransferase, and triose phosphate transporter, show shifted expression patterns compared with their C3 counterparts. A number of conserved short DNA motifs between maize C4 genes and their rice orthologous genes were identified not only in the promoter, 5'UTR, 3'UTR, and coding sequences, but also in the introns of core C4 genes. We also identified cis-regulatory motifs that exist in maize C4 genes and also in genes showing similar expression patterns as maize C4 genes but that do not exist in rice C3 orthologs, suggesting a possible recruitment of pre-existing cis-elements from genes unrelated to C4 photosynthesis into C4 photosynthesis genes during C4 evolution. © The Author 2016. Published by Oxford University Press on behalf of the Society for Experimental Biology.

Prospects of Understanding the Molecular Biology of Disease Resistance in Rice

PubMed Central

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

2018-01-01

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

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

PubMed

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

2015-01-01

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

Progressive Colonization of Bacteria and Degradation of Rice Straw in the Rumen by Illumina Sequencing

PubMed Central

Cheng, Yanfen; Wang, Ying; Li, Yuanfei; Zhang, Yipeng; Liu, Tianyi; Wang, Yu; Sharpton, Thomas J.; Zhu, Weiyun

2017-01-01

The aim of this study was to improve the utilization of rice straw as forage in ruminants by investigating the degradation pattern of rice straw in the dairy cow rumen. Ground up rice straw was incubated in situ in the rumens of three Holstein cows over a period of 72 h. The rumen fluid at 0 h and the rice straw at 0.5, 1, 2, 4, 6, 12, 24, 48, and 72 h were collected for analysis of the bacterial community and the degradation of the rice straw. The bacterial community and the carbohydrate-active enzymes in the rumen fluid were analyzed by metagenomics. The diversity of bacteria loosely and tightly attached to the rice straw was investigated by scanning electron microscopy and Miseq sequencing of 16S rRNA genes. The predominant genus in the rumen fluid was Prevotella, followed by Bacteroides, Butyrivibrio, unclassified Desulfobulbaceae, Desulfovibrio, and unclassified Sphingobacteriaceae. The main enzymes were members of the glycosyl hydrolase family, divided into four categories (cellulases, hemicellulases, debranching enzymes, and oligosaccharide-degrading enzymes), with oligosaccharide-degrading enzymes being the most abundant. No significant degradation of rice straw was observed between 0.5 and 6 h, whereas the rice straw was rapidly degraded between 6 and 24 h. The degradation then gradually slowed between 24 and 72 h. A high proportion of unclassified bacteria were attached to the rice straw and that Prevotella, Ruminococcus, and Butyrivibrio were the predominant classified genera in the loosely and tightly attached fractions. The composition of the loosely attached bacterial community remained consistent throughout the incubation, whereas a significant shift in composition was observed in the tightly attached bacterial community after 6 h of incubation. This shift resulted in a significant reduction in numbers of Bacteroidetes and a significant increase in numbers of Firmicutes. In conclusion, the degradation pattern of rice straw in the dairy cow rumen

Effects of different treatments of fly ash and mining soil on growth and antioxidant protection of Indian wild rice.

PubMed

Bisoi, Sidhanta Sekhar; Mishra, Swati S; Barik, Jijnasa; Panda, Debabrata

2017-05-04

The aim of the present study was investigation of the effects of fly ash and mining soil on growth and antioxidant protection of two cultivars of Indian wild rice (Oryza nivara and Oryza rufipogon) for possible phytoremediation and restoration of metal-contaminated site. In this study, Indian wild rice showed significant changes in germination, growth, and biochemical parameters after exposure to different ratio of fly ash and mining soil with garden soil. There was significant reduction of germination, fresh weight, dry weight, leaf chlorophyll content, leaf area, Special Analysis Device Chlorophyll (SPAD) Index, proteins, and activities of antioxidant enzymes in both cultivars of the wild rice grown in 100% fly ash and mining soil compared to the plants grown in 100% garden soil. Results from this study showed that in both cultivars of wild rice, all growth and antioxidant parameters increased when grown in 50% fly ash and mining soil. Taken together, Indian wild rice has the capacity to tolerate 50% of fly ash and mining soil, and can be considered as a good candidate for possible phytoremediation of contaminated soils.

Polyphasic characterization of bacteria obtained from upland rice cultivated in Cerrado soil.

PubMed

Braga, Lívia Fabiana; Oliveira, Fênix Araújo de; Couto, Eva Aparecida Prado do; Santos, Karina Freire d'Eça Nogueira; Ferreira, Enderson Petrônio de Brito; Martin-Didonet, Claudia Cristina Garcia

This work aimed to characterize 20 isolates obtained from upland rice plants, based on phenotypic (morphology, enzymatic activity, inorganic phosphate solubilization, carbon source use, antagonism), genotypic assays (16S rRNA sequencing) and plant growth promotion. Results showed a great morphological, metabolic and genetic variability among bacterial isolates. All isolates showed positive activity for catalase and protease enzymes and, 90% of the isolates showed positive activity for amylase, catalase and, nitrogenase. All isolates were able to metabolize sucrose and malic acid in contrast with mannitol, which was metabolized only by one isolate. For the other carbon sources, we observed a great variability in its use by the isolates. Most isolates showed antibiosis against Rhizoctonia solani (75%) and Sclerotinia sclerotiorum (55%) and, 50% of them showed antibiosis against both pathogens. Six isolates showed simultaneous ability of antibiosis, inorganic phosphate solubilization and protease activity. Based on phylogenetic analysis of the 16S rRNA gene all the isolates belong to Bacillus genus. Under greenhouse conditions, two isolates (S4 and S22) improved to about 24%, 25%, 30% and 31% the Total N, leaf area, shoot dry weight and root dry weight, respectively, of rice plants, indicating that they should be tested for this ability under field conditions. Copyright © 2017 Sociedade Brasileira de Microbiologia. Published by Elsevier Editora Ltda. All rights reserved.

Promoter variants of Xa23 alleles affect bacterial blight resistance and evolutionary pattern

PubMed Central

Xu, Feifei; Tang, Yongchao; Gao, Ying

2017-01-01

Bacterial blight, caused by Xanthomonas oryzae pv. oryzae (Xoo), is the most important bacterial disease in rice (Oryza sativa L.). Our previous studies have revealed that the bacterial blight resistance gene Xa23 from wild rice O. rufipogon Griff. confers the broadest-spectrum resistance against all the naturally occurring Xoo races. As a novel executor R gene, Xa23 is transcriptionally activated by the bacterial avirulence (Avr) protein AvrXa23 via binding to a 28-bp DNA element (EBEAvrXa23) in the promoter region. So far, the evolutionary mechanism of Xa23 remains to be illustrated. Here, a rice germplasm collection of 97 accessions, including 29 rice cultivars (indica and japonica) and 68 wild relatives, was used to analyze the evolution, phylogeographic relationship and association of Xa23 alleles with bacterial blight resistance. All the ~ 473 bp DNA fragments consisting of promoter and coding regions of Xa23 alleles in the germplasm accessions were PCR-amplified and sequenced, and nine single nucleotide polymorphisms (SNPs) were detected in the promoter regions (~131 bp sequence upstream from the start codon ATG) of Xa23/xa23 alleles while only two SNPs were found in the coding regions. The SNPs in the promoter regions formed 5 haplotypes (Pro-A, B, C, D, E) which showed no significant difference in geographic distribution among these 97 rice accessions. However, haplotype association analysis indicated that Pro-A is the most favored haplotype for bacterial blight resistance. Moreover, SNP changes among the 5 haplotypes mostly located in the EBE/ebe regions (EBEAvrXa23 and corresponding ebes located in promoters of xa23 alleles), confirming that the EBE region is the key factor to confer bacterial blight resistance by altering gene expression. Polymorphism analysis and neutral test implied that Xa23 had undergone a bottleneck effect, and selection process of Xa23 was not detected in cultivated rice. In addition, the Xa23 coding region was found highly

Promoter variants of Xa23 alleles affect bacterial blight resistance and evolutionary pattern.

PubMed

Cui, Hua; Wang, Chunlian; Qin, Tengfei; Xu, Feifei; Tang, Yongchao; Gao, Ying; Zhao, Kaijun

2017-01-01

Bacterial blight, caused by Xanthomonas oryzae pv. oryzae (Xoo), is the most important bacterial disease in rice (Oryza sativa L.). Our previous studies have revealed that the bacterial blight resistance gene Xa23 from wild rice O. rufipogon Griff. confers the broadest-spectrum resistance against all the naturally occurring Xoo races. As a novel executor R gene, Xa23 is transcriptionally activated by the bacterial avirulence (Avr) protein AvrXa23 via binding to a 28-bp DNA element (EBEAvrXa23) in the promoter region. So far, the evolutionary mechanism of Xa23 remains to be illustrated. Here, a rice germplasm collection of 97 accessions, including 29 rice cultivars (indica and japonica) and 68 wild relatives, was used to analyze the evolution, phylogeographic relationship and association of Xa23 alleles with bacterial blight resistance. All the ~ 473 bp DNA fragments consisting of promoter and coding regions of Xa23 alleles in the germplasm accessions were PCR-amplified and sequenced, and nine single nucleotide polymorphisms (SNPs) were detected in the promoter regions (~131 bp sequence upstream from the start codon ATG) of Xa23/xa23 alleles while only two SNPs were found in the coding regions. The SNPs in the promoter regions formed 5 haplotypes (Pro-A, B, C, D, E) which showed no significant difference in geographic distribution among these 97 rice accessions. However, haplotype association analysis indicated that Pro-A is the most favored haplotype for bacterial blight resistance. Moreover, SNP changes among the 5 haplotypes mostly located in the EBE/ebe regions (EBEAvrXa23 and corresponding ebes located in promoters of xa23 alleles), confirming that the EBE region is the key factor to confer bacterial blight resistance by altering gene expression. Polymorphism analysis and neutral test implied that Xa23 had undergone a bottleneck effect, and selection process of Xa23 was not detected in cultivated rice. In addition, the Xa23 coding region was found highly

Differential distribution of proteins expressed in companion cells in the sieve element-companion cell complex of rice plants.

PubMed

Fukuda, Akari; Fujimaki, Syu; Mori, Tomoko; Suzui, Nobuo; Ishiyama, Keiki; Hayakawa, Toshihiko; Yamaya, Tomoyuki; Fujiwara, Toru; Yoneyama, Tadakatsu; Hayashi, Hiroaki

2005-11-01

Sieve tubes are comprised of sieve elements, enucleated cells that are incapable of RNA and protein synthesis. The proteins in sieve elements are supplied from the neighboring companion cells through plasmodesmata. In rice plants, it was unclear whether or not all proteins produced in companion cells had the same distribution pattern in the sieve element-companion cell complex. In this study, the distribution pattern of four proteins, beta-glucuronidase (GUS), green fluorescent protein (GFP), thioredoxin h (TRXh) and glutathione S-transferase (GST) were analyzed. The foreign proteins GUS and GFP were expressed in transgenic rice plants under the control of the TRXh gene promoter (PTRXh), a companion cell-specific promoter. Analysis of leaf cross-sections of PTRXh-GUS and PTRXh-GFP plants indicated high accumulation of GUS and GFP, respectively, in companion cells rather than in sieve elements. GUS and GFP were also detected in phloem sap collected from leaf sheaths of the transgenic rice plants, suggesting these proteins could enter sieve elements. Relative amounts of GFP and endogenous phloem proteins, TRXh and GST, in phloem sap and total leaf extracts were compared. Compared to TRXh and GST, GFP content was higher in total leaf extracts, but lower in phloem sap, suggesting that GFP accumulated mainly in companion cells rather than in sieve elements. On the other hand, TRXh and GST appeared to accumulate in sieve elements rather than in companion cells. These results indicate the evidence for differential distribution of proteins between sieve elements and companion cells in rice plants.

Fructose-Bisphophate Aldolase Exhibits Functional Roles between Carbon Metabolism and the hrp System in Rice Pathogen Xanthomonas oryzae pv. oryzicola

PubMed Central

Li, Yu-rong; Cui, Yi-ping; Ji, Zhi-yuan; Cai, Lu-lu; Zou, Hua-song; Hutchins, William C.; Yang, Ching-hong; Chen, Gong-you

2012-01-01

Fructose-bisphophate aldolase (FbaB), is an enzyme in glycolysis and gluconeogenesis in living organisms. The mutagenesis in a unique fbaB gene of Xanthomonas oryzae pv. oryzicola, the causal agent of rice bacterial leaf streak, led the pathogen not only unable to use pyruvate and malate for growth and delayed its growth when fructose was used as the sole carbon source, but also reduced extracellular polysaccharide (EPS) production and impaired bacterial virulence and growth in rice. Intriguingly, the fbaB promoter contains an imperfect PIP-box (plant-inducible promoter) (TTCGT-N9-TTCGT). The expression of fbaB was negatively regulated by a key hrp regulatory HrpG and HrpX cascade. Base substitution in the PIP-box altered the regulation of fbaB with the cascade. Furthermore, the expression of fbaB in X. oryzae pv. oryzicola RS105 strain was inducible in planta rather than in a nutrient-rich medium. Except other hrp-hrc-hpa genes, the expression of hrpG and hrpX was repressed and the transcripts of hrcC, hrpE and hpa3 were enhanced when fbaB was deleted. The mutation in hrcC, hrpE or hpa3 reduced the ability of the pathogen to acquire pyruvate and malate. In addition, bacterial virulence and growth in planta and EPS production in RΔfbaB mutant were completely restored to the wild-type level by the presence of fbaB in trans. This is the first report to demonstrate that carbohydrates, assimilated by X. oryzae pv. oryzicola, play critical roles in coordinating hrp gene expression through a yet unknown regulator. PMID:22384086

Gas film retention and underwater photosynthesis during field submergence of four contrasting rice genotypes

PubMed Central

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

2014-01-01

Floods can completely submerge some rice (Oryza sativa L.) fields. Leaves of rice have gas films that aid O2 and CO2 exchange under water. The present study explored the relationship between gas film persistence and underwater net photosynthesis (PN) as influenced by genotype and submergence duration. Four contrasting genotypes (FR13A, IR42, Swarna, and Swarna-Sub1) were submerged for 13 days in the field and leaf gas films, chlorophyll, and the capacity for underwater PN at near ambient and high CO2 were assessed with time of submergence. At high CO2 during the PN assay, all genotypes initially showed high rates of underwater PN, and this rate was not affected by time of submergence in FR13A. This superior photosynthetic performance of FR13A was not evident in Swarna-Sub1 (carrying the SUB1 QTL) and the declines in underwater PN in both Swarna-Sub1 and Swarna were equal to that in IR42. At near ambient CO2 concentration, underwater PN declined in all four genotypes and this corresponded with loss of leaf gas films with time of submergence. FR13A retained leaf gas films moderately longer than the other genotypes, but gas film retention was not linked to SUB1. Diverse rice germplasm should be screened for gas film persistence during submergence, as this trait could potentially increase carbohydrate status and internal aeration owing to increased underwater PN, which contributes to submergence tolerance in rice. PMID:24759881

Dynamic Cytology and Transcriptional Regulation of Rice Lamina Joint Development1[OPEN

PubMed Central

2017-01-01

Rice (Oryza sativa) leaf angle is determined by lamina joint and is an important agricultural trait determining leaf erectness and, hence, the photosynthesis efficiency and grain yield. Genetic studies reveal a complex regulatory network of lamina joint development; however, the morphological changes, cytological transitions, and underlying transcriptional programming remain to be elucidated. A systemic morphological and cytological study reveals a dynamic developmental process and suggests a common but distinct regulation of the lamina joint. Successive and sequential cell division and expansion, cell wall thickening, and programmed cell death at the adaxial or abaxial sides form the cytological basis of the lamina joint, and the increased leaf angle results from the asymmetric cell proliferation and elongation. Analysis of the gene expression profiles at four distinct developmental stages ranging from initiation to senescence showed that genes related to cell division and growth, hormone synthesis and signaling, transcription (transcription factors), and protein phosphorylation (protein kinases) exhibit distinct spatiotemporal patterns during lamina joint development. Phytohormones play crucial roles by promoting cell differentiation and growth at early stages or regulating the maturation and senescence at later stages, which is consistent with the quantitative analysis of hormones at different stages. Further comparison with the gene expression profile of leaf inclination1, a mutant with decreased auxin and increased leaf angle, indicates the coordinated effects of hormones in regulating lamina joint. These results reveal a dynamic cytology of rice lamina joint that is fine-regulated by multiple factors, providing informative clues for illustrating the regulatory mechanisms of leaf angle and plant architecture. PMID:28500269

Evaluation of indigenous bacterial strains for biocontrol of the frogeye leaf spot of soya bean caused by Cercospora sojina.

PubMed

Simonetti, E; Carmona, M A; Scandiani, M M; García, A F; Luque, A G; Correa, O S; Balestrasse, K B

2012-08-01

Assessment of biological control of Cercospora sojina, causal agent of frogeye leaf spot (FLS) of soya bean, using three indigenous bacterial strains, BNM297 (Pseudomonas fluorescens), BNM340 and BNM122 (Bacillus amyloliquefaciens). From cultures of each bacterial strain, cell suspensions and cell-free supernatants were obtained and assayed to determine their antifungal activity against C. sojina. Both mycelial growth and spore germination in vitro were more strongly inhibited by bacterial cell suspensions than by cell-free supernatants. The Bacillus strains BNM122 and BNM340 inhibited the fungal growth to a similar degree (I ≈ 52-53%), while cells from P. fluorescens BNM297 caused a lesser reduction (I ≈ 32-34%) in the fungus colony diameter. The foliar application of the two Bacillus strains on soya bean seedlings, under greenhouse conditions, significantly reduced the disease severity with respect to control soya bean seedlings and those sprayed with BNM297. This last bacterial strain was not effective in controlling FLS in vivo. Our data demonstrate that the application of antagonistic bacteria may be a promising and environmentally friendly alternative to control the FLS of soya bean.   To our knowledge, this is the first report of biological control of C. sojina by using native Bacillus strains. © 2012 The Authors. Letters in Applied Microbiology © 2012 The Society for Applied Microbiology.

Agronomic performance of F1, F2 and F3 hybrids between weedy rice and transgenic glufosinate-resistant rice.

PubMed

Song, Xiaoling; Wang, Zhou; Qiang, Sheng

2011-08-01

Studies of hybrid fitness, of which agronomic performance may be an indicator, can help in evaluating the potential for introgression of a transgene from a transgenic crop to wild relatives. The objective of this study was to assess the agronomic performance of reciprocal hybrids between two transgenic glufosinate-resistant rice lines, Y0003 and 99-t, and two weedy rice accessions, WR1 and WR2, in the greenhouse. F1 hybrids displayed heterosis in height, flag leaf area and number of spikelets per panicle. The agronomic performance of F1 between WR1 and Y0003 was not affected by crossing direction. The tiller and panicle numbers of F1 individuals were higher than their F2 counterparts. However, these traits did not change significantly from the F2 to the F3 generation or in hybrids with weedy rice as maternal or paternal plants. For all hybrids, the in vitro germination rates of fresh pollen were similar and significantly lower than those of their parents, seed sets were similar to or of lower value than those of weedy rice parents and seed shattering characteristics were partially suppressed, but the survival of hybrids over winter in the field was similar to that of weedy rice parents. All F1, F2 and F3 hybrids had similar composite agronomic performance to weedy rice parents. There was no significant decrease in the composite agronomic performance of any of the hybrids compared with weedy rice. This implies that gene flow from transgenic cultivated rice to weedy rice could occur under natural conditions. Copyright © 2011 Society of Chemical Industry.

Transgenic rice expressing the cry2AX1 gene confers resistance to multiple lepidopteran pests.

PubMed

Chakraborty, M; Reddy, P Sairam; Mustafa, G; Rajesh, G; Narasu, V M Laxmi; Udayasuriyan, V; Rana, Debashis

2016-10-01

A chimeric Bacillus thuringiensis toxin (Bt) gene, cry2AX1was cloned in a bi-selectable marker free binary vector construct. The cry2AX1 gene, driven by the Chrysanthemum rbcS1 promoter, was introduced into JK1044R, the restorer line (Oryza sativa L. ssp. Indica) of a notified commercially grown rice hybrid in India, by Agrobacterium-mediated transformation. Its effect against two major lepidopteran insect pests viz., yellow stem borer (YSB) Scirpophaga incertulas, rice leaf folder (RLF) Cnaphalocrocis medinalis and one minor insect pest, oriental army worm (OAW) Mythimna separata was demonstrated through bioassays of transgenic rice plants under laboratory and greenhouse conditions. The rbcS1 promoter with chloroplast signal peptide was used to avoid Cry2AX1 protein expression in rice seed endosperm tissue. A total of 37 independent transformants were generated, of which after preliminary molecular characterization and YSB bioassay screening, five events were selected for their protein expression and bioefficacy against all three rice insect. One elite transgenic rice line, BtE15, was identified with Cry2AX1 expression ranging from 0.68 to 1.34 µg g(-1) leaf fresh weight and with 80-92 % levels of resistance against rice pests at the vegetative and reproductive stages. Increase in Cry2AX1 protein concentration was also observed with crop maturity. The Cry2AX1protein concentration in the de-husked seeds was negligible (as low as 2.7-3.6 ng g(-1)). These results indicate the potential application of cry2AX1 gene in rice for protection against YSB, RLF and OAW.

Three-dimensional intracellular structure of a whole rice mesophyll cell observed with FIB-SEM.

PubMed

Oi, Takao; Enomoto, Sakiko; Nakao, Tomoyo; Arai, Shigeo; Yamane, Koji; Taniguchi, Mitsutaka

2017-07-01

Ultrathin sections of rice leaf blades observed two-dimensionally using a transmission electron microscope (TEM) show that the chlorenchyma is composed of lobed mesophyll cells, with intricate cell boundaries, and lined with chloroplasts. The lobed cell shape and chloroplast positioning are believed to enhance the area available for the gas exchange surface for photosynthesis in rice leaves. However, a cell image revealing the three-dimensional (3-D) ultrastructure of rice mesophyll cells has not been visualized. In this study, a whole rice mesophyll cell was observed using a focused ion beam scanning electron microscope (FIB-SEM), which provides many serial sections automatically, rapidly and correctly, thereby enabling 3-D cell structure reconstruction. Rice leaf blades were fixed chemically using the method for conventional TEM observation, embedded in resin and subsequently set in the FIB-SEM chamber. Specimen blocks were sectioned transversely using the FIB, and block-face images were captured using the SEM. The sectioning and imaging were repeated overnight for 200-500 slices (each 50 nm thick). The resultant large-volume image stacks ( x = 25 μm, y = 25 μm, z = 10-25 μm) contained one or two whole mesophyll cells. The 3-D models of whole mesophyll cells were reconstructed using image processing software. The reconstructed cell models were discoid shaped with several lobes around the cell periphery. The cell shape increased the surface area, and the ratio of surface area to volume was twice that of a cylinder having the same volume. The chloroplasts occupied half the cell volume and spread as sheets along the cell lobes, covering most of the inner cell surface, with adjacent chloroplasts in close contact with each other. Cellular and sub-cellular ultrastructures of a whole mesophyll cell in a rice leaf blade are demonstrated three-dimensionally using a FIB-SEM. The 3-D models and numerical information support the hypothesis that rice mesophyll

Seed-vectored endophytic bacteria modulate development of rice seedlings.

PubMed

Verma, S K; Kingsley, K; Irizarry, I; Bergen, M; Kharwar, R N; White, J F

2017-06-01

The aim of the present study was to evaluate the effects of the removal of indigenous bacteria from rice seeds on seedling growth and development. Here we report the presence of three indigenous endophytic bacteria in rice seeds that play important roles in modulating seedling development (shoot and root lengths, and formation of root hairs and secondary roots) and defence against pathogens. Seed-associated bacteria were removed using surface sterilization with NaOCl (bleach) followed by antibiotic treatment. When bacteria were absent, growth of seedlings in terms of root hair development and overall seedling size was less than that of seedlings that contained bacteria. Reactive oxygen staining of seedlings showed that endophytic bacteria became intracellular in root parenchyma cells and root hairs. Roots containing endophytic bacteria were seen to stain densely for reactive oxygen, while roots free of bacteria stained lightly for reactive oxygen. Bacteria were isolated and identified as Enterobacter asburiae (VWB1), Pantoea dispersa (VWB2) and Pseudomonas putida (VWB3) by 16S rDNA sequencing. Bacteria were found to produce indole acetic acid (auxins), inhibited the pathogen Fusarium oxysporum and solubilized phosphate. Reinoculation of bacteria onto seedlings derived from surface-disinfected rice and Bermuda grass seeds significantly restored seedling growth and development. Rice seeds harbour indigenous bacterial endophytes that greatly influence seedling growth and development, including root and shoot lengths, root hair formation and disease susceptibility of rice seedlings. This study shows that seeds of rice naturally harbour bacterial endophytes that play key roles in modulation of seedling development. © 2017 The Society for Applied Microbiology.

Risk assessment and vertical distribution of thallium in paddy soils and uptake in rice plants irrigated with acid mine drainage.

PubMed

Huang, Xuexia; Li, Ning; Wu, Qihang; Long, Jianyou; Luo, Dinggui; Zhang, Ping; Yao, Yan; Huang, Xiaowu; Li, Dongmei; Lu, Yayin; Liang, Jianfeng

2016-12-01

The objective of this paper is to assess the influence of irritating paddy fields with acid mine drainage containing thallium (Tl) to rice plant-soil system and potential health risks for local residents. Vertical distribution of Tl, pH, organic matter (OM), and cation exchange capacity (CEC) in 24 paddy soil profiles around Yunfu pyrite mine area was investigated. Rice plant samples were collected from the corresponding soil sampling site. The results showed that Tl concentrations in paddy soils at 0-60 cm depth range from 3.07 to 9.42 mg kg -1 , with a mean of 5.74 mg kg -1 , which were significantly higher than the background value of soil in China (0.58 mg kg -1 ). On the whole, Tl contents in paddy soil profiles increased quickly with soil depth from 0 to 30 cm and decreased slowly with soil depth from 30 to 60 cm. The soil Tl content was significant negatively correlated with soil pH. The mean content of Tl in the root, stem, leaf, and rice was 4.36, 1.83, 2.74, and 1.42 mg kg -1 , respectively, which exceeded the proposed permissible limits for foods and feedstuffs in Germany. The Tl content in various tissues of the rice plants followed the order root > leaf > stem (rice), which suggested that most Tl taken up by rice plants retained in the root, and a little migrated to the leaf, stem, and rice. Correlation analysis showed that Tl content in root was significant positively correlated with Tl content in leaf and rice. The ranges of hazard quotient (HQ) values were 4.08∼24.50 and 3.84∼22.38 for males and females, respectively. Males have higher health risk than females in the same age group. In childhood age groups (2 to <21 years) and adult age groups (21 to <70 years), the highest health risk level was observed in the 11 to 16 age group and 21 to 50 age group, respectively. The findings indicated that regular irrigation with Tl-bearing acid mine drainage led to considerable contamination of Tl in paddy soil and rice plant. Local government

Succession of bacterial and fungal communities during a traditional pot fermentation of rice vinegar assessed by PCR-mediated denaturing gradient gel electrophoresis.

PubMed

Haruta, Shin; Ueno, Shintaro; Egawa, Isao; Hashiguchi, Kazunori; Fujii, Akira; Nagano, Masanobu; Ishii, Masaharu; Igarashi, Yasuo

2006-05-25

Denaturing gradient gel electrophoresis (DGGE) based on small subunit rRNA gene was applied to a traditional rice vinegar fermentation process in which the conversion of rice starch into acetic acid proceeded in a pot. The fungal DGGE profile indicated that the transition from Aspergillus oryzae to Saccharomyces sp. took place at the initial stage at which alcohol production was observed. The early stage was characterized by the coexistence of Saccharomyces sp. and lactic acid bacteria. Almost all of the bacterial DGGE bands related to lactic acid bacteria were replaced by bands derived from Lactobacillus acetotolerance and Acetobacter pasteurianus at the stage at which acetic acid started to accumulate. The microbial succession, tested in three different pots, was found to be essentially identical. Among the bacteria isolated at the early stage, some species differed from those detected by DGGE. This is the first report to reveal the microbial community succession that occurs during a unique vinegar fermentation process, as determined by a culture-independent method.

Metagenomic and metaproteomic insights into bacterial communities in leaf-cutter ant fungus gardens

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

Aylward, Frank O.; Burnum, Kristin E.; Scott, Jarrod J.

2012-09-01

Herbivores gain access to nutrients stored in plant biomass largely by harnessing the metabolic activities of microbes. Leaf-cutter ants of the genus Atta are a hallmark example; these dominant Neotropical herbivores cultivate symbiotic fungus gardens on massive quantities of fresh plant forage. As the external digestive system of the ants, fungus gardens facilitate the production and sustenance of millions of workers in mature Atta colonies. Here we use metagenomic, and metaproteomic techniques to characterize the bacterial diversity and overall physiological potential of fungus gardens from two species of Atta. Our analysis of over 1.2 Gbp of community metagenomic sequence andmore » three 16S pyrotag libraries reveals that, in addition to harboring the dominant fungal crop, these ecosystems contain abundant populations of Enterobacteriaceae, including the genera Enterobacter, Pantoea, Klebsiella, Citrobacter, and Escherichia. We show that these bacterial communities possess genes commonly associated with lignocellulose degradation, and likely participate in the processing of plant biomass. Additionally, we demonstrate that bacteria in these environments encode a diverse suite of biosynthetic pathways, and that they may enrich the nitrogen-poor forage of the ants with B-vitamins, amino acids, and proteins. These results are consistent with the hypothesis that fungus gardens are highly-specialized fungus-bacteria communities that efficiently convert plant material into usable energy for their ant hosts. Together with recent investigations into the microbial symbionts of vertebrates, our work underscores the importance of microbial communities to the ecology and evolution of herbivorous metazoans.« less

Climate Change Implications to Irrigated Rice Production in Southern Brazil: A Modelling Approach

NASA Astrophysics Data System (ADS)

Dos Santos, Thiago

Rice is one of the staple foods for more than three billion people worldwide. When cultivated under irrigated conditions (i.e. lowland rice), rice is one of the most intensive water consumer crops globally. Therefore, representation of rice growth should be integrated into the latest land surface models to allow studies on food security and to ensure that accurate simulations of the bidirectional feedbacks between the land surface and atmosphere take place. In this study, I present a new process-based model for rice fields that includes rice growth and rice irrigation as modules within the Agro-IBIS dynamic agro-ecosystem model. The model includes a series of equations, agricultural management parameters and an irrigation scheme that are specifically tailored for rice crops. The model was evaluated against leaf area index and biomass observations, obtained for one growing season in Rio Grande do Sul state (southern Brazil), and in Los Banos, Philippines. The model accurately captured the temporal dynamics of leaf area index in both the Brazilian and the Philippine sites, and predicted end-of-season biomass with an error of between -9.5% and 11.3% depending on the location and the plant organ. Rice phenology is predicted by the model based on experimentally-derived growth rates, and was evaluated by comparing simulated and observed durations of the four growth phases considered by the model. Agro-IBIS showed a tendency to overestimate the duration of the growth stages between 3% and 16%, but underestimated by 8% the duration of the panicle formation phase in one growing season. The new irrigation model is based on the water balance at the surface and applies irrigation in order to keep the water layer at the paddy field always in the optimum level. A set of climate projections from global climate models under two emission scenarios, and excluding and considering CO2 fertilizations effects, was used to drive the updated Agro-IBIS to estimate the effects of climate

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. © 2012 The Authors. New Phytologist © 2012 New Phytologist Trust.

The rice nuclear gene, VIRESCENT 2, is essential for chloroplast development and encodes a novel type of guanylate kinase targeted to plastids and mitochondria.

PubMed

Sugimoto, Hiroki; Kusumi, Kensuke; Noguchi, Ko; Yano, Masahiro; Yoshimura, Atsushi; Iba, Koh

2007-11-01

Guanylate kinase (GK) is a critical enzyme in guanine nucleotide metabolism pathways, catalyzing the phosphorylation of (d)GMP to (d)GDP. Here we show that a novel gene, VIRESCENT 2 (V2), encodes a new type of GK (designated pt/mtGK) that is localized in plastids and mitochondria. We initially identified the V2 gene by positional cloning of the rice v2 mutant. The v2 mutant is temperature-sensitive and develops chlorotic leaves at restrictive temperatures. The v2 mutation causes inhibition of chloroplast differentiation; in particular, it disrupts the chloroplast translation machinery during early leaf development [Sugimoto et al. (2004)Plant Cell Physiol. 45, 985]. In the bacterial and animal species studied to date, GK is localized in the cytoplasm and participates in maintenance of the guanine nucleotide pools required for many fundamental cellular processes. Phenotypic analysis of rice seedlings with RNAi knockdown of cytosolic GK (designated cGK) showed that cGK is indispensable for the growth and development of plants, but not for chloroplast development. Thus, rice has two types of GK, as does Arabidopsis, suggesting that higher plants have two types of GK. Our results suggest that, of the two types of GK, only pt/mtGK is essential for chloroplast differentiation.

Aquaporins are major determinants of water use efficiency of rice plants in the field.

PubMed

Nada, Reham M; Abogadallah, Gaber M

2014-10-01

This study aimed at specifying the reasons of unbalanced water relations of rice in the field at midday which results in slowing down photosynthesis and reducing water use efficiency (WUE) in japonica and indica rice under well-watered and droughted conditions. Leaf relative water content (RWC) decreased in the well-watered plants at midday in the field, but more dramatically in the droughted indica (75.6 and 71.4%) than japonica cultivars (85.5 and 80.8%). Gas exchange was measured at three points during the day (9:00, 13:00 and 17:00). Leaf internal CO2 (Ci) was not depleted when midday stomatal depression was highest indicating that Ci was not limiting to photosynthesis. Most aquaporins were predominantly expressed in leaves suggesting higher water permeability in leaves than in roots. The expression of leaf aquaporins was further induced by drought at 9:00 without comparable responses in roots. The data suggest that aquaporin expression in the root endodermis was limiting to water uptake. Upon removal of the radial barriers to water flow in roots, transpiration increased instantly and photosynthesis increased after 4h resulting in increasing WUE after 4h, demonstrating that WUE in rice is largely limited by the inadequate aquaporin expression profiles in roots. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Isolation of a rice endophytic bacterium, Pantoea sp. Sd-1, with ligninolytic activity and characterization of its rice straw degradation ability.

PubMed

Xiong, X Q; Liao, H D; Ma, J S; Liu, X M; Zhang, L Y; Shi, X W; Yang, X L; Lu, X N; Zhu, Y H

2014-02-01

This study focused on an endophytic bacterial strain, Pantoea sp. Sd-1, which can be used to degrade lignin and rice straw. This strain was isolated from rice seeds by an optimized surface sterilization method. Pantoea sp. Sd-1 showed exceptional ability to degrade rice straw and lignin. In rice straw or kraft lignin-containing medium supplemented with 1% glucose and 0.5% peptone, Pantoea sp. Sd-1 effectively reduced the rice straw mass weight by 54.5% after 6 days of treatment. The strain was also capable of reducing the lignin colour (52.4%) and content (69.1%) after 4 days of incubation. The findings suggested that the rice endophytic bacterium Pantoea sp. Sd-1 could be applied for the degradation of lignocellulose biomass, such as rice straw. Rice straw, an abundant agricultural by-product in China, is very difficult to degrade because of its high lignin content. Due to the immense environmental adaptability and biochemical versatility of bacteria, endophytic bacteria are useful resources for biodegradation. In this study, we screened for endophytic bacteria capable of biodegrading rice straw and lignin and obtained one strain, Pantoea sp. Sd-1, with suitable characteristics. Sd-1 could be used for degradation of rice straw and lignin, and may play an important role in biodegradation of this agricultural by-product. © 2013 The Society for Applied Microbiology.

The mechanism of improved aeration due to gas films on leaves of submerged rice.

PubMed

Verboven, Pieter; Pedersen, Ole; Ho, Quang Tri; Nicolai, Bart M; Colmer, Timothy D

2014-10-01

Some terrestrial wetland plants, such as rice, have super-hydrophobic leaf surfaces which retain a gas film when submerged. O2 movement through the diffusive boundary layer (DBL) of floodwater, gas film and stomata into leaf mesophyll was explored by means of a reaction-diffusion model that was solved in a three-dimensional leaf anatomy model. The anatomy and dark respiration of leaves of rice (Oryza sativa L.) were measured and used to compute O2 fluxes and partial pressure of O2 (pO2 ) in the DBL, gas film and leaf when submerged. The effects of floodwater pO2 , DBL thickness, cuticle permeability, presence of gas film and stomatal opening were explored. Under O2 -limiting conditions of the bulk water (pO2  < 10 kPa), the gas film significantly increases the O2 flux into submerged leaves regardless of whether stomata are fully or partly open. With a gas film, tissue pO2 substantially increases, even for the slightest stomatal opening, but not when stomata are completely closed. The effect of gas films increases with decreasing cuticle permeability. O2 flux and tissue pO2 decrease with increasing DBL thickness. The present modelling analysis provides a mechanistic understanding of how leaf gas films facilitate O2 entry into submerged plants. © 2014 John Wiley & Sons Ltd.

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

NASA Astrophysics Data System (ADS)

Li, Lianjie; Cheng, Long

2017-10-01

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

Construction of an 800-kb contig in the near-centromeric region of the rice blast resistance gene Pi-ta2 using a highly representative rice BAC library.

PubMed

Nakamura, S; Asakawa, S; Ohmido, N; Fukui, K; Shimizu, N; Kawasaki, S

1997-05-01

We constructed a rice Bacterial Artificial Chromosome (BAC) library from green leaf protoplasts of the cultivar Shimokita harboring the rice blast resistance gene Pi-ta. The average insert size of 155 kb and the library size of seven genome equivalents make it one of the most comprehensive BAC libraries available, and larger than many plant YAC libraries. The library clones were plated on seven high density membranes of microplate size, enabling efficient colony identification in colony hybridization experiments. Seven percent of clones carried chloroplast DNA. By probing with markers close to the blast resistance genes Pi-ta2(closely linked to Pi-ta) and Pi-b, respectively located in the centromeric region of chromosome 12 and near the telomeric end of chromosome 2, on average 2.2 +/- 1.3 and 8.0 +/- 2.6 BAC clones/marker were isolated. Differences in chromosomal structures may contribute to this wide variation in yield. A contig of about 800 kb, consisting of 19 clones, was constructed in the Pi-ta2 region. This region had a high frequency of repetitive sequences. To circumvent this difficulty, we devised a "two-step walking" method. The contig spanned a 300 kb region between markers located at 0 cM and 0.3 cM from Pi-ta. The ratio of physical to genetic distances (> 1,000 kb/cM) was more than three times larger than the average of rice (300 kb/cM). The low recombination rate and high frequency of repetitive sequences may also be related to the near centromeric character of this region. Fluorescent in situ hybridization (FISH) with a BAC clone from the Pi-b region yielded very clear signals on the long arm of chromosome 2, while a clone from the Pi-ta2 region showed various cross-hybridizing signals near the centromeric regions of all chromosomes.

Fine mapping QTL for drought resistance traits in rice (Oryza sativa L.) using bulk segregant analysis.

PubMed

Salunkhe, Arvindkumar Shivaji; Poornima, R; Prince, K Silvas Jebakumar; Kanagaraj, P; Sheeba, J Annie; Amudha, K; Suji, K K; Senthil, A; Babu, R Chandra

2011-09-01

Drought stress is a major limitation to rice (Oryza sativa L.) yields and its stability, especially in rainfed conditions. Developing rice cultivars with inherent capacity to withstand drought stress would improve rainfed rice production. Mapping quantitative trait loci (QTLs) linked to drought resistance traits will help to develop rice cultivars suitable for water-limited environments through molecular marker-assisted selection (MAS) strategy. However, QTL mapping is usually carried out by genotyping large number of progenies, which is labour-intensive, time-consuming and cost-ineffective. Bulk segregant analysis (BSA) serves as an affordable strategy for mapping large effect QTLs by genotyping only the extreme phenotypes instead of the entire mapping population. We have previously mapped a QTL linked to leaf rolling and leaf drying in recombinant inbred (RI) lines derived from two locally adapted indica rice ecotypes viz., IR20/Nootripathu using BSA. Fine mapping the QTL will facilitate its application in MAS. BSA was done by bulking DNA of 10 drought-resistant and 12 drought-sensitive RI lines. Out of 343 rice microsatellites markers genotyped, RM8085 co-segregated among the RI lines constituting the respective bulks. RM8085 was mapped in the middle of the QTL region on chromosome 1 previously identified in these RI lines thus reducing the QTL interval from 7.9 to 3.8 cM. Further, the study showed that the region, RM212-RM302-RM8085-RM3825 on chromosome 1, harbours large effect QTLs for drought-resistance traits across several genetic backgrounds in rice. Thus, the QTL may be useful for drought resistance improvement in rice through MAS and map-based cloning.

Gas film retention and underwater photosynthesis during field submergence of four contrasting rice genotypes.

PubMed

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

2014-07-01

Floods can completely submerge some rice (Oryza sativa L.) fields. Leaves of rice have gas films that aid O2 and CO2 exchange under water. The present study explored the relationship between gas film persistence and underwater net photosynthesis (PN) as influenced by genotype and submergence duration. Four contrasting genotypes (FR13A, IR42, Swarna, and Swarna-Sub1) were submerged for 13 days in the field and leaf gas films, chlorophyll, and the capacity for underwater PN at near ambient and high CO2 were assessed with time of submergence. At high CO2 during the PN assay, all genotypes initially showed high rates of underwater PN, and this rate was not affected by time of submergence in FR13A. This superior photosynthetic performance of FR13A was not evident in Swarna-Sub1 (carrying the SUB1 QTL) and the declines in underwater PN in both Swarna-Sub1 and Swarna were equal to that in IR42. At near ambient CO2 concentration, underwater PN declined in all four genotypes and this corresponded with loss of leaf gas films with time of submergence. FR13A retained leaf gas films moderately longer than the other genotypes, but gas film retention was not linked to SUB1. Diverse rice germplasm should be screened for gas film persistence during submergence, as this trait could potentially increase carbohydrate status and internal aeration owing to increased underwater PN, which contributes to submergence tolerance in rice. © The Author 2014. Published by Oxford University Press on behalf of the Society for Experimental Biology.

Rice monitoring with multi-temporal and dual-polarimetric TerraSAR-X data

NASA Astrophysics Data System (ADS)

Koppe, Wolfgang; Gnyp, Martin L.; Hütt, Christoph; Yao, Yinkun; Miao, Yuxin; Chen, Xinping; Bareth, Georg

2013-04-01

This study assesses the use of TerraSAR-X data for monitoring rice cultivation in the Sanjiang Plain in Heilongjiang Province, Northeast China. The main objective is the understanding of the coherent co-polarized X-band backscattering signature of rice at different phenological stages in order to retrieve growth status. For this, multi-temporal dual polarimetric TerraSAR-X High Resolution SpotLight data (HH/VV) as well as single polarized StripMap (VV) data were acquired over the test site. In conjunction with the satellite data acquisition, a ground truth field campaign was carried out. The backscattering coefficients at HH and VV of the observed fields were extracted on the different dates and analysed as a function of rice phenology to provide a physical interpretation for the co-polarized backscatter response in a temporal and spatial manner. Then, a correlation analysis was carried out between TerraSAR-X backscattering signal and rice biomass of stem, leaf and head to evaluate the relationship with different vertical layers within the rice vegetation. HH and VV signatures show two phases of backscatter increase, one at the beginning up to 46 days after transplanting and a second one from 80 days after transplanting onwards. The first increase is related to increasing double bounce reflection from the surface-stem interaction. Then, a decreasing trend of both polarizations can be observed due to signal attenuation by increasing leaf density. A second slight increase is observed during senescence. Correlation analysis showed a significant relationship with different vertical layers at different phenological stages which prove the physical interpretation of X-band backscatter of rice. The seasonal backscatter coefficient showed that X-band is highly sensitive to changes in size, orientation and density of the dominant elements in the upper canopy.

Influence of temperature regimes on resistance gene-mediated response to rice bacterial blight

USDA-ARS?s Scientific Manuscript database

Increasing temperatures could reduce yield growth rate of rice by 10% in several rice production areas. Similarly, higher temperatures are predicted to accelerate the breakdown of plant disease resistance through higher disease pressure or altered resistance (R) gene effectiveness in many host-path...

Rice rhizosphere soil and root surface bacterial community response to water management changes

USDA-ARS?s Scientific Manuscript database

Different water management practices could affect microbial populations in the rice rhizosphere. A field-scale study was conducted to evaluate microbial populations in the root plaque and rhizosphere of rice in response to continuous and intermittent flooding conditions. Microbial populations in rhi...

Heat shock suppresses mating and sperm transfer in the rice leaf folder Cnaphalocrocis medinalis.

PubMed

Liao, H J; Qian, Q; Liu, X D

2014-06-01

Temperature is a key environmental factor in determining the population size of Cnaphalocrocis medinalis in summer. High temperatures inhibit survival, development and fecundity of this insect. However, biological responses of female and male adults to heat shock, and physiological mechanism of high temperature suppressing population development are still ambiguous. We experimentally tested the impact of heat shock (5 h day-1) on biological traits, spermatogenesis and sperm transfer of adults of C. medinalis. The result showed that heat exposure to 39 and 40 °C for 5 h reduced longevity and copulation frequency of adults, and hatchability of eggs. Immediate survival rate of males was lower than that of females after 3 days of exposure to 41 °C. The oviposition period, copulation frequency, fecundity of adults and hatchability of eggs were significantly lower when male adults were exposed to 40 or 41 °C for 3 days. Heat shock decreased frequency and success rate of mating when males were exposed, and it also resulted in postponement of mating behaviour and prolongation of mating duration as both the female and male adults were exposed. Heat shock did not affect spermatogenesis, but significantly inhibited sperms maturation. Moreover, males could not ejaculate sperm into females during copulation when these male moths received heat shock. Heat shock remarkably suppressed mating behaviour and sperm transfer, which led to a dramatic decline of rice leaf folder populations.

Changes in carbon stability and microbial activity in size fractions of micro-aggregates in a rice soil chronosequence under long term rice cultivation

NASA Astrophysics Data System (ADS)

Pan, Genxing; Liu, Yalong; Wang, Ping; Li, Lianqinfg; Cheng, Kun; Zheng, Jufeng; Zhang, Xuhui; Zheng, Jinwei; Bian, Rongjun; Ding, Yuanjun; Ma, Chong

2016-04-01

Recent studies have shown soil carbon sequestration through physical protection of relative labile carbon intra micro-aggregates with formation of large sized macro-aggregates under good management of soil and agricultural systems. While carbon stabilization had been increasingly concerned as ecosystem properties, the mechanisms underspin bioactivity of soil carbon with increased carbon stability has been still poorly understood. In this study, topsoil samples were collected from rice soils derived from salt marsh under different length of rice cultivation up to 700 years from eastern China. Particle size fractions (PSF) of soil aggregates were separated using a low energy dispersion protocol. Carbon fractions in the PSFs were analyzed either with FTIR spectroscopy. Soil microbial community of bacterial, fungal and archaeal were analyzed with molecular fingerprinting using specific gene primers. Soil respiration and carbon gain from amended maize as well as enzyme activities were measured using lab incubation protocols. While the PSFs were dominated by the fine sand (200-20μm) and silt fraction (20-2μm), the mass proportion both of sand (2000-200μm) and clay (<2μm) fraction increased with prolonged rice cultivation, giving rise to an increasing trend of mean weight diameter of soil aggregates (also referred to aggregate stability). Soil organic carbon was found most enriched in coarse sand fraction (40-60g/kg), followed by the clay fraction (20-24.5g/kg), but depleted in the silt fraction (~10g/kg). Phenolic and aromatic carbon as recalcitrant pool were high (33-40% of total SOC) in both coarse sand and clay fractions than in both fine sand and silt fractions (20-29% of total SOC). However, the ratio of LOC/total SOC showed a weak decreasing trend with decreasing size of the aggregate fractions. Total gene content in the size fractions followed a similar trend to that of SOC. Bacterial and archaeal gene abundance was concentrated in both sand and clay fractions

Antixenosis and Antibiosis Resistance in Rice Cultivars against Chilo suppressalis (Walker) (Lepidoptera: Crambidae).

PubMed

Tabari, M A; Fathi, S A A; Nouri-Ganbalani, G; Moumeni, A; Razmjou, J

2017-08-01

The striped stem borer, Chilo suppressalis (Walker) (Lepidoptera: Crambidae), is an important pest afflicting rice in most rice-growing countries in the world. Deliniating the categories of resistance in rice genotypes under field conditions could be helpful in managment of this pest. Two categories of resistance, antixenosis and antibiosis, were examined in ten popular and diverse rice genotypes of different origin that had been selected for their resistance to the striped stem borer in a previous study. Significant differences were found between genotypes for the number of egg masses, number of eggs, preference index, larval and pupal weight, larval development time, larval survival rate, larval mine length, and leaf trichome density. It was found that the rice genotypes Novator, A7801, and Nemat had the more pronounced antixenosis-type resistance, whereas AB1 and Shirodi had better antiobiosis-type resistance. Interestingly, the rice genotype AN-74 for which Nemat is the parental line showed both types of resistance and could be effectively used in an integrated pest management of the rice striped stem borer.

Exogenous superoxide dismutase may lose its antidotal ability on rice leaves

USDA-ARS?s Scientific Manuscript database

Leaf diffusates of the resistant rice cultivars suppressed spore germination of blast fungus (Magnaporthe grisea). Bovine Cu-Zn superoxide dismutase (SOD) added to the diffusate abolished its toxicity. However, the enzyme added to the inoculum did not affect the toxicity of the diffusate. Even the s...

Evaporation kinetics of surfactant solution droplets on rice (Oryza sativa) leaves

PubMed Central

Cao, Li-Dong; Zheng, Li; Xu, Jun; Li, Feng-Min; Huang, Qi-Liang

2017-01-01

The dynamics of evaporating sessile droplets on hydrophilic or hydrophobic surfaces is widely studied, and many models for these processes have been developed based on experimental evidence. However, few research has been explored on the evaporation of sessile droplets of surfactant or pesticide solutions on target crop leaves. Thus, in this paper the impact of surfactant concentrations on contact angle, contact diameter, droplet height, and evolution of the droplets’ evaporative volume on rice leaf surfaces have been investigated. The results indicate that the evaporation kinetics of surfactant droplets on rice leaves were influenced by both the surfactant concentrations and the hydrophobicity of rice leaf surfaces. When the surfactant concentration is lower than the surfactant CMC (critical micelle concentration), the droplet evaporation time is much longer than that of the high surfactant concentration. This is due to the longer existence time of a narrow wedge region under the lower surfactant concentration, and such narrow wedge region further restricts the droplet evaporation. Besides, our experimental data are shown to roughly collapse onto theoretical curves based on the model presented by Popov. This study could supply theoretical data on the evaporation of the adjuvant or pesticide droplets for practical applications in agriculture. PMID:28472108

Mutation in Mg-Protoporphyrin IX Monomethyl Ester Cyclase Decreases Photosynthesis Capacity in Rice

PubMed Central

Wang, Xuexia; Huang, Rongfeng; Quan, Ruidang

2017-01-01

In photosynthesis, the pigments chlorophyll a/b absorb light energy to convert to chemical energy in chloroplasts. Though most enzymes of chlorophyll biosynthesis from glutamyl-tRNA to chlorophyll a/b have been identified, the exact composition and regulation of the multimeric enzyme Mg-protoporphyrin IX monomethyl ester cyclase (MPEC) is largely unknown. In this study, we isolated a rice pale-green leaf mutant m167 with yellow-green leaf phenotype across the whole lifespan. Chlorophyll content decreases 43–51% and the granal stacks of chloroplasts becomes thinner in m167. Chlorophyll fluorescence parameters, including Fv/Fm (the maximum quantum efficiency of PSII) and quantum yield of PSII (Y(II)), were lower in m167 than those in wild type plants (WT), and photosynthesis rate decreases 40% in leaves of m167 mutant compared with WT plants, which lead to yield reduction in m167. Genetic analysis revealed that yellow-green leaf phenotype of m167 is controlled by a single recessive genetic locus. By positional cloning, a single mutated locus, G286A (Alanine 96 to Threonine in protein), was found in the coding sequence of LOC_Os01g17170 (Rice Copper Response Defect 1, OsCRD1), encoding a putative subunit of MPEC. Expression profile analysis demonstrated that OsCRD1 is mainly expressed in green tissues of rice. Sequence alignment analysis of CRD1 indicated that Alanine 96 is very conserved in all green plants and photosynthetic bacteria. OsCRD1 protein mainly locates in chloroplast and the point mutation A96T in OsCRD1 does not change its location. Therefore, Alanine96 of OsCRD1 might be fundamental for MPEC activity, mutation of which leads to deficiency in chlorophyll biosynthesis and chloroplast development and decreases photosynthetic capacity in rice. PMID:28129387

Autumn leaf subsidies influence spring dynamics of freshwater plankton communities.

PubMed

Fey, Samuel B; Mertens, Andrew N; Cottingham, Kathryn L

2015-07-01

While ecologists primarily focus on the immediate impact of ecological subsidies, understanding the importance of ecological subsidies requires quantifying the long-term temporal dynamics of subsidies on recipient ecosystems. Deciduous leaf litter transferred from terrestrial to aquatic ecosystems exerts both immediate and lasting effects on stream food webs. Recently, deciduous leaf additions have also been shown to be important subsidies for planktonic food webs in ponds during autumn; however, the inter-seasonal effects of autumn leaf subsidies on planktonic food webs have not been studied. We hypothesized that autumn leaf drop will affect the spring dynamics of freshwater pond food webs by altering the availability of resources, water transparency, and the metabolic state of ponds. We created leaf-added and no-leaf-added field mesocosms in autumn 2012, allowed mesocosms to ice-over for the winter, and began sampling the physical, chemical, and biological properties of mesocosms immediately following ice-off in spring 2013. At ice-off, leaf additions reduced dissolved oxygen, elevated total phosphorus concentrations and dissolved materials, and did not alter temperature or total nitrogen. These initial abiotic effects contributed to higher bacterial densities and lower chlorophyll concentrations, but by the end of spring, the abiotic environment, chlorophyll and bacterial densities converged. By contrast, zooplankton densities diverged between treatments during the spring, with leaf additions stimulating copepods but inhibiting cladocerans. We hypothesized that these differences between zooplankton orders resulted from resource shifts following leaf additions. These results suggest that leaf subsidies can alter both the short- and long-term dynamics of planktonic food webs, and highlight the importance of fully understanding how ecological subsidies are integrated into recipient food webs.

Root bacterial endophytes alter plant phenotype, but not physiology

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

Henning, Jeremiah A.; Weston, David J.; Pelletier, Dale A.

Plant traits, such as root and leaf area, influence how plants interact with their environment and the diverse microbiota living within plants can influence plant morphology and physiology. Here, we explored how three bacterial strains isolated from the Populus root microbiome, influenced plant phenotype. Here, we chose three bacterial strains that differed in predicted metabolic capabilities, plant hormone production and metabolism, and secondary metabolite synthesis. We inoculated each bacterial strain on a single genotype of Populus trichocarpa and measured the response of plant growth related traits (root:shoot, biomass production, root and leaf growth rates) and physiological traits (chlorophyll content, netmore » photosynthesis, net photosynthesis at saturating light–A sat, and saturating CO 2–A max). Overall, we found that bacterial root endophyte infection increased root growth rate up to 184% and leaf growth rate up to 137% relative to non-inoculated control plants, evidence that plants respond to bacteria by modifying morphology. However, endophyte inoculation had no influence on total plant biomass and photosynthetic traits (net photosynthesis, chlorophyll content). In sum, bacterial inoculation did not significantly increase plant carbon fixation and biomass, but their presence altered where and how carbon was being allocated in the plant host.« less

Root bacterial endophytes alter plant phenotype, but not physiology

DOE PAGES

Henning, Jeremiah A.; Weston, David J.; Pelletier, Dale A.; ...

2016-11-01

Plant traits, such as root and leaf area, influence how plants interact with their environment and the diverse microbiota living within plants can influence plant morphology and physiology. Here, we explored how three bacterial strains isolated from the Populus root microbiome, influenced plant phenotype. Here, we chose three bacterial strains that differed in predicted metabolic capabilities, plant hormone production and metabolism, and secondary metabolite synthesis. We inoculated each bacterial strain on a single genotype of Populus trichocarpa and measured the response of plant growth related traits (root:shoot, biomass production, root and leaf growth rates) and physiological traits (chlorophyll content, netmore » photosynthesis, net photosynthesis at saturating light–A sat, and saturating CO 2–A max). Overall, we found that bacterial root endophyte infection increased root growth rate up to 184% and leaf growth rate up to 137% relative to non-inoculated control plants, evidence that plants respond to bacteria by modifying morphology. However, endophyte inoculation had no influence on total plant biomass and photosynthetic traits (net photosynthesis, chlorophyll content). In sum, bacterial inoculation did not significantly increase plant carbon fixation and biomass, but their presence altered where and how carbon was being allocated in the plant host.« less

Mechanism of Methane Transport from the Rhizosphere to the Atmosphere through Rice Plants 1

PubMed Central

Nouchi, Isamu; Mariko, Shigeru; Aoki, Kazuyuki

1990-01-01

To clarify the mechanisms of methane transport from the rhizosphere into the atmosphere through rice plants (Oryza sativa L.), the methane emission rate was measured from a shoot whose roots had been kept in a culture solution with a high methane concentration or exposed to methane gas in the gas phase by using a cylindrical chamber. No clear correlation was observed between change in the transpiration rate and that in the methane emission rate. Methane was mostly released from the culm, which is an aggregation of leaf sheaths, but not from the leaf blade. Micropores which are different from stomata were newly found at the abaxial epidermis of the leaf sheath by scanning electron microscopy. The measured methane emission rate was much higher than the calculated methane emission rate that would result from transpiration and the methane concentration in the culture solution. Rice roots could absorb methane gas in the gas phase without water uptake. These results suggest that methane dissolved in the soil water surrounding the roots diffuses into the cell-wall water of the root cells, gasifies in the root cortex, and then is mostly released through the micropores in the leaf sheaths. Images Figure 7 PMID:16667719

HrpE3 is a type III effector protein required for full virulence of Xanthomonas oryzae pv. oryzicola in rice.

PubMed

Cui, Yiping; Zou, Lifang; Zou, Huasong; Li, Yurong; Zakria, Muhammad; Chen, Gongyou

2013-09-01

Xanthomonas oryzae pv. oryzicola (Xoc) is the causal agent of bacterial leaf streak, a devastating disease in rice. Xoc uses a type III secretion (T3S) system, which is encoded by the hrp-hrc-hpa (hypersensitive response and pathogenicity, hrp-conserved and hrp-associated) genes, to inject repertoires of T3S effectors (T3Es) into plant cells. Many of the hrp-hrc-hpa genes have roles in pathogenesis, but the role of hrpE3, which shows homology to hpaE in X. campestris pv. vesicatoria (Xcv), is poorly understood. In this study, hrpE3 was shown to be transcribed independent of the hrpD operon, and its expression was dependent on a promoter within hpaB. The expression of hrpE3 was positively regulated by HrpG and HrpX, a finding probably caused by an imperfect plant-inducible promoter (PIP) box (TTCGT-N16 -TTCGA) in the hrpE3 promoter. The secretion of HrpE3 was dependent on T3S, and subcellular localization of HrpE3 was cytoplasmic and nuclear in plant cells. A mutation in hrpE3 reduced the virulence of Xoc by decreasing disease lesion length and bacterial growth in planta. Full virulence was restored to the mutant when Xoc hrpE3, but not Xcv hpaE, was expressed in trans. The differences in transcription, secretion via the T3S system and bacterial virulence in plants were attributed to N-terminal amino acid differences between Xoc HrpE3 and Xcv HpaE. Collectively, the results demonstrate that hrpE3 encodes a T3E protein which is delivered into the plant cell through the T3S system, localizes to the cytoplasm and nucleus, and is required for full virulence in rice. © 2013 BSPP AND JOHN WILEY & SONS LTD.

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, ZnCl 2 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, ZnCl 2 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. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

Exogenously Applied Plant Growth Regulators Enhance the Morpho-Physiological Growth and Yield of Rice under High Temperature.

PubMed

Fahad, Shah; Hussain, Saddam; Saud, Shah; Hassan, Shah; Ihsan, Zahid; Shah, Adnan N; Wu, Chao; Yousaf, Muhammad; Nasim, Wajid; Alharby, Hesham; Alghabari, Fahad; Huang, Jianliang

2016-01-01

A 2-year experiment was conducted to ascertain the effects of exogenously applied plant growth regulators (PGR) on rice growth and yield attributes under high day (HDT) and high night temperature (HNT). Two rice cultivars (IR-64 and Huanghuazhan) were subjected to temperature treatments in controlled growth chambers and four different combinations of ascorbic acid (Vc), alpha-tocopherol (Ve), brassinosteroids (Br), methyl jasmonates (MeJA), and triazoles (Tr) were applied. High temperature severely affected rice morphology, and also reduced leaf area, above-, and below-ground biomass, photosynthesis, and water use efficiency, while increased the leaf water potential of both rice cultivars. Grain yield and its related attributes except number of panicles, were reduced under high temperature. The HDT posed more negative effects on rice physiological attributes, while HNT was more detrimental for grain formation and yield. The Huanghuazhan performed better than IR-64 under high temperature stress with better growth and higher grain yield. Exogenous application of PGRs was helpful in alleviating the adverse effects of high temperature. Among PGR combinations, the Vc+Ve+MejA+Br was the most effective treatment for both cultivars under high temperature stress. The highest grain production by Vc+Ve+MejA+Br treated plants was due to enhanced photosynthesis, spikelet fertility and grain filling, which compensated the adversities of high temperature stress. Taken together, these results will be of worth for further understanding the adaptation and survival mechanisms of rice to high temperature and will assist in developing heat-resistant rice germplasm in future.

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

PubMed

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

2014-06-01

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

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

PubMed

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

2013-12-01

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

Comparative Proteomic Analysis of Susceptible and Resistant Rice Plants during Early Infestation by Small Brown Planthopper

PubMed Central

Dong, Yan; Fang, Xianping; Yang, Yong; Xue, Gang-Ping; Chen, Xian; Zhang, Weilin; Wang, Xuming; Yu, Chulang; Zhou, Jie; Mei, Qiong; Fang, Wang; Yan, Chengqi; Chen, Jianping

2017-01-01

The small brown planthopper (Laodelphax striatellus Fallén, Homoptera, Delphacidae-SBPH) is one of the major destructive pests of rice (Oryza sativa L.). Understanding on how rice responds to SBPH infestation will contribute to developing strategies for SBPH control. However, the response of rice plant to SBPH is poorly understood. In this study, two contrasting rice genotypes, Pf9279-4 (SBPH-resistant) and 02428 (SBPH-susceptible), were used for comparative analysis of protein profiles in the leaf sheath of rice plants in responses to SBPH infestation. One hundred and thirty-two protein spots that were differentially expressed between the resistant and susceptible rice lines were identified with significant intensity differences (≥2-fold, P < 0.05) at 0, 6, and 12 h after SBPH infestation. Protein expression profile analysis in the leaf sheath of SBPH-resistant and SBPH-susceptible rice lines after SBPH infestation showed that proteins induced by SBPH feeding were involved mainly in stress response, photosynthesis, protein metabolic process, carbohydrate metabolic process, energy metabolism, cell wall-related proteins, amino acid metabolism and transcriptional regulation. Gene expression analysis of 24 differentially expressed proteins (DEPs) showed that more than 50% DEPs were positively correlated with their mRNA levels. Analysis of some physiological indexes mainly involved in the removal of oxygen reactive species showed that the levels of superoxide dismutase (SOD) and glutathione (GSH) were considerably higher in Pf9279-4 than 02428 during SBPH infestation. The catalase (CAT) activity and hydroxyl radical inhibition were lower in Pf9279-4 than 02428. Analysis of enzyme activities indicates that Pf9279-4 rice plants defend against SBPH through the activation of the pathway of the salicylic acid (SA)-dependent systemic acquired resistance. In conclusion, this study provides some insights into the molecular networks involved on cellular and physiological

Rice crop growth monitoring using ENVISAT-1/ASAR AP mode

NASA Astrophysics Data System (ADS)

Konishi, Tomohisa; Suga, Yuzo; Omatu, Shigeru; Takeuchi, Shoji; Asonuma, Kazuyoshi

2007-10-01

Hiroshima Institute of Technology (HIT) is operating the direct down-links of microwave and optical earth observation satellite data in Japan. This study focuses on the validation for rice crop monitoring using microwave remotely sensed image data acquired by ENIVISAT-1 referring to ground truth data such as height of rice crop, vegetation cover rate and leaf area index in the test sites of Hiroshima district, the western part of Japan. ENVISAT-1/ASAR data has the capabilities for the monitoring of the rice crop growing cycle by using alternating cross polarization mode images. However, ASAR data is influenced by several parameters such as land cover structure, direction and alignment of rice crop fields in the test sites. In this study, the validation was carried out to be combined with microwave image data and ground truth data regarding rice crop fields to investigate the above parameters. Multi-temporal, multi-direction (descending and ascending) and multi-angle ASAR alternating cross polarization mode images were used to investigate during the rice crop growing cycle. On the other hand, LANDSAT-7/ETM+ data were used to detect land cover structure, direction and alignment of rice crop fields corresponding to the backscatter of ASAR. Finally, the extraction of rice planted area was attempted by using multi-temporal ASAR AP mode data such as VV/VH and HH/HV. As the result of this study, it is clear that the estimated rice planted area coincides with the existing statistical data for area of the rice crop field. In addition, HH/HV is more effective than VV/VH in the rice planted area extraction.

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

PubMed Central

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

2001-01-01

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

A transcriptome-wide study on the microRNA- and the Argonaute 1-enriched small RNA-mediated regulatory networks involved in plant leaf senescence.

PubMed

Qin, J; Ma, X; Yi, Z; Tang, Z; Meng, Y

2016-03-01

Leaf senescence is an important physiological process during the plant life cycle. However, systemic studies on the impact of microRNAs (miRNAs) on the expression of senescence-associated genes (SAGs) are lacking. Besides, whether other Argonaute 1 (AGO1)-enriched small RNAs (sRNAs) play regulatory roles in leaf senescence remains unclear. In this study, a total of 5,123 and 1,399 AGO1-enriched sRNAs, excluding miRNAs, were identified in Arabidopsis thaliana and rice (Oryza sativa), respectively. After retrieving SAGs from the Leaf Senescence Database, all of the AGO1-enriched sRNAs and the miRBase-registered miRNAs of these two plants were included for target identification. Supported by degradome signatures, 200 regulatory pairs involving 120 AGO1-enriched sRNAs and 40 SAGs, and 266 regulatory pairs involving 64 miRNAs and 42 SAGs were discovered in Arabidopsis. Moreover, 13 genes predicted to interact with some of the above-identified target genes at protein level were validated as regulated by 17 AGO1-enriched sRNAs and ten miRNAs in Arabidopsis. In rice, only one SAG was targeted by three AGO1-enriched sRNAs, and one SAG was targeted by miR395. However, five AGO1-enriched sRNAs were conserved between Arabidopsis and rice. Target genes conserved between the two plants were identified for three of the above five sRNAs, pointing to the conserved roles of these regulatory pairs in leaf senescence or other developmental procedures. Novel targets were discovered for three of the five AGO1-enriched sRNAs in rice, indicating species-specific functions of these sRNA-target pairs. These results could advance our understanding of the sRNA-involved molecular processes modulating leaf senescence. © 2015 German Botanical Society and The Royal Botanical Society of the Netherlands.

Zinc allocation and re-allocation in rice.

PubMed

Stomph, Tjeerd Jan; Jiang, Wen; Van Der Putten, Peter E L; Struik, Paul C

2014-01-01

Agronomy and breeding actively search for options to enhance cereal grain Zn density. Quantifying internal (re-)allocation of Zn as affected by soil and crop management or genotype is crucial. We present experiments supporting the development of a conceptual model of whole plant Zn allocation and re-allocation in rice. Two solution culture experiments using (70)Zn applications at different times during crop development and an experiment on within-grain distribution of Zn are reported. In addition, results from two earlier published experiments are re-analyzed and re-interpreted. A budget analysis showed that plant zinc accumulation during grain filling was larger than zinc allocation to the grains. Isotope data showed that zinc taken up during grain filling was only partly transported directly to the grains and partly allocated to the leaves. Zinc taken up during grain filling and allocated to the leaves replaced zinc re-allocated from leaves to grains. Within the grains, no major transport barrier was observed between vascular tissue and endosperm. At low tissue Zn concentrations, rice plants maintained concentrations of about 20 mg Zn kg(-1) dry matter in leaf blades and reproductive tissues, but let Zn concentrations in stems, sheath, and roots drop below this level. When plant zinc concentrations increased, Zn levels in leaf blades and reproductive tissues only showed a moderate increase while Zn levels in stems, roots, and sheaths increased much more and in that order. In rice, the major barrier to enhanced zinc allocation towards grains is between stem and reproductive tissues. Enhancing root to shoot transfer will not contribute proportionally to grain zinc enhancement.

Zinc allocation and re-allocation in rice

PubMed Central

Stomph, Tjeerd Jan; Jiang, Wen; Van Der Putten, Peter E. L.; Struik, Paul C.

2014-01-01

Aims: Agronomy and breeding actively search for options to enhance cereal grain Zn density. Quantifying internal (re-)allocation of Zn as affected by soil and crop management or genotype is crucial. We present experiments supporting the development of a conceptual model of whole plant Zn allocation and re-allocation in rice. Methods: Two solution culture experiments using 70Zn applications at different times during crop development and an experiment on within-grain distribution of Zn are reported. In addition, results from two earlier published experiments are re-analyzed and re-interpreted. Results: A budget analysis showed that plant zinc accumulation during grain filling was larger than zinc allocation to the grains. Isotope data showed that zinc taken up during grain filling was only partly transported directly to the grains and partly allocated to the leaves. Zinc taken up during grain filling and allocated to the leaves replaced zinc re-allocated from leaves to grains. Within the grains, no major transport barrier was observed between vascular tissue and endosperm. At low tissue Zn concentrations, rice plants maintained concentrations of about 20 mg Zn kg−1 dry matter in leaf blades and reproductive tissues, but let Zn concentrations in stems, sheath, and roots drop below this level. When plant zinc concentrations increased, Zn levels in leaf blades and reproductive tissues only showed a moderate increase while Zn levels in stems, roots, and sheaths increased much more and in that order. Conclusions: In rice, the major barrier to enhanced zinc allocation towards grains is between stem and reproductive tissues. Enhancing root to shoot transfer will not contribute proportionally to grain zinc enhancement. PMID:24478788

Enhanced leaf photosynthesis as a target to increase grain yield: insights from transgenic rice lines with variable Rieske FeS protein content in the cytochrome b6 /f complex.

PubMed

Yamori, Wataru; Kondo, Eri; Sugiura, Daisuke; Terashima, Ichiro; Suzuki, Yuji; Makino, Amane

2016-01-01

Although photosynthesis is the most important source for biomass and grain yield, a lack of correlation between photosynthesis and plant yield among different genotypes of various crop species has been frequently observed. Such observations contribute to the ongoing debate whether enhancing leaf photosynthesis can improve yield potential. Here, transgenic rice plants that contain variable amounts of the Rieske FeS protein in the cytochrome (cyt) b6 /f complex between 10 and 100% of wild-type levels have been used to investigate the effect of reductions of these proteins on photosynthesis, plant growth and yield. Reductions of the cyt b6 /f complex did not affect the electron transport rates through photosystem I but decreased electron transport rates through photosystem II, leading to concomitant decreases in CO2 assimilation rates. There was a strong control of plant growth and grain yield by the rate of leaf photosynthesis, leading to the conclusion that enhancing photosynthesis at the single-leaf level would be a useful target for improving crop productivity and yield both via conventional breeding and biotechnology. The data here also suggest that changing photosynthetic electron transport rates via manipulation of the cyt b6 /f complex could be a potential target for enhancing photosynthetic capacity in higher plants. © 2015 John Wiley & Sons Ltd.

Native arbuscular mycorrhizal symbiosis alters foliar bacterial community composition.

PubMed

Poosakkannu, Anbu; Nissinen, Riitta; Kytöviita, Minna-Maarit

2017-11-01

The effects of arbuscular mycorrhizal (AM) fungi on plant-associated microbes are poorly known. We tested the hypothesis that colonization by an AM fungus affects microbial species richness and microbial community composition of host plant tissues. We grew the grass, Deschampsia flexuosa in a greenhouse with or without the native AM fungus, Claroideoglomus etunicatum. We divided clonally produced tillers into two parts: one inoculated with AM fungus spores and one without AM fungus inoculation (non-mycorrhizal, NM). We characterized bacterial (16S rRNA gene) and fungal communities (internal transcribed spacer region) in surface-sterilized leaf and root plant compartments. AM fungus inoculation did not affect microbial species richness or diversity indices in leaves or roots, but the AM fungus inoculation significantly affected bacterial community composition in leaves. A total of three OTUs in leaves belonging to the phylum Firmicutes positively responded to the presence of the AM fungus in roots. Another six OTUs belonging to the Proteobacteria (Alpha, Beta, and Gamma) and Bacteroidetes were significantly more abundant in NM plants when compared to AM fungus-inoculated plants. Further, there was a significant correlation between plant dry weight and leaf microbial community compositional shift. Also, there was a significant correlation between leaf bacterial community compositional shift and foliar nitrogen content changes due to AM fungus inoculation. The results suggest that AM fungus colonization in roots has a profound effect on plant physiology that is reflected in leaf bacterial community composition.

Relationships among bulk soil physicochemical, biochemical, and microbiological parameters in an organic alfalfa-rice rotation system.

PubMed

Lopes, Ana R; Bello, Diana; Prieto-Fernández, Ángeles; Trasar-Cepeda, Carmen; Manaia, Célia M; Nunes, Olga C

2015-08-01

The microbial communities of bulk soil of rice paddy fields under an ancient organic agriculture regimen, consisting on an alfalfa-rice rotation system, were characterized. The drained soil of two adjacent paddies at different stages of the rotation was compared before rice seeding and after harvesting. The relationships among the soil microbial, physicochemical, and biochemical parameters were investigated using multivariate analyses. In the first year of rice cropping, aerobic cultivable heterotrophic populations correlated with lineages of presumably aerobic bacteria (e.g., Sphingobacteriales, Sphingomonadales). In the second year of rice cropping, the total C content correlated with presumable anaerobic bacteria (e.g., Anaerolineae). Independently of the year of rice cropping, before rice seeding, proteolytic activity correlated positively with the cultivable aerobic heterotrophic and ammonifier populations, the soil catabolic profile and with presumable aerobes (e.g., Sphingobacteriales, Rhizobiales) and anaerobes (e.g., Bacteroidales, Anaerolineae). After harvesting, strongest correlations were observed between cultivable diazotrophic populations and bacterial groups described as comprising N2 fixing members (e.g., Chloroflexi-Ellin6529, Betaproteobacteria, Alphaproteobacteria). It was demonstrated that chemical parameters and microbial functions were correlated with variations on the total bacterial community composition and structure occurring during rice cropping. A better understanding of these correlations and of their implications on soil productivity may be valid contributors for sustainable agriculture practices, based on ancient processes.

Involvement of NADPH oxidase isoforms in the production of O2- manipulated by ABA in the senescing leaves of early-senescence-leaf (esl) mutant rice (Oryza sativa).

PubMed

Li, Zhaowei; Wang, Fubiao; Zhao, Qian; Liu, Jianchao; Cheng, Fangmin

2018-01-01

In this study, the differences in reactive oxygen species (ROS) generation and abscisic acid (ABA) accumulation in senescing leaves were investigated by early-senescence-leaf (esl) mutant and its wild type, to clarify the relationship among ABA levels, ROS generation, and NADPH oxidase (Nox) in senescing leaves of rice (Oryza sativa). The temporal expression levels of OsNox isoforms in senescing leaves and their expression patterns in response to ABA treatment were determined through quantitative real-time reverse transcription PCR (qRT-PCR). Results showed that the flag leaf of the esl mutant generated more O2- concentrations and accumulated higher ABA levels than the wild-type cultivar did in the grain-filling stage. Exogenous ABA treatment induced O2- generation; however, it was depressed by diphenyleneiodonium chloride (DPI) pretreatment in the detached leaf segments. This finding suggested the involvement of NADPH oxidase in ABA-induced O2- generation. The esl mutant exhibited significantly higher expression of OsNox2, OsNox5, OsNox6, and OsNox7 in the initial of grain-filling stage, followed by sharply decrease. The transcriptional levels of OsNox1, OsNox3, and OsFR07 in the flag leaf of the esl mutant were significantly lower than those in the wild-type cultivar. The expression levels of OsNox2, OsNox5, OsNox6, and OsNox7 were significantly enhanced by exogenous ABA treatments. The enhanced expression levels of OsNox2 and OsNox6 were dependent on the duration of ABA treatment. The inducible expression levels of OsNox5 and OsNox7 were dependent on ABA concentrations. By contrast, exogenous ABA treatment severely repressed the transcripts of OsNox1, OsNox3, and OsFR07 in the detached leaf segments. Therefore, OsNox2, OsNox5, OsNox6, and OsNox7 were probably involved in the ABA-induced O2- generation in the initial stage of leaf senescence. Subsequently, other oxidases activated in deteriorating cells were associated with ROS generation and accumulation in the

Growth and production of new superior rice varieties in the shade intensity

NASA Astrophysics Data System (ADS)

Alridiwirsah; Harahap, E. M.; Akoeb, E. N.; Hanum, H.

2018-02-01

Shade intensity is one of the most important requirements for plant growth, affecting growth, development, survival, and crop productivity. This study aims to evaluate the growth and productiom of New Superior Rice Varieties In The shade Intensity. This study was conducted in Balai Pengkajian Teknologi Pertanian, Pagar Merbau, Deli Serdang, North Sumatra. The research used completely randomized design with twofactors. The shade intensity (N) were 25%, 50% and no shade intensity as a control. Whereas new superior rice varieties were V1: Inpara 2, V2: Suluttan Unsrat 2, V3: Inpari Mugibat, V4: Inpari Sidenuk, V5: Mekongga, V6: Ciherang, V7:Inpari 10, V8: Inpari 3, V9: Inpari 4, V10: Inpari 30, dan V11: Cibogo. The result indicated that new superior rice varietiesshowedsignificant effectonthe growth and productionvariablesuch as leaf area, where Inpari Sidenuk variety was the highest among the varieties. Total chorophyll, the highest was found on Inpari variety. Number of tillers and plant height where the highest was found on Ciherang variety. The shade intensity showed significant effect on leaf area, where 25% shade intensity was the highest. Total chlorophyll, the highest was found on 50% shade intensity, number of tillers, the highest was found on no shade intensity.

Persistence behavior of metamifop and its metabolite in rice ecosystem.

PubMed

Barik, Suhrid Ranjan; Ganguly, Pritam; Patra, Sandip; Dutta, Swaraj Kumar; Goon, Arnab; Bhattacharyya, Anjan

2018-02-01

A field experiment was conducted to determine the persistence of metamifop in transplanted rice crop for two seasons. Metamifop 10% EC was applied at two doses: 100 g a.i. ha -1 and 200 g a.i. ha -1 at 2-3 leaf stage of Echinochloa crusgalli. The residues of metamifop along with its major metabolite, N-(2-fluorophenyl)-2-hydroxy-N-methylpropionamide (HFMPA), were estimated in rice plant, field water and soil using Liquid Chromatography Mass Spectrometry. Limit of detection and limit of quantification of the method for both the compounds were set at 0.003 μg g -1 and 0.010 μg g -1 respectively. Metamifop showed less persistence in field water and rice plant as compared to soil samples. Presence of HFMPA was recorded in rice plant and soil. Both the compounds were found below level of quantification in harvest samples of straw, grains, husk and soil. A safe waiting period of 52 d was suggested for harvesting of rice when metamifop was applied at 100 g a.i. ha -1 (recommended dose). Copyright © 2017 Elsevier Ltd. All rights reserved.

Phenotypical, physiological and biochemical analyses provide insight into selenium-induced phytotoxicity in rice plants.

PubMed

Mostofa, Mohammad Golam; Hossain, Mohammad Anwar; Siddiqui, Md Nurealam; Fujita, Masayuki; Tran, Lam-Son

2017-07-01

The present study investigated the phenotypical, physiological and biochemical changes of rice plants exposed to high selenium (Se) concentrations to gain an insight into Se-induced phytotoxicity. Results showed that exposure of rice plants to excessive Se resulted in growth retardation and biomass reduction in connection with the decreased levels of chlorophyll, carotenoids and soluble proteins. The reduced water status and an associated increase in sugar and proline levels indicated Se-induced osmotic stress in rice plants. Measurements of Se contents in roots, leaf sheaths and leaves revealed that Se was highly accumulated in leaves followed by leaf sheaths and roots. Se also potentiated its toxicity by impairing oxidative metabolism, as evidenced by enhanced accumulation of hydrogen peroxide, superoxide and lipid peroxidation product. Se toxicity also displayed a desynchronized antioxidant system by elevating the level of glutathione and the activities of superoxide dismutase, glutathione-S-transferase and glutathione peroxidase, whereas decreasing the level of ascorbic acid and the activities of catalase, glutathione reductase and dehydroascorbate reductase. Furthermore, Se triggered methylglyoxal toxicity by inhibiting the activities of glyoxalases I and II, particularly at higher concentrations of Se. Collectively, our results suggest that excessive Se caused phytotoxic effects on rice plants by inducing chlorosis, reducing sugar, protein and antioxidant contents, and exacerbating oxidative stress and methylglyoxal toxicity. Accumulation levels of Se, proline and glutathione could be considered as efficient biomarkers to indicate degrees of Se-induced phytotoxicity in rice, and perhaps in other crops. Copyright © 2017 Elsevier Ltd. All rights reserved.

Litter Breakdown and Microbial Succession on Two Submerged Leaf Species in a Small Forested Stream

PubMed Central

Newman, Molli M.; Liles, Mark R.; Feminella, Jack W.

2015-01-01

Microbial succession during leaf breakdown was investigated in a small forested stream in west-central Georgia, USA, using multiple culture-independent techniques. Red maple (Acer rubrum) and water oak (Quercus nigra) leaf litter were incubated in situ for 128 days, and litter breakdown was quantified by ash-free dry mass (AFDM) method and microbial assemblage composition using phospholipid fatty acid analysis (PLFA), ribosomal intergenic spacer analysis (RISA), denaturing gradient gel electrophoresis (DGGE), and bar-coded next-generation sequencing of 16S rRNA gene amplicons. Leaf breakdown was faster for red maple than water oak. PLFA revealed a significant time effect on microbial lipid profiles for both leaf species. Microbial assemblages on maple contained a higher relative abundance of bacterial lipids than oak, and oak microbial assemblages contained higher relative abundance of fungal lipids than maple. RISA showed that incubation time was more important in structuring bacterial assemblages than leaf physicochemistry. DGGE profiles revealed high variability in bacterial assemblages over time, and sequencing of DGGE-resolved amplicons indicated several taxa present on degrading litter. Next-generation sequencing revealed temporal shifts in dominant taxa within the phylum Proteobacteria, whereas γ-Proteobacteria dominated pre-immersion and α- and β-Proteobacteria dominated after 1 month of instream incubation; the latter groups contain taxa that are predicted to be capable of using organic material to fuel further breakdown. Our results suggest that incubation time is more important than leaf species physicochemistry in influencing leaf litter microbial assemblage composition, and indicate the need for investigation into seasonal and temporal dynamics of leaf litter microbial assemblage succession. PMID:26098687

Effects of elevated carbon dioxide, elevated temperature, and rice growth stage on the community structure of rice root-associated bacteria.

PubMed

Okubo, Takashi; Tokida, Takeshi; Ikeda, Seishi; Bao, Zhihua; Tago, Kanako; Hayatsu, Masahito; Nakamura, Hirofumi; Sakai, Hidemitsu; Usui, Yasuhiro; Hayashi, Kentaro; Hasegawa, Toshihiro; Minamisawa, Kiwamu

2014-01-01

The effects of free-air carbon dioxide enrichment (FACE) and elevated soil and water temperature (warming) on the rice root-associated bacterial community were evaluated by clone library analysis of the 16S ribosomal RNA gene. Roots were sampled at the panicle initiation and ripening stages 41 and 92 days after transplanting (DAT), respectively. The relative abundances of the methanotrophs Methylosinus and Methylocystis were increased by warming and decreased by FACE at 92 DAT, which indicated that microbial methane (CH4) oxidation in rice roots may have been influenced by global warming. The relative abundance of Burkholderia kururiensis was increased by warming at 41 DAT and by FACE or warming at 92 DAT. The abundances of methanotrophs increased during rice growth, which was likely induced by an enhancement in the emission of CH4 from the paddy fields, suggesting that CH4 is one of the predominant factors affecting the structure of the microbial community in rice roots. Marked variations in the community structure were also observed during rice growth in other genera: Bradyrhizobium, Clostridium, and an unknown genus close to Epsilonproteobacteria were abundant at 92 DAT, whereas Achromobacter was abundant at 41 DAT. These results demonstrated that the community structures of rice root-associated bacteria were markedly affected by FACE, temperature, and the rice growth stage.

OsLYP4 and OsLYP6 play critical roles in rice defense signal transduction.

PubMed

Liu, Bing; Li, Jian-Feng; Ao, Ying; Li, Zhangqun; Liu, Jun; Feng, Dongru; Qi, Kangbiao; He, Yanming; Zeng, Liexian; Wang, Jinfa; Wang, Hong-Bin

2013-02-01

Plant innate immunity relies on successful detection of trespassing pathogens through recognizing their microbe-associated molecular patterns (MAMPs) by pattern recognition receptors (PRRs) at the cell surface. We recently reported two rice lysin motif (LysM)-containing proteins, OsLYP4 and OsLYP6, as dual functional PRRs sensing bacterial peptidoglycan (PGN) and fungal chitin. Here we further demonstrated the important roles of OsLYP4 and OsLYP6 in rice defense signaling, as silencing of either LYP impaired the defense marker gene activation induced by either bacterial pathogen Xanthomonas oryzaecola or fungal pathogen Magnaporthe oryzae. Moreover, we found that OsLYP4 and OsLYP6 could form homo- and hetero-dimers, and could interact with CEBiP, suggesting an unexpected complexity of chitin perception in rice.

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

Rice terpene synthase 24 (OsTPS24) encodes a jasmonate-responsive monoterpene synthase that produces an antibacterial γ-terpinene against rice pathogen.

PubMed

Yoshitomi, Kayo; Taniguchi, Shiduku; Tanaka, Keiichiro; Uji, Yuya; Akimitsu, Kazuya; Gomi, Kenji

2016-02-01

Rice is one of the most important crops worldwide and is widely used as a model plant for molecular studies of monocotyledonous species. The plant hormone jasmonic acid (JA) is involved in rice-pathogen interactions. In addition, volatile compounds, including terpenes, whose production is induced by JA, are known to be involved in the rice defense system. In this study, we analyzed the JA-induced terpene synthase OsTPS24 in rice. We found that OsTPS24 was localized in chloroplasts and produced a monoterpene, γ-terpinene. The amount of γ-terpinene increased after JA treatment. γ-Terpinene had significant antibacterial activity against Xanthomonas oryzae pv. oryzae (Xoo); however, it did not show significant antifungal activity against Magnaporthe oryzae. The antibacterial activity of the γ-terpinene against Xoo was caused by damage to bacterial cell membranes. These results suggest that γ-terpinene plays an important role in JA-induced resistance against Xoo, and that it functions as an antibacterial compound in rice. Copyright © 2015 Elsevier GmbH. All rights reserved.

Spatial variability of chlorophyll and nitrogen content of rice from hyperspectral imagery

NASA Astrophysics Data System (ADS)

Moharana, Shreedevi; Dutta, Subashisa

2016-12-01

Chlorophyll and nitrogen are the most essential parameters for paddy crop growth. Spectroradiometric measurements were collected at canopy level during critical growth period of rice. Chemical analysis was performed to quantify the total leaf content. By exploiting the ground based measurements, regression models were established for chlorophyll and nitrogen aimed indices with their corresponding crop growth variables. Vegetation index models were developed for mapping these parameters from Hyperion imagery in an agriculture system. It was inferred that the present Simple Ratio (SR) and Leaf Nitrogen Concentration (LNC) indices, which followed a linear and nonlinear relationship respectively, were completely different from published Tian et al. (2011). The nitrogen content varied widely from 1 to 4% and only 2 to 3% for paddy crop using present modified index models and Tian et al. (2011) respectively. The modified LNC index model performed better than the established Tian et al. (2011) model as far as estimated nitrogen content from Hyperion imagery was concerned. Furthermore, within the observed chlorophyll range obtained from the studied rice varieties grown in the rice agriculture system, the index models (LNC, OASVI, Gitelson, mSR and MTCI) performed well in the spatial distribution of rice chlorophyll content from Hyperion imagery. Spatial distribution of total chlorophyll content varied widely from 1.77 to 5.81 mg/g (LNC), 3.0 to 13 mg/g (OASVI), 0.5 to 10.43 mg/g (Gitelson), 2.18 to 10.61 mg/g (mSR) and 2.90 to 5.40 mg/g (MTCI). The spatial information of these parameters will help in proper nutrient management, yield forecasting, and will serve as inputs for crop growth and forecasting models for a precision rice agriculture system.

Molecular Mapping of High Resistance to Bacterial Leaf Spot in Lettuce PI 358001-1.

PubMed

Wang, Yunwen; Lu, Huangjun; Hu, Jinguo

2016-11-01

Lettuce (Lactuca sativa L.) is a diploid (2n = 18) with a genome size of 2,600 Mbp, and belongs to the family Compositae. Bacterial leaf spot (BLS), caused by Xanthomonas campestris pv. vitians, is a major disease of lettuce worldwide. Leaf lettuce PI 358001-1 has been characterized as an accession highly resistant to BLS and has white seed. In order to understand inheritance of the high resistance in this germplasm line, an F 3 population consisting of 163 families was developed from the cross PI 358001-1 × 'Tall Guzmaine' (a susceptible Romaine lettuce variety with black seed). The segregation ratio of reaction to disease by seedling inoculation with X. campestris pv. vitians L7 strain in the F 3 families was shown to be 32:82:48 homozygous resistant/heterozygous/homozygous susceptible, fitting to 1:2:1 (n = 162, χ 2 = 3.19, P = 0.20). The segregation ratio of seed color by checking F 2 plants was 122:41 black/white, fitting to 3:1 (n = 163, χ 2 = 0.002, P = 0.96). The results indicated that both BLS resistance and seed color were inherited as a dominant gene mode. A genetic linkage map based on 124 randomly selected F 2 plants was developed to enable molecular mapping of the BLS resistance and the seed color trait. In total, 199 markers, comprising 176 amplified fragment length polymorphisms, 16 simple-sequence repeats, 5 resistant gene candidate markers, and 2 cleaved amplified polymorphic sequences (CAPS) markers were assigned to six linkage groups. The dominant resistance gene to BLS (Xcvr) was mapped on linkage group 2 and the gene locus y for seed color was identified on linkage group 5. Due to the nature of a single gene inheritance, the high-resistance gene should be readily transferred to adapted lettuce cultivars to battle against the devastating disease of lettuce.

Expression of Chlamydophila psittaci MOMP heat-labile toxin B subunit fusion gene in transgenic rice.

PubMed

Zhang, Xiuxiang; Yuan, Ziguo; Guo, Xuejun; Li, Jingwen; Li, Zhaonan; Wang, Qingyu

2008-09-01

A DNA fragment encoding the MOMP gene of Chlamydophila psittaci was fused to the heat-labile toxin B subunit gene (LTB-MOMP) and transferred into rice callus by Agrobacterium tumefaciens-mediated transformation. The LTB-MOMP fusion gene was detected in genomic DNA from transformed rice leaves by Southern blot and RT-PCR amplification. Synthesis and assembly of the LTB-MOMP fusion protein into pentamers was detected in transformed leaf extracts by immunoblot analysis. Binding of the pentamers to intestinal epithelial cell membrane glycolipid receptors was quantified by GM1-ganglioside enzyme-linked immunosorbent assay (GM1-ELISA). The ELISA results indicated that LTB-MOMP fusion protein made up 0.0033-0.0054% of the total soluble leaf protein. Meanwhile, this suggested that the fusion protein retained both its native antigenicity and the ability to form pentamers.

Bacterial community of the rice floodwater using cultivation-independent approaches

USDA-ARS?s Scientific Manuscript database

In agricultural systems, interactions between plants and symbiotic microorganisms are important to maintaining production and profitability. In addition, the water layer and its interface with the soil play an important role in rice plant nutrition while nutrients levels in floodwaters can shape env...

Development of a new lactic acid bacterial inoculant for fresh rice straw silage.

PubMed

Kim, Jong Geun; Ham, Jun Sang; Li, Yu Wei; Park, Hyung Soo; Huh, Chul-Sung; Park, Byung-Chul

2017-07-01

Effects of newly isolated Lactobacillus plantarum on the fermentation and chemical composition of fresh rice straw silage was evaluated in this study. Lactic acid bacteria (LAB) from good crop silage were screened by growing them in MRS broth and a minimal medium with low carbohydrate content. Selected LAB (LAB 1821) were Gram-positive, rods, catalase negative, and were identified to be Lactobacillus plantarum based on their biochemical characteristics and a 16S rRNA analysis. Fresh rice straw was ensiled with two isolated LAB (1821 and 1841), two commercial inoculants (HM/F and P1132) and no additive as a control. After 2 months of storage at ambient temperature, rice straw silages treated with additives were well-preserved, the pH values and butyric and acetic acid contents were lower, and the lactic acid content and lactic/acetic acid ratio were higher than those in the control (p<0.05). Acidity (pH) was lowest, and lactic acid highest, in 1821-treated silage (p<0.05). The NH 3 -N content decreased significantly in inoculant-treated silage (p<0.05) and the NH 3 -N content in 1821-treated silage was lowest among the treatments. The dry matter (DM) content of the control silage was lower than that of fresh rice straw (p<0.05), while that of the 1841- and p1174-inoculant-treated silages was significantly higher than that of HM/F-treated silage. Microbial additives did not have any significant (p>0.05) effect on acid detergent fiber or neutral detergent fiber contents. Crude protein (CP) content and in vitro DM digestibility (IVDMD) increased after inoculation of LAB 1821 (p<0.05). LAB 1821 increased the CP, IVDMD, lactic acid content and ratio of lactic acid to acetic acid in rice straw silage and decreased the pH, acetic acid, NH 3 -N, and butyric acid contents. Therefore, adding LAB 1821 improved the fermentation quality and feed value of rice straw silage.

2D-DIGE-based proteome expression changes in leaves of rice seedlings exposed to low-level gamma radiation at Iitate village, Fukushima

PubMed Central

Hayashi, Gohei; Moro, Carlo F; Rohila, Jai Singh; Shibato, Junko; Kubo, Akihiro; Imanaka, Tetsuji; Kimura, Shinzo; Ozawa, Shoji; Fukutani, Satoshi; Endo, Satoru; Ichikawa, Katsuki; Agrawal, Ganesh Kumar; Shioda, Seiji; Hori, Motohide; Fukumoto, Manabu; Rakwal, Randeep

2015-01-01

The present study continues our previous research on investigating the biological effects of low-level gamma radiation in rice at the heavily contaminated Iitate village in Fukushima, by extending the experiments to unraveling the leaf proteome. 14-days-old plants of Japonica rice (Oryza sativa L. cv. Nipponbare) were subjected to gamma radiation level of upto 4 µSv/h, for 72 h. Following exposure, leaf samples were taken from the around 190 µSv/3 d exposed seedling and total proteins were extracted. The gamma irradiated leaf and control leaf (harvested at the start of the experiment) protein lysates were used in a 2-D differential gel electrophoresis (2D-DIGE) experiment using CyDye labeling in order to asses which spots were differentially represented, a novelty of the study. 2D-DIGE analysis revealed 91 spots with significantly different expression between samples (60 positive, 31 negative). MALDI-TOF and TOF/TOF mass spectrometry analyses revealed those as comprising of 59 different proteins (50 up-accumulated, 9 down-accumulated). The identified proteins were subdivided into 10 categories, according to their biological function, which indicated that the majority of the differentially expressed proteins consisted of the general (non-energy) metabolism and stress response categories. Proteome-wide data point to some effects of low-level gamma radiation exposure on the metabolism of rice leaves. PMID:26451896

Rice Crop Monitoring Using Microwave and Optical Remotely Sensed Image Data

NASA Astrophysics Data System (ADS)

Suga, Y.; Konishi, T.; Takeuchi, S.; Kitano, Y.; Ito, S.

Hiroshima Institute of Technology HIT is operating the direct down-links of microwave and optical satellite data in Japan This study focuses on the validation for rice crop monitoring using microwave and optical remotely sensed image data acquired by satellites referring to ground truth data such as height of crop ratio of crop vegetation cover and leaf area index in the test sites of Japan ENVISAT-1 ASAR data has a capability to capture regularly and to monitor during the rice growing cycle by alternating cross polarization mode images However ASAR data is influenced by several parameters such as landcover structure direction and alignment of rice crop fields in the test sites In this study the validation was carried out combined with microwave and optical satellite image data and ground truth data regarding rice crop fields to investigate the above parameters Multi-temporal multi-direction descending and ascending and multi-angle ASAR alternating cross polarization mode images were used to investigate rice crop growing cycle LANDSAT data were used to detect landcover structure direction and alignment of rice crop fields corresponding to the backscatter of ASAR As the result of this study it was indicated that rice crop growth can be precisely monitored using multiple remotely sensed data and ground truth data considering with spatial spectral temporal and radiometric resolutions

Microbial decomposition is highly sensitive to leaf litter emersion in a permanent temperate stream.

PubMed

Mora-Gómez, Juanita; Duarte, Sofia; Cássio, Fernanda; Pascoal, Cláudia; Romaní, Anna M

2018-04-15

Drought frequency and intensity in some temperate regions are forecasted to increase under the ongoing global change, which might expose permanent streams to intermittence and have severe repercussions on stream communities and ecosystem processes. In this study, we investigated the effect of drought duration on microbial decomposition of Populus nigra leaf litter in a temperate permanent stream (Oliveira, NW Portugal). Specifically, we measured the response of the structural (assemblage composition, bacterial and fungal biomass) and functional (leaf litter decomposition, extracellular enzyme activities (EEA), and fungal sporulation) parameters of fungal and bacterial communities on leaf litter exposed to emersion during different time periods (7, 14 and 21d). Emersion time affected microbial assemblages and litter decomposition, but the response differed among variables. Leaf decomposition rates and the activity of β-glucosidase, cellobiohydrolase and phosphatase were gradually reduced with increasing emersion time, while β-xylosidase reduction was similar when emersion last for 7 or more days, and the phenol oxidase reduction was similar at 14 and 21days of leaf emersion. Microbial biomass and fungal sporulation were reduced after 21days of emersion. The structure of microbial assemblages was affected by the duration of the emersion period. The shifts in fungal assemblages were correlated with a decreased microbial capacity to degrade lignin and hemicellulose in leaf litter exposed to emersion. Additionally, some resilience was observed in leaf litter mass loss, bacterial biomass, some enzyme activities and structure of fungal assemblages. Our study shows that drought can strongly alter structural and functional aspects of microbial decomposers. Therefore, the exposure of leaf litter to increasing emersion periods in temperate streams is expected to affect decomposer communities and overall decomposition of plant material by decelerating carbon cycling in

The HD-GYP Domain Protein RpfG of Xanthomonas oryzae pv. oryzicola Regulates Synthesis of Extracellular Polysaccharides that Contribute to Biofilm Formation and Virulence on Rice

PubMed Central

Zhang, Yuanbao; Wei, Chao; Jiang, Wendi; Wang, Lei; Li, Churui; Wang, Yunyue; Dow, John Maxwell; Sun, Wenxian

2013-01-01

Bacterial leaf streak caused by Xanthomonas oryzae pv. oryzicola (Xoc) is one of the most important diseases in rice. However, little is known about the pathogenicity mechanisms of Xoc. Here we have investigated the function of three HD-GYP domain regulatory proteins in biofilm formation, the synthesis of virulence factors and virulence of Xoc. Deletion of rpfG resulted in altered production of extracellular polysaccharides (EPS), abolished virulence on rice and enhanced biofilm formation, but had little effect on the secretion of proteases and motility. In contrast, mutational analysis showed that the other two HD-GYP domain proteins had no effect on virulence factor synthesis and tested phenotypes. Mutation of rpfG led to up-regulation of the type III secretion system and altered expression of three putative glycosyltransferase genes gumD, pgaC and xagB, which are part of operons directing the synthesis of different extracellular polysaccharides. The pgaABCD and xagABCD operons were greatly up-regulated in the Xoc ΔrpfG mutant, whereas the expression of the gum genes was unaltered or slightly enhanced. The elevated biofilm formation of the Xoc ΔrpfG mutant was dramatically reduced upon deletion of gumD, xagA and xagB, but not when pgaA and pgaC were deleted. Interestingly, only the ΔgumD mutant, among these single gene mutants, exhibits multiple phenotype alterations including reduced biofilm and EPS production and attenuated virulence on rice. These data indicate that RpfG is a global regulator that controls biofilm formation, EPS production and bacterial virulence in Xoc and that both gumD- and xagB-dependent EPS contribute to biofilm formation under different conditions. PMID:23544067

MicroRNA166 Modulates Cadmium Tolerance and Accumulation in Rice.

PubMed

Ding, Yanfei; Gong, Shaohua; Wang, Yi; Wang, Feijuan; Bao, Hexigeduleng; Sun, Junwei; Cai, Chong; Yi, Keke; Chen, Zhixiang; Zhu, Cheng

2018-06-20

MicroRNAs (miRNAs) are 20- to 24-nucleotide small non-coding RNAs that regulate gene expression in eukaryotic organisms. Several plant miRNAs, such as miR166, have vital roles in plant growth, development and responses to environmental stresses. One such environmental stress encountered by crop plants is exposure to cadmium (Cd), an element highly toxic to most organisms, including humans and plants. In this study, we analyzed the role of miR166 in Cd accumulation and tolerance in rice (Oryza sativa). The expression levels of miR166 in both root and leaf tissues were significantly higher in the reproductive stage than in the seedling stage in rice. The expression of miR166 in the roots of rice seedlings was reduced after Cd treatment. Overexpression of miR166 in rice improved Cd tolerance, a result associated with the reduction of Cd-induced oxidative stress in transgenic rice plants. Furthermore, overexpression of miR166 reduced both Cd translocation from roots to shoots and Cd accumulation in the grains. miR166 targets genes encoding the class-III homeodomain-leucine zipper (HD-Zip) family proteins in plants. In rice, HOMEODOMAIN CONTAINING PROTEIN 4 (OsHB4) gene (Os03g43930), which encodes an HD-Zip protein, was up-regulated by Cd treatment but down-regulated by overexpression of miR166 in transgenic rice plants. Overexpression of OsHB4 increased Cd sensitivity and Cd accumulation in the leaves and grains of transgenic rice plants. By contrast, silencing OsHB4 by RNA interference enhanced Cd tolerance in transgenic rice plants. These results indicate a critical role for miR166 in Cd accumulation and tolerance through regulation of its target gene, OsHB4, in rice. {copyright, serif} 2018 American Society of Plant Biologists. All rights reserved.

Novel components of leaf bacterial communities of field-grown tomato plants and their potential for plant growth promotion and biocontrol of tomato diseases.

PubMed

Romero, Fernando M; Marina, María; Pieckenstain, Fernando L

2016-04-01

This work aimed to characterize potentially endophytic culturable bacteria from leaves of cultivated tomato and analyze their potential for growth promotion and biocontrol of diseases caused by Botrytis cinerea and Pseudomonas syringae. Bacteria were obtained from inner tissues of surface-disinfected tomato leaves of field-grown plants. Analysis of 16S rRNA gene sequences identified bacterial isolates related to Exiguobacterium aurantiacum (isolates BT3 and MT8), Exiguobacterium spp. (isolate GT4), Staphylococcus xylosus (isolate BT5), Pantoea eucalypti (isolate NT6), Bacillus methylotrophicus (isolate MT3), Pseudomonas veronii (isolates BT4 and NT2), Pseudomonas rhodesiae (isolate BT2) and Pseudomonas cichorii (isolate NT3). After seed inoculation, BT2, BT4, MT3, MT8, NT2 and NT6 were re-isolated from leaf extracts. NT2, BT2, MT3 and NT6 inhibited growth of Botrytis cinerea and Pseudomonas syringae pv. tomato in vitro, produced antimicrobial compounds and reduced leaf damage caused by B. cinerea. Some of these isolates also promoted growth of tomato plants, produced siderophores, the auxin indole-3-acetic and solubilized inorganic phosphate. Thus, bacterial communities of leaves from field-grown tomato plants were found to harbor potentially endophytic culturable beneficial bacteria capable of antagonizing pathogenic microorganisms and promoting plant growth, which could be used as biological control agents and biofertilizers/biostimulators for promotion of tomato plant growth. Copyright © 2015 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

A Rice PECTATE LYASE-LIKE Gene Is Required for Plant Growth and Leaf Senescence.

PubMed

Leng, Yujia; Yang, Yaolong; Ren, Deyong; Huang, Lichao; Dai, Liping; Wang, Yuqiong; Chen, Long; Tu, Zhengjun; Gao, Yihong; Li, Xueyong; Zhu, Li; Hu, Jiang; Zhang, Guangheng; Gao, Zhenyu; Guo, Longbiao; Kong, Zhaosheng; Lin, Yongjun; Qian, Qian; Zeng, Dali

2017-06-01

To better understand the molecular mechanisms behind plant growth and leaf senescence in monocot plants, we identified a mutant exhibiting dwarfism and an early-senescence leaf phenotype, termed dwarf and early-senescence leaf1 ( del1 ). Histological analysis showed that the abnormal growth was caused by a reduction in cell number. Further investigation revealed that the decline in cell number in del1 was affected by the cell cycle. Physiological analysis, transmission electron microscopy, and TUNEL assays showed that leaf senescence was triggered by the accumulation of reactive oxygen species. The DEL1 gene was cloned using a map-based approach. It was shown to encode a pectate lyase (PEL) precursor that contains a PelC domain. DEL1 contains all the conserved residues of PEL and has strong similarity with plant PelC. DEL1 is expressed in all tissues but predominantly in elongating tissues. Functional analysis revealed that mutation of DEL1 decreased the total PEL enzymatic activity, increased the degree of methylesterified homogalacturonan, and altered the cell wall composition and structure. In addition, transcriptome assay revealed that a set of cell wall function- and senescence-related gene expression was altered in del1 plants. Our research indicates that DEL1 is involved in both the maintenance of normal cell division and the induction of leaf senescence. These findings reveal a new molecular mechanism for plant growth and leaf senescence mediated by PECTATE LYASE-LIKE genes. © 2017 American Society of Plant Biologists. All Rights Reserved.

Inhibitory activities of Moringa oleifera leaf extract against α-glucosidase enzyme in vitro

NASA Astrophysics Data System (ADS)

Natsir, H.; Wahab, A. W.; Laga, A.; Arif, A. R.

2018-03-01

Alpha-glucosidase is a key enzyme in the final process of breaking carbohydrates into glucose. Inhibition of α-glucosidase affected more absorption of glucose, so it can reduce hyperglycemia condition. The aims of this study is to determine the effectiveness of inhibition wet and dried Moringa oleifera leaf extract through α-glucosidase activity in vitro. The effectiveness study of inhibition on the activity of α-glucosidase enzyme obtained from white glutinous rice (Oryza sativa glutinosa) was carried out using wet and dried kelor leaf extract of 13% (w/v) with 10 mM α-D-glucopyranoside (PNPG) substrate. A positive control used 1% acarbose and substrate without addition of extract was a negative control. Inhibitory activity was measured using spectrophotometers at a wavelength of 400 nm. The result showed that the inhibition activity against α-glucosidase enzyme of dried leaf extract, wet leaf extract and acarbose was 81,39%, 83,94%, and 95,4%, respectively on pH 7,0. The effectiveness inhibition of the wet Moringa leaf extract was greater than the dried leaf extract. The findings suggest that M. oleifera leaf has the potential to be developed as an alternative food therapy for diabetics.

Diversity analysis of lactic acid bacteria in takju, Korean rice wine.

PubMed

Jin, Jianbo; Kim, So-Young; Jin, Qing; Eom, Hyun-Ju; Han, Nam Soo

2008-10-01

To investigate the lactic acid bacterial population in Korean traditional rice wines, biotyping was performed using cell morphology and whole-cell protein pattern analysis by SDSPAGE, and then the isolates were identified by 16S rRNA sequencing analysis. Based on the morphological characteristics, 103 LAB isolates were detected in wine samples, characterized by whole-cell protein pattern analysis, and they were then divided into 18 patterns. By gene sequencing of 16S rRNA, the isolates were identified as Lactobacillus paracasei, Lb. arizonensis, Lb. plantarum, Lb. harbinensis, Lb. parabuchneri, Lb. brevis, and Lb. hilgardii when listed by their frequency of occurrence. It was found that the difference in bacterial diversity between rice and grape wines depends on the raw materials, especially the composition of starch and glucose.

Marker-free transgenic rice expressing the vegetative insecticidal protein (Vip) of Bacillus thuringiensis shows broad insecticidal properties.

PubMed

Pradhan, Subrata; Chakraborty, Anirban; Sikdar, Narattam; Chakraborty, Saikat; Bhattacharyya, Jagannath; Mitra, Joy; Manna, Anulina; Dutta Gupta, Snehasish; Sen, Soumitra Kumar

2016-10-01

Genetically engineered rice lines with broad insecticidal properties against major lepidopteran pests were generated using a synthetic, truncated form of vegetative insecticidal protein (Syn vip3BR) from Bacillus thuringiensis. The selectable marker gene and the redundant transgene(s) were eliminated through Cre/ lox mediated recombination and genetic segregation to make consumer friendly Bt -rice. For sustainable resistance against lepidopteran insect pests, chloroplast targeted synthetic version of bioactive core component of a vegetative insecticidal protein (Syn vip3BR) of Bacillus thuringiensis was expressed in rice under the control of green-tissue specific ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit gene promoter. The transgenic plants (in Oryza sativa indica Swarna cultivar) showed high insect mortality rate in vitro against major rice pests, yellow stem borer (Scirpophaga incertulas), rice leaf folder (Cnaphalocrocis medinalis) and rice horn caterpillar (Melanitis leda ismene) in T1 generation, indicating insecticidal potency of Syn vip3BR. Under field conditions, the T1 plants showed considerable resistance against leaf folders and stem borers. The expression cassette (vip-lox-hpt-lox) as well as another vector with chimeric cre recombinase gene under constitutive rice ubiquitin1 gene promoter was designed for the elimination of selectable marker hygromycin phosphotransferase (hptII) gene. Crossing experiments were performed between T1 plants with single insertion site of vip-lox-hpt-lox T-DNA and one T1 plant with moderate expression of cre recombinase with linked bialaphos resistance (syn bar) gene. Marker gene excision was achieved in hybrids with up to 41.18 % recombination efficiency. Insect resistant transgenic lines, devoid of selectable marker and redundant transgene(s) (hptII + cre-syn bar), were established in subsequent generation through genetic segregation.

Lysin Motif–Containing Proteins LYP4 and LYP6 Play Dual Roles in Peptidoglycan and Chitin Perception in Rice Innate Immunity[W][OA

PubMed Central

Liu, Bing; Li, Jian-Feng; Ao, Ying; Qu, Jinwang; Li, Zhangqun; Su, Jianbin; Zhang, Yang; Liu, Jun; Feng, Dongru; Qi, Kangbiao; He, Yanming; Wang, Jinfa; Wang, Hong-Bin

2012-01-01

Plant innate immunity relies on successful detection of microbe-associated molecular patterns (MAMPs) of invading microbes via pattern recognition receptors (PRRs) at the plant cell surface. Here, we report two homologous rice (Oryza sativa) lysin motif–containing proteins, LYP4 and LYP6, as dual functional PRRs sensing bacterial peptidoglycan (PGN) and fungal chitin. Live cell imaging and microsomal fractionation consistently revealed the plasma membrane localization of these proteins in rice cells. Transcription of these two genes could be induced rapidly upon exposure to bacterial pathogens or diverse MAMPs. Both proteins selectively bound PGN and chitin but not lipopolysaccharide (LPS) in vitro. Accordingly, silencing of either LYP specifically impaired PGN- or chitin- but not LPS-induced defense responses in rice, including reactive oxygen species generation, defense gene activation, and callose deposition, leading to compromised resistance against bacterial pathogen Xanthomonas oryzae and fungal pathogen Magnaporthe oryzae. Interestingly, pretreatment with excess PGN dramatically attenuated the alkalinization response of rice cells to chitin but not to flagellin; vice versa, pretreatment with chitin attenuated the response to PGN, suggesting that PGN and chitin engage overlapping perception components in rice. Collectively, our data support the notion that LYP4 and LYP6 are promiscuous PRRs for PGN and chitin in rice innate immunity. PMID:22872757

Determining the migration duration of rice leaf folder (Cnaphalocrocis medinalis (Guenée)) moths using a trajectory analytical approach

PubMed Central

Wang, Feng-Ying; Yang, Fan; Lu, Ming-Hong; Luo, Shan-Yu; Zhai, Bao-Ping; Lim, Ka-Sing; McInerney, Caitríona E.; Hu, Gao

2017-01-01

Many moths finish their long distance migration after consecutive nights, but little is known about migration duration and distance. This information is key to predicting migration pathways and understanding their evolution. Tethered flight experiments have shown that ovarian development of rice leaf folder (Cnaphalocrocis medinalis [Guenée]) moths was accelerated and synchronized by flight in the first three nights, whereby most females were then matured for mating and reproduction. Thus, it was supposed that this moth might fly three nights to complete its migration. To test this hypothesis, 9 year’s field data for C. medinalis was collected from Nanning, Guangxi Autonomous Region in China. Forward trajectories indicated that most moths arrived at suitable breeding areas after three nights’ flight. Thus, for C. medinalis this migration duration and distance was a reasonable adaptation to the geographic distribution of suitable habitat. The development of female moth ovaries after three consecutive night flights appears to be a well-balanced survival strategy for this species to strike between migration and reproduction benefits. Hence, an optimum solution of migration-reproduction trade-offs in energy allocation evolved in response to the natural selection on migration route and physiological traits. PMID:28051132

Relationships between phyllosphere bacterial communities and plant functional traits in a neotropical forest

PubMed Central

Kembel, Steven W.; O’Connor, Timothy K.; Arnold, Holly K.; Hubbell, Stephen P.; Wright, S. Joseph; Green, Jessica L.

2014-01-01

The phyllosphere—the aerial surfaces of plants, including leaves—is a ubiquitous global habitat that harbors diverse bacterial communities. Phyllosphere bacterial communities have the potential to influence plant biogeography and ecosystem function through their influence on the fitness and function of their hosts, but the host attributes that drive community assembly in the phyllosphere are poorly understood. In this study we used high-throughput sequencing to quantify bacterial community structure on the leaves of 57 tree species in a neotropical forest in Panama. We tested for relationships between bacterial communities on tree leaves and the functional traits, taxonomy, and phylogeny of their plant hosts. Bacterial communities on tropical tree leaves were diverse; leaves from individual trees were host to more than 400 bacterial taxa. Bacterial communities in the phyllosphere were dominated by a core microbiome of taxa including Actinobacteria, Alpha-, Beta-, and Gammaproteobacteria, and Sphingobacteria. Host attributes including plant taxonomic identity, phylogeny, growth and mortality rates, wood density, leaf mass per area, and leaf nitrogen and phosphorous concentrations were correlated with bacterial community structure on leaves. The relative abundances of several bacterial taxa were correlated with suites of host plant traits related to major axes of plant trait variation, including the leaf economics spectrum and the wood density–growth/mortality tradeoff. These correlations between phyllosphere bacterial diversity and host growth, mortality, and function suggest that incorporating information on plant–microbe associations will improve our ability to understand plant functional biogeography and the drivers of variation in plant and ecosystem function. PMID:25225376

Comparative proteomic analysis reveals alterations in development and photosynthesis-related proteins in diploid and triploid rice.

PubMed

Wang, Shuzhen; Chen, Wenyue; Yang, Changdeng; Yao, Jian; Xiao, Wenfei; Xin, Ya; Qiu, Jieren; Hu, Weimin; Yao, Haigen; Ying, Wu; Fu, Yaping; Tong, Jianxin; Chen, Zhongzhong; Ruan, Songlin; Ma, Huasheng

2016-09-13

Polyploidy has pivotal influences on rice (Oryza sativa L.) morphology and physiology, and is very important for understanding rice domestication and improving agricultural traits. Diploid (DP) and triploid (TP) rice shows differences in morphological parameters, such as plant height, leaf length, leaf width and the physiological index of chlorophyll content. However, the underlying mechanisms determining these morphological differences are remain to be defined. To better understand the proteomic changes between DP and TP, tandem mass tags (TMT) mass spectrometry (MS)/MS was used to detect the significant changes to protein expression between DP and TP. Results indicated that both photosynthesis and metabolic pathways were highly significantly associated with proteomic alteration between DP and TP based on biological process and pathway enrichment analysis, and 13 higher abundance chloroplast proteins involving in these two pathways were identified in TP. Quantitative real-time PCR analysis demonstrated that 5 of the 13 chloroplast proteins ATPF, PSAA, PSAB, PSBB and RBL in TP were higher abundance compared with those in DP. This study integrates morphology, physiology and proteomic profiling alteration of DP and TP to address their underlying different molecular mechanisms. Our finding revealed that ATPF, PSAA, PSAB, PSBB and RBL can induce considerable expression changes in TP and may affect the development and growth of rice through photosynthesis and metabolic pathways.

A transcription activator-like effector from Xanthomonas oryzae pv. oryzicola elicits dose-dependent resistance in rice.

PubMed

Hummel, Aaron W; Wilkins, Katherine E; Wang, Li; Cernadas, R Andres; Bogdanove, Adam J

2017-01-01

Xanthomonas spp. reduce crop yields and quality worldwide. During infection of their plant hosts, many strains secrete transcription activator-like (TAL) effectors, which enter the host cell nucleus and activate specific corresponding host genes at effector binding elements (EBEs) in the promoter. TAL effectors may contribute to disease by activating the expression of susceptibility genes or trigger resistance associated with the hypersensitive reaction (HR) by activating an executor resistance (R) gene. The rice bacterial leaf streak pathogen X. oryzae pv. oryzicola (Xoc) is known to suppress host resistance, and no host R gene has been identified against it, despite considerable effort. To further investigate Xoc suppression of host resistance, we conducted a screen of effectors from BLS256 and identified Tal2a as an HR elicitor in rice when delivered heterologously by a strain of the closely related rice bacterial blight pathogen X. oryzae pv. oryzae (Xoo) or by the soybean pathogen X. axonopodis pv. glycines. The HR required the Tal2a activation domain, suggesting an executor R gene. Tal2a activity was differentially distributed among geographically diverse Xoc isolates, being largely conserved among Asian isolates. We identified four genes induced by Tal2a in next-generation RNA sequencing experiments and confirmed them using quantitative real-time reverse transcription-polymerase chain reaction (qPCR). However, neither individual nor collective activation of these genes by designer TAL effectors resulted in HR. A tal2a knockout mutant of BLS256 showed virulence comparable with the wild-type, but plasmid-based overexpression of tal2a at different levels in the wild-type reduced virulence in a directly corresponding way. Overall, the results reveal that host resistance suppression by Xoc plays a critical role in pathogenesis. Further, the dose-dependent avirulence activity of Tal2a and the apparent lack of a single canonical target that accounts for HR point to

Dark septate endophyte decreases stress on rice plants.

PubMed

Santos, Silvana Gomes Dos; Silva, Paula Renata Alves da; Garcia, Andres Calderin; Zilli, Jerri Édson; Berbara, Ricardo Luis Louro

Abiotic stress is one of the major limiting factors for plant development and productivity, which makes it important to identify microorganisms capable of increasing plant tolerance to stress. Dark septate endophytes can be symbionts of plants. In the present study, we evaluated the ability of dark septate endophytes isolates to reduce the effects of water stress in the rice varieties Nipponbare and Piauí. The experiments were performed under gnotobiotic conditions, and the water stress was induced with PEG. Four dark septate endophytes were isolated from the roots of wild rice (Oryza glumaepatula) collected from the Brazilian Amazon. Plant height as well as shoot and root fresh and dry matter were measured. Leaf protein concentrations and antioxidant enzyme activity were also estimated. The dark septate endophytes were grown in vitro in Petri dishes containing culture medium; they exhibited different levels of tolerance to salinity and water stress. The two rice varieties tested responded differently to inoculation with dark septate endophytes. Endophytes promoted rice plant growth both in the presence and in the absence of a water deficit. Decreased oxidative stress in plants in response to inoculation was observed in nearly all inoculated treatments, as indicated by the decrease in antioxidant enzyme activity. Dark septate endophytes fungi were shown to increase the tolerance of rice plants to stress caused by water deficiency. Copyright © 2016 Sociedade Brasileira de Microbiologia. Published by Elsevier Editora Ltda. All rights reserved.

Structure and function of the methanogenic microbial communities in Uruguayan soils shifted between pasture and irrigated rice fields.

PubMed

Scavino, Ana Fernandez; Ji, Yang; Pump, Judith; Klose, Melanie; Claus, Peter; Conrad, Ralf

2013-09-01

Irrigated rice fields in Uruguay are temporarily established on soils used as cattle pastures. Typically, 4 years of cattle pasture are alternated with 2 years of irrigated rice cultivation. Thus, oxic upland conditions are rotated with seasonally anoxic wetland conditions. Only the latter conditions are suitable for the production of CH4 from anaerobic degradation of organic matter. We studied soil from a permanent pasture as well as soils from different years of the pasture-rice rotation hypothesizing that activity and structure of the bacterial and archaeal communities involved in production of CH4 change systematically with the duration of either oxic or anoxic conditions. Soil samples were taken from drained fields, air-dried and used for the experiments. Indeed, methanogenic archaeal gene copy numbers (16S rRNA, mcrA) were lower in soil from the permanent pasture than from the pasture-rice alternation fields, but within the latter, there was no significant difference. Methane production started to accumulate after 16 days and 7 days of anoxic incubation in soil from the permanent pasture and the pasture-rice alternation fields respectively. Then, CH4 production rates were slightly higher in the soils used for pasture than for rice production. Analysis of δ(13) C in CH4, CO2 and acetate in the presence and absence of methyl fluoride, an inhibitor of aceticlastic methanogenesis, indicated that CH4 was mainly (58-75%) produced from acetate, except in the permanent pasture soil (42%). Terminal restriction fragment length polymorphism (T-RFLP) of archaeal 16S rRNA genes showed no difference among the soils from the pasture-rice alternation fields with Methanocellaceae and Methanosarcinaceae as the main groups of methanogens, but in the permanent pasture soil, Methanocellaceae were relatively less abundant. T-RFLP analysis of bacterial 16S rRNA genes allowed the distinction of permanent pasture and fields from the pasture-rice rotation, but nevertheless with a

Bacterial, archaeal, and fungal community responses to acid mine drainage-laden pollution in a rice paddy soil ecosystem.

PubMed

Wang, Han; Zeng, Yufei; Guo, Chuling; Bao, Yanping; Lu, Guining; Reinfelder, John R; Dang, Zhi

2018-03-01

Lacking sufficient clean water, the paddy soils along the Hengshi River have suffered from long-term acid mine drainage (AMD) contamination. The impacted cropland is too heavily contaminated to grow food safely. The microbial communities inhabiting the environment play pivotal roles in the crop growth, health, and ecological services. In this study, the bacterial, archaeal, and fungal communities in the impacted paddy soil were examined using high-throughput Illumina MiSeq sequencing. The results showed that AMD irrigation considerably enriched the bacterial phylum Acidobacteria and the archaeal phylum Crenarchaeota, while the fungal community was more stable. The abundances of Acidobacteria and Crenarchaeota were significantly positively correlated with the AMD-related environmental factors of pH and heavy metals (Cu, Pb, and Zn). In the most contaminated samples, communities were dominated by the bacteria Candidatus Solibacter and Candidatus Koribacter from the Acidobacteria family. Functional gene profile analysis demonstrated that the energy metabolic processes of the microbial communities, especially C/N related pathways, have adjusted and are well-adapted to tolerating AMD contamination. The present study described the structural and functional differentiation of microbial communities in the rice paddy soil under AMD irrigation. The results are useful for the development of bioremediation strategies using native microbes in the cleanup and biorestoration of AMD-contaminated agriculture soil. Copyright © 2017 Elsevier B.V. All rights reserved.

Bacterial Diversity Analysis during the Fermentation Processing of Traditional Chinese Yellow Rice Wine Revealed by 16S rDNA 454 Pyrosequencing.

PubMed

Fang, Ruo-si; Dong, Ya-chen; Chen, Feng; Chen, Qi-he

2015-10-01

Rice wine is a traditional Chinese fermented alcohol drink. Spontaneous fermentation with the use of the Chinese starter and wheat Qu lead to the growth of various microorganisms during the complete brewing process. It's of great importance to fully understand the composition of bacteria diversity in rice wine in order to improve the quality and solve safety problems. In this study, a more comprehensive bacterial description was shown with the use of bacteria diversity analysis, which enabled us to have a better understanding. Rarefaction, rank abundance, alpha Diversity, beta diversity and principal coordinates analysis simplified their complex bacteria components and provide us theoretical foundation for further investigation. It has been found bacteria diversity is more abundant at mid-term and later stage of brewing process. Bacteria community analysis reveals there is a potential safety hazard existing in the fermentation, since most of the sequence reads are assigned to Enterobacter (7900 at most) and Pantoea (7336 at most), followed by Staphylococcus (2796 at most) and Pseudomonas (1681 at most). Lactic acid bacteria are rare throughout the fermentation process which is not in accordance with other reports. This work may offer us an opportunity to investigate micro ecological fermentation system in food industry. © 2015 Institute of Food Technologists®

Rice MADS6 Interacts with the Floral Homeotic Genes SUPERWOMAN1, MADS3, MADS58, MADS13, and DROOPING LEAF in Specifying Floral Organ Identities and Meristem Fate[C][W][OA

PubMed Central

Li, Haifeng; Liang, Wanqi; Hu, Yun; Zhu, Lu; Yin, Changsong; Xu, Jie; Dreni, Ludovico; Kater, Martin M.; Zhang, Dabing

2011-01-01

AGAMOUS-LIKE6 (AGL6) genes play essential roles in flower development, but whether and how they work with floral organ identity genes remain less understood. Here, we describe interactions of the rice (Oryza sativa) AGL6 gene MADS6 with other rice floral homeotic genes in flower development. Genetic analyses revealed that MADS6 specifies the identity of the three inner whorls and floral meristem determinacy redundantly with SUPERWOMAN1/MADS16 (B-gene) or MADS3 (C-gene). MADS6 was shown to define carpel/ovule development and floral determinacy by interacting with MADS13 (D-gene) and control the palea and floral meristem identities together with the YABBY gene DROOPING LEAF. Expression analyses revealed that the transcript levels of six B-, C-, and E-class genes were reduced in mads6-1 at the early flower developmental stage, suggesting that MADS6 is a key regulator of early flower development. Moreover, MADS6 can directly bind to a putative regulatory motif on MADS58 (C-gene), and mads6-1 mads58 displayed phenotypes similar to that of mads6-1. These results suggest that MADS6 is a key player in specifying flower development via interacting with other floral homeotic genes in rice, thus providing new insights into the mechanism by which flower development is controlled. PMID:21784949

Anti-fouling properties of microstructured surfaces bio-inspired by rice leaves and butterfly wings.

PubMed

Bixler, Gregory D; Theiss, Andrew; Bhushan, Bharat; Lee, Stephen C

2014-04-01

Material scientists often look to biology for new engineering solutions to materials science problems. For example, unique surface characteristics of rice leaves and butterfly wings combine the shark skin (antifouling) and lotus leaf (self-cleaning) effects, producing the so-called rice and butterfly wing effect. In this paper, we study antifouling properties of four microstructured surfaces inspired by rice leaves and fabricated with photolithography and hot embossing techniques. Anti-biofouling effectiveness is determined with bioassays using Escherichia coli whilst inorganic fouling with simulated dirt particles. Antifouling data are presented to understand the role of surface geometrical features resistance to fouling. Conceptual modeling provides design guidance when developing novel antifouling surfaces for applications in the medical, marine, and industrial fields. Copyright © 2013 Elsevier Inc. All rights reserved.

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

PubMed Central

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

2016-01-01

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

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

PubMed

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

2016-05-02

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

Potential of Bacillus cereus strain RS87 for partial replacement of chemical fertilisers in the production of Thai rice cultivars.

PubMed

Jetiyanon, Kanchalee; Plianbangchang, Pinyupa

2012-03-30

There is increasing interest in the development of technologies which can reduce the requirement for chemical fertilisers in rice production. The objective of this study was to investigate the efficacy of Bacillus cereus strain RS87 for the partial replacement of chemical fertiliser in rice production. A greenhouse experiment was designed using different fertiliser regimes, with and without strain RS87. Six Thai rice cultivars were tested separately. Maximum rice growth and yield were obtained in rice receiving the full recommended fertiliser rate in combination with the strain RS87. Interestingly, all rice cultivars which were treated with strain RS87 and 50% recommended fertiliser rate provided equivalent plant growth and yield to that receiving the full recommended fertiliser rate only. A paired comparison between rice treated with 50% of the recommended fertiliser rate with the bacterial inoculant and the full fertiliser rate alone was further examined in small experimental rice paddy fields. Growth and yield of all rice cultivars which received the 50% fertiliser rate supplemented with strain RS87 gave a similar yield to that receiving the full fertiliser rate alone. Bacterial strain RS87 showed the potential to replace 50% of the recommended fertiliser rate for yield production. Integration of plant growth-promoting rhizobacterial inoculants with reduced application rates of chemical fertiliser appears promising for future agriculture. Copyright © 2012 Society of Chemical Industry.

Structural features of the rice chromosome 4 centromere.

PubMed

Zhang, Yu; Huang, Yuchen; Zhang, Lei; Li, Ying; Lu, Tingting; Lu, Yiqi; Feng, Qi; Zhao, Qiang; Cheng, Zhukuan; Xue, Yongbiao; Wing, Rod A; Han, Bin

2004-01-01

A complete sequence of a chromosome centromere is necessary for fully understanding centromere function. We reported the sequence structures of the first complete rice chromosome centromere through sequencing a large insert bacterial artificial chromosome clone-based contig, which covered the rice chromosome 4 centromere. Complete sequencing of the 124-kb rice chromosome 4 centromere revealed that it consisted of 18 tracts of 379 tandemly arrayed repeats known as CentO and a total of 19 centromeric retroelements (CRs) but no unique sequences were detected. Four tracts, composed of 65 CentO repeats, were located in the opposite orientation, and 18 CentO tracts were flanked by 19 retroelements. The CRs were classified into four types, and the type I retroelements appeared to be more specific to rice centromeres. The preferential insert of the CRs among CentO repeats indicated that the centromere-specific retroelements may contribute to centromere expansion during evolution. The presence of three intact retrotransposons in the centromere suggests that they may be responsible for functional centromere initiation through a transcription-mediated mechanism.

Final report on the safety assessment of AloeAndongensis Extract, Aloe Andongensis Leaf Juice,aloe Arborescens Leaf Extract, Aloe Arborescens Leaf Juice, Aloe Arborescens Leaf Protoplasts, Aloe Barbadensis Flower Extract, Aloe Barbadensis Leaf, Aloe Barbadensis Leaf Extract, Aloe Barbadensis Leaf Juice,aloe Barbadensis Leaf Polysaccharides, Aloe Barbadensis Leaf Water, Aloe Ferox Leaf Extract, Aloe Ferox Leaf Juice, and Aloe Ferox Leaf Juice Extract.

PubMed

2007-01-01

Plant materials derived from the Aloe plant are used as cosmetic ingredients, including Aloe Andongensis Extract, Aloe Andongensis Leaf Juice, Aloe Arborescens Leaf Extract, Aloe Arborescens Leaf Juice, Aloe Arborescens Leaf Protoplasts, Aloe Barbadensis Flower Extract, Aloe Barbadensis Leaf, Aloe Barbadensis Leaf Extract, Aloe Barbadensis Leaf Juice, Aloe Barbadensis Leaf Polysaccharides, Aloe Barbadensis Leaf Water, Aloe Ferox Leaf Extract, Aloe Ferox Leaf Juice, and Aloe Ferox Leaf Juice Extract. These ingredients function primarily as skin-conditioning agents and are included in cosmetics only at low concentrations. The Aloe leaf consists of the pericyclic cells, found just below the plant's skin, and the inner central area of the leaf, i.e., the gel, which is used for cosmetic products. The pericyclic cells produce a bitter, yellow latex containing a number of anthraquinones, phototoxic compounds that are also gastrointestinal irritants responsible for cathartic effects. The gel contains polysaccharides, which can be acetylated, partially acetylated, or not acetylated. An industry established limit for anthraquinones in aloe-derived material for nonmedicinal use is 50 ppm or lower. Aloe-derived ingredients are used in a wide variety of cosmetic product types at concentrations of raw material that are 0.1% or less, although can be as high as 20%. The concentration of Aloe in the raw material also may vary from 100% to a low of 0.0005%. Oral administration of various anthraquinone components results in a rise in their blood concentrations, wide systemic distribution, accumulation in the liver and kidneys, and excretion in urine and feces; polysaccharide components are distributed systemically and metabolized into smaller molecules. aloe-derived material has fungicidal, antimicrobial, and antiviral activities, and has been effective in wound healing and infection treatment in animals. Aloe barbadensis (also known as Aloe vera)-derived ingredients were not toxic

Effect of heavy ion beam irradiation on germination of local Toraja rice seed (M1-M2) mutant generation