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1.
Potential of vegetation indices combined with laser-induced fluorescence parameters for monitoring leaf nitrogen content in paddy rice.
Yang, J, Du, L, Gong, W, Shi, S, Sun, J, Chen, B
PloS one. 2018;(1):e0191068
Abstract
Nitrogen (N) is important for the growth of crops. Leaf nitrogen content (LNC) serves as a crucial indicator of the growth status of crops and can help determine the dose of N fertilizer. Laser-induced fluorescence (LIF) technology and the reflectance spectra of crops are widely used to detect the biochemical content of leaves. Many vegetation indices (VIs) and fluorescence parameters have been developed to estimate LNC. However, the comparison among VIs and between fluorescence parameters and VIs has been rarely studied in the estimation of LNC. In this study, the performances of several published empirical VIs and fluorescence parameters for the estimation of paddy rice LNC were analyzed using the support vector machine (SVM) algorithm. Then, the optimal VIs (TVI, MTVI1, MTVI2, and MSAVI) and fluorescence parameters (F735/F460 and F685/F460), which were suitable for LNC monitoring in this study, were chosen. In addition, the combination of the VIs and fluorescence parameters was proposed as the input variables in the SVM model and used to estimate the LNC. Experimental results exhibited the promising potential of the LIF technology combined with reflectance for the accurate estimation of LNC, which provided guidance for monitoring the LNC.
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2.
Genetic dissection of QTLs and differentiation analysis of alleles for heading date genes in rice.
Zhang, H, Liu, S, Chen, G, Liu, X, Xuan, N, Yang, Y, Liu, W, Ding, H, Yao, F
PloS one. 2018;(1):e0190491
Abstract
Heading date is an important agronomic trait in rice (Oryza sativa L.); it determines the geographical and seasonal adaptability of the crop. Single segment substitution lines (SSSLs) have become the preferred experimental materials in mapping functional genetic variations as the particular chromosome segments from donor genotypes can be evaluated for their impact on the phenotype in a recurrent recipient background. The phenotypic differences can be attributed to the control of quantitative trait loci (QTLs). Here, we evaluated a library consisting of 1,123 SSSLs in the same genetic background of an elite rice variety, Huajingxian74 (HJX74), and revealed four SSSLs, W05-1-11-2-7-6 (W05), W08-16-3-2 (W08), W12-28-58-03-19-1 (W12), and W22-9-5-2-4-9-3 (W22), which had a significantly different heading date compared to HJX74. To further genetically dissect the QTLs controlling heading date on chromosomes 3, 6, and 10, four SSSLs were used to develop 15 secondary SSSLs with the smaller substituted segments. The qHD-3 heading date QTL detected in W05 and W08 was delimited to an interval of 4.15 cM, whereas qHD-6-1 and qHD-6-2 heading date QTLs dissected from the substituted segments in W12 were mapped to the intervals of 2.25-cM and 2.55-cM, respectively. The qHD-10 QTL detected on the substituted segment in W22 was mapped to an interval of 6.85-cM. The nucleotide and amino acid sequence changes for those genes in the secondary SSSLs were also revealed. The allele variations of those genes might contribute to the heading date QTLs on chromosome 3 (DTH3, OsDof12, and EHD4), chromosome 6 (Hd3a, Hd17, and RFT1), and chromosome 10 (Ehd1 and Ehd2). These sequence variations in heading date genes would be useful resources for further studying the function of genes, and would be important for rice breeding. Overall, our results indicate that secondary SSSLs were powerful tools for genetic dissection of QTLs and identification of differentiation in the genes.
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3.
Mining and Development of Novel SSR Markers Using Next Generation Sequencing (NGS) Data in Plants.
Taheri, S, Lee Abdullah, T, Yusop, MR, Hanafi, MM, Sahebi, M, Azizi, P, Shamshiri, RR
Molecules (Basel, Switzerland). 2018;(2)
Abstract
Microsatellites, or simple sequence repeats (SSRs), are one of the most informative and multi-purpose genetic markers exploited in plant functional genomics. However, the discovery of SSRs and development using traditional methods are laborious, time-consuming, and costly. Recently, the availability of high-throughput sequencing technologies has enabled researchers to identify a substantial number of microsatellites at less cost and effort than traditional approaches. Illumina is a noteworthy transcriptome sequencing technology that is currently used in SSR marker development. Although 454 pyrosequencing datasets can be used for SSR development, this type of sequencing is no longer supported. This review aims to present an overview of the next generation sequencing, with a focus on the efficient use of de novo transcriptome sequencing (RNA-Seq) and related tools for mining and development of microsatellites in plants.
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4.
Current understanding of pattern-triggered immunity and hormone-mediated defense in rice (Oryza sativa) in response to Magnaporthe oryzae infection.
Nasir, F, Tian, L, Chang, C, Li, X, Gao, Y, Tran, LP, Tian, C
Seminars in cell & developmental biology. 2018;:95-105
Abstract
Plant pathogens represent a huge threat to world food security, affecting both crop production and quality. Although significant progress has been made in improving plant immunity by expressing key, defense-related genes and proteins from different species in transgenic crops, a challenge remains for molecular breeders and biotechnologists to successfully engineer elite, transgenic crop varieties with improved resistance against critical plant pathogens. Upon pathogen attack, including infection of rice (Oryza sativa) by Magnaporthe oryzae, host plants initiate a complex defense response at molecular, biochemical and physiological levels. Plants perceive the presence of pathogens by detecting microbe-associated molecular patterns via pattern recognition receptors, and initiate a first line of innate immunity, the so-called pattern-triggered immunity (PTI). This results in a series of downstream defense responses, including the production of hormones, which collectively function to fend off pathogen attacks. A variety of studies have demonstrated that many genes are involved in the defense response of rice to M. oryzae. In this review, the current understanding of mechanisms that improve rice defense response to M. oryzae will be discussed, with special focus on PTI and the phytohormones ethylene, jasmonic acid, salicylic acid, and abscisic acid; as well as on the mediation of defense signaling mechanisms by PTI and these hormones. Potential target genes that may serve as promising candidates for improving rice immunity against M. oryzae will also be discussed.
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5.
Rapid Detection of Ustilaginoidea virens from Rice using Loop-Mediated Isothermal Amplification Assay.
Yang, X, Al-Attala, MN, Zhang, Y, Zhang, AF, Zang, HY, Gu, CY, Gao, TC, Chen, Y, Al-Attala, MN, Ali, F, et al
Plant disease. 2018;(9):1741-1747
Abstract
Ustilaginoidea virens is an important fungus that causes rice false smut disease. This disease significantly reduces both grain yield and quality. Various methods have been developed for the detection of U. virens but most of these methods need sophisticated equipment such as a thermal cycler. Here, we present a loop-mediated isothermal amplification (LAMP) assay for the specific detection of U. virens. This assay used a specific region of the UvG-β1 gene (212-bp region) to design six LAMP primers. The LAMP assay was optimized by the combination of rapidity, simplicity, and high sensitivity for the detection of about 1 pg of target genomic DNA in the reaction whereas, with polymerase chain reaction (PCR), there was no amplification of DNA with concentrations less than 1 ng. Among the genomic DNA of 22 fungus species and two strains of U. virens, only the tube containing the DNA of U. virens changed to yellowish green with SYBR Green I. The color change was indicative of DNA amplification. No DNA was amplified from either the other 22 fungus species or the negative control. Moreover, 20 spikelets and 22 rice seed samples were used for the detection of rice false smut via LAMP. The results were comparable with conventional PCR. We conclude that gene UvG-β1 coupled with LAMP assay, can be used for the detection and identification of U. virens gene via LAMP.
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6.
Molecular mechanisms underpinning phosphorus-use efficiency in rice.
Dissanayaka, DMSB, Plaxton, WC, Lambers, H, Siebers, M, Marambe, B, Wasaki, J
Plant, cell & environment. 2018;(7):1483-1496
Abstract
Orthophosphate (H2 PO4- , Pi) is an essential macronutrient integral to energy metabolism as well as a component of membrane lipids, nucleic acids, including ribosomal RNA, and therefore essential for protein synthesis. The Pi concentration in the solution of most soils worldwide is usually far too low for maximum growth of crops, including rice. This has prompted the massive use of inefficient, polluting, and nonrenewable phosphorus (P) fertilizers in agriculture. We urgently need alternative and more sustainable approaches to decrease agriculture's dependence on Pi fertilizers. These include manipulating crops by (a) enhancing the ability of their roots to acquire limiting Pi from the soil (i.e. increased P-acquisition efficiency) and/or (b) increasing the total biomass/yield produced per molecule of Pi acquired from the soil (i.e. increased P-use efficiency). Improved P-use efficiency may be achieved by producing high-yielding plants with lower P concentrations or by improving the remobilization of acquired P within the plant so as to maximize growth and biomass allocation to developing organs. Membrane lipid remodelling coupled with hydrolysis of RNA and smaller P-esters in senescing organs fuels P remobilization in rice, the world's most important cereal crop.
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7.
A randomized, double-blind, placebo-controlled trial investigating cholesterol-lowering effects and safety of yellow yeast rice in adults with mild to moderate hypercholesterolemia: A study protocol.
Jeong, S, Lee, J, Kwon, O, Kim, JW, Oh, B
Medicine. 2018;(30):e11634
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Abstract
BACKGROUND Elevated levels of blood lipids are well-documented risk factors for cardiovascular disease. For cardiovascular risk reduction, preventive strategies to lower blood cholesterol levels are essential, and these strategies include lifestyle modification and cholesterol-lowering agents. We aim to investigate the cholesterol-lowering effects and safety of yellow yeast rice in a randomized, controlled, double-blind, and parallel group study. METHODS Participants for this study will be selected based on the following inclusion criteria:Participants are randomly allocated to the placebo or yellow-yeast-rice-treated group. Participants with mild to moderately elevated LDL-C levels will consume 1 pouch of yellow yeast rice powder (containing monacolin K) or placebo twice daily for 8 weeks. Next, the lipid profiles will be evaluated. RESULTS The number of participants required for this study is 68, and is currently recruiting participants. Participants are randomly assigned to control group and intervention group. CONCLUSION This is the first human intervention study to investigate the cholesterol-lowering effects and safety of yellow yeast rice in adults with mild to moderate hypercholesterolemia. Also, this is a randomized, double-blind, placebo-controlled trial that considers confounders, such as dietary habits, lifestyle factors, and genetic factors.
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8.
Leaf gas films contribute to rice (Oryza sativa) submergence tolerance during saline floods.
Herzog, M, Konnerup, D, Pedersen, O, Winkel, A, Colmer, TD
Plant, cell & environment. 2018;(5):885-897
Abstract
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, chlorophylla and tissue porosity. Submergence was more detrimental to leaf PN and growth than the additional effect of 50 mm NaCl, as salt did not significantly affect underwater PN at 200 μm CO2 nor growth.
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9.
Rice Protein Matrix Enhances Circulating Levels of Xanthohumol Following Acute Oral Intake of Spent Hops in Humans.
O'Connor, A, Konda, V, Reed, RL, Christensen, JM, Stevens, JF, Contractor, N
Molecular nutrition & food research. 2018;(6):e1700692
Abstract
SCOPE Xanthohumol (XN), a prenylated flavonoid found in hops, exhibits anti-inflammatory and antioxidant properties. However, poor bioavailability may limit therapeutic applications. As food components are known to modulate polyphenol absorption, the objective is to determine whether a protein matrix could enhance the bioavailability of XN post oral consumption in humans. METHODS AND RESULTS This is a randomized, double-blind, crossover study in healthy participants (n = 6) evaluating XN and its major metabolites (isoxanthohumol [IX], 6- and 8-prenylnaringenin [6-PN, 8-PN]) for 6 h following consumption of 12.4 mg of XN delivered via a spent hops-rice protein matrix preparation or a control spent hops preparation. Plasma XN and metabolites are measured by LC-MS/MS. Cmax , Tmax , and area-under-the-curve (AUC) values were determined. Circulating XN and metabolite response to each treatment was not bioequivalent. Plasma concentrations of XN and XN + metabolites (AUC) are greater with consumption of the spent hops-rice protein matrix preparation. CONCLUSION Compared to a standard spent hops powder, a protein-rich spent hops matrix demonstrates enhanced plasma levels of XN and metabolites following acute oral intake.
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10.
Chrysoviruses in Magnaporthe oryzae.
Moriyama, H, Urayama, SI, Higashiura, T, Le, TM, Komatsu, K
Viruses. 2018;(12)
Abstract
Magnaporthe oryzae, the fungus that causes rice blast, is the most destructive pathogen of rice worldwide. A number of M. oryzae mycoviruses have been identified. These include Magnaporthe oryzae. viruses 1, 2, and 3 (MoV1, MoV2, and MoV3) belonging to the genus, Victorivirus, in the family, Totiviridae; Magnaporthe oryzae. partitivirus 1 (MoPV1) in the family, Partitiviridae; Magnaporthe oryzae. chrysovirus 1 strains A and B (MoCV1-A and MoCV1-B) belonging to cluster II of the family, Chrysoviridae; a mycovirus related to plant viruses of the family, Tombusviridae (Magnaporthe oryzae. virus A); and a (+)ssRNA mycovirus closely related to the ourmia-like viruses (Magnaporthe oryzae. ourmia-like virus 1). Among these, MoCV1-A and MoCV1-B were the first reported mycoviruses that cause hypovirulence traits in their host fungus, such as impaired growth, altered colony morphology, and reduced pigmentation. Recently we reported that, although MoCV1-A infection generally confers hypovirulence to fungi, it is also a driving force behind the development of physiological diversity, including pathogenic races. Another example of modulated pathogenicity caused by mycovirus infection is that of Alternaria alternata chrysovirus 1 (AaCV1), which is closely related to MoCV1-A. AaCV1 exhibits two contrasting effects: Impaired growth of the host fungus while rendering the host hypervirulent to the plant, through increased production of the host-specific AK-toxin. It is inferred that these mycoviruses might be epigenetic factors that cause changes in the pathogenicity of phytopathogenic fungi.