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28 September 2019, Volume 26 Issue 5 Previous Issue    Next Issue
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Letter

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Quantitative Trait Loci Mapping for Rice Yield-Related Traits Using Chromosomal Segment Substitution Lines Zihe Li, Riaz Aamir, Yingxin Zhang, Bakr Anis Galal, Aike Zhu, Liyong Cao, Shihua Cheng 2019, 26(5): 261-264.  DOI: 10.1016/j.rsci.2019.02.001 Abstract ( )   HTML ( )   PDF (722KB) ( )

Review

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CRISPR/Cas9: Development and Application in Rice Breeding Matías Romero Fernando, Gatica-Arias Andrés 2019, 26(5): 265-281.  DOI: 10.1016/j.rsci.2019.08.001 Abstract ( )   HTML ( )   PDF (810KB) ( )   Rice (Oryza sativa L.) is an important staple food crop worldwide due to its adaptability to different environmental conditions. Because of its great economic and social importance, there is a constant requirement for new varieties with improved agronomic characteristics, such as tolerance to different biotic (such as bacterium, fungus, insect and virus) and abiotic stresses (such as salinity, drought and temperature), higher yield and better organoleptic and nutritional value. Among the new genome editing technologies, the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) (CRISPR/Cas) system allows precise and specific edition in a targeted genome region. It is one of the most frequently used techniques for the study of the function of new genes and for the development of mutant lines with enhanced tolerance to biotic and abiotic stresses, herbicide resistance or improved yield. The wide varieties of applications for this technology include simple non-homologous end joining, homologous recombination, gene replacement, and base editing. In this review, we analyzed how some of these applications have been used in rice cultivars to obtain rice varieties better adapted to current environmental conditions and market requirements.

Research Papers

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Differential RNA Editing of Mitochondrial Genes in WA-Cytoplasmic Based Male Sterile Line Pusa 6A, and Its Maintainer and Restorer Lines Ngangkham Umakanta, Kumar Parida Swarup, Kumar Singh Ashok, Mohapatra Trilochan 2019, 26(5): 282-289.  DOI: 10.1016/j.rsci.2019.08.002 Abstract ( )   HTML ( )   PDF (824KB) ( )   RNA editing changes the nucleotides at the transcript level of mitochondrial genes which results in synthesis of functional proteins. This study was designed to find the editing sites which could be implicated in male fertility restoration and to develop editing based markers for differentiation of cytoplasmic male sterility and maintainer lines from each other. DNA and RNA from young panicles were isolated from three-line system of hybrid rice PRH10, wild abortive (WA) cytoplasm based male sterile (A line Pusa 6A), maintainer (B line Pusa 6B) and restorer (R line PRR78) lines. Pusa 6A and PRR78 having the same WA cytoplasm are allo-nuclear and iso-cytpolasmic lines. The genomic and cDNA amplicons for eight mitochondrial genes (18SrRNA, atp6, atp9, cobII, coxI, coxIII, nadI and rps3) were sequenced and compared. Differences in genomic and cDNA sequences were considered as editing. Two hundred and thirty editing sites having base substitution or insertion/deletion were identified with the highest in 18SrRNA (5.74%) and the lowest in coxI (0.60%). The highest editing sites were observed in fertile maintainer Pusa 6B followed by PRR78 and Pusa 6A, of which random five editing sites in five different rice mitochondrial transcripts namely atp9, cobII, coxIII, rps3 and 18SrRNA were chosen and validated through cleaved amplified polymorphism sequence (CAPS) analysis and found to be partially edited in four genes. The identical editing sites of different mitochondrial genes from maintainer and restorer lines might reflect their possible contribution to fertility restoration of sterile WA cytoplasm.

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Fusarium solani Upregulated Sesquiterpene Synthase Expression, Sesquiterpene Production and Allelopathic Activity in Piper betle Woranoot Kamrai, Buaruang Rattikarn, Aranyakanon Kodchakorn, Ratanasut Kumrop, Kongbangkerd Anupan, Jannoey Panatda, Nangngam Pranee, Choopayak Chonnanit 2019, 26(5): 290-299.  DOI: 10.1016/j.rsci.2019.08.003 Abstract ( )   HTML ( )   PDF (1115KB) ( )   Activators of sesquiterpene synthase (STS) gene expression and sesquiterpene production in Piper betle L. were examined using quantitative real time PCR and gas chromatography mass spectrometry methods, and the allelopathic activity of untreated and Fusarium solani-treated betel extracts was tested on seed germination and on the shoot and root growth of Thai rice variety PSL2 (Oryza sativa cv. Phitsanulok 2) and three dominant paddy weeds (Eclipta prostrata, Echinochloa crus-galli and Chloris barbata). The results demonstrated that F. solani dramatically upregulated STS expression and productions of β-cubebene, β-caryophyllene and germacrene D sesquiterpene when compared with the untreated control, and that betel extracts had a greater inhibitory effect on weeds than on rice. The effects were more clearly detected on seed germination and root growth than on shoot growth, and they were found to be dose-dependent. It is also noted that F. solani-treated extract had stronger effects than the untreated extract. The species most sensitive to the allelopathic effects was C. barbata, germination of which was completely inhibited even at a dose of 0.1 mg/mL untreated extract. With regards to rice, although betel extract at 1.0 mg/mL showed no inhibition on germination, it affected the elongation of rice roots, in addition to those of the tested weeds. The obtained data suggested that F. solani has potential as an activator of sesquiterpene allelochemical production via STS expression, the latter leading to the treated betel extract having a stronger phytotoxic effect. These results were beneficial in the promotion of natural herbicide production using biotechnology.

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Quinclorac Resistance in Echinochloa crus-galli from China Qiong Peng, Heping Han, Xia Yang, Lianyang Bai, Qin Yu, B. Powles Stephen 2019, 26(5): 300-308.  DOI: 10.1016/j.rsci.2019.08.004 Abstract ( )   HTML ( )   PDF (1180KB) ( )   Echinochloa crus-galli is a major weed in rice fields in China, and quinclorac has been long used for its control. Over-reliance of quinclorac has resulted in quinclorac resistance in E. crus-galli. Two resistant (R) E. crus-galli populations from Hunan, China were confirmed to be at least 78-fold more resistant to quinclorac than the susceptible (S) population. No difference in foliar uptake of 14C-labelled quinclorac was detected between the R and S plants. However, a higher level of 14C translocation and a lower level of quinclorac metabolism were found in the R plants. Basal and induced expression levels of β-cyanoalanine synthase (β-CAS) gene and β-CAS activity were not significantly different between the R and S plants. However, the induction expression of 1-aminocyclopropane-1-carboxylic acid oxidase (ACO1) gene by quinclorac treatment was evident in the S plants but not in the R plants. Quinclorac resistance in the two resistant E. crus-galli populations was not likely to be related to foliar uptake, translocation or metabolism of quinclorac, nor to cyanide detoxification via β-CAS. Thus, target-site based quinclorac signal reception and transduction and regulation of the ethylene synthesis pathway should be the focus for further research.

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Effects of Integrated Organic and Inorganic Fertilizers on Yield and Growth Parameters of Rice Varieties Moe Kyi, Moh Moh Seinn, Zaw Htwe Aung, Kajihara Yoshinori, Yamakawa Takeo 2019, 26(5): 309-318.  DOI: 10.1016/j.rsci.2019.08.005 Abstract ( )   HTML ( )   PDF (1123KB) ( )   We investigated the effects of integrated organic and inorganic fertilizers on the growth and yield of indica rice variety Manawthukha and japonica rice variety Genkitsukushi. In a split-plot design, the two rice varieties were assigned as main plot factors, and the integrated treatments were the subplot factors, including no-N fertilizer (N0), 50% chemical fertilizer (CF) (CF50), 100% CF (CF100), 50% CF + 50% poultry manure (PM) (CF50PM50), 50% CF + 50% cow manure (CM) (CF50CM50), and 50% CF + 50% compost (CP) (CF50CP50). CF100 was equivalent to N at 85 kg/hm2. Manure was applied based on the estimated mineralizable nitrogen (EMN) level, which is dependent on total N (%) of each manure type. Manawthukha rice plants were taller with higher tiller number and dry matter content. However, higher soil-plant analysis development (SPAD) values were measured in Genkitsukushi throughout the crop growth period, resulting in higher seed-setting rate (%) and greater yield. At the same N level, CF50PM50 application in both rice varieties resulted in higher SPAD values, plant height and tiller number than CF100. CF50PM50 containing total N more than 4% supplied synchronized N for the demands of the rice plants, resulting in maximum dry matter, yield and yield components. CF50CM50 and CF50CP50 treatments containing total N less than 4% resulted in lower yields which were similar to CF100. These results indicated that integrating organic and inorganic fertilizers enhanced growth parameters and yields of Manawthukha and Genkitsukushi, while reducing the dose of chemical fertilizer.

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Strategies for Fermentable Sugar Production by Using Pressurized Acid Hydrolysis for Rice Husks B. Pedroso Giovanni, R. Philippsen Michael, F. Saldanha Loisleini, B. Araujo Raiara, F. Martins Ayrton 2019, 26(5): 319-330.  DOI: 10.1016/j.rsci.2019.08.006 Abstract ( )   HTML ( )   PDF (2024KB) ( )   This study investigated the use of leftover biomass (rice husks) as the raw material for the biotechnological production of platform chemicals and biopolymers. Following the biorefinery concept, different acid hydrolysates were studied and resulted into a wide range of treatment strategies. Chemometrics were applied throughout the procedures in multivariate experimental conditions. By using the best hydrolytic conditions of 6.0% H3PO4, 135 ºC (45 MPa) and reaction time of 62 min, 21.0 g/L sugar hydrolysates were produced; by using the best hydrolytic condition of 4.5% HNO3, 135 ºC/35 min, 16.1 g/L sugar hydrolysates were produced; and with the hydrolysates use of 1.5% H2SO4 and 1.5% HCl, 135 ºC/62 min, 18.2 and 17.8 g/L sugar hydrolysates were produced, respectively. The highest productivity, in terms of fermentable sugars, reached 68% of integral cellulose/hemicellulose fraction and surpassed those found in the literature, with regard to the processing of rice husks, by considering just one step process. Sulfuric hydrolysate, detoxified with active carbon, was used to prove this proposal viability, resulting in a fermentation substrate for A. terreus (ATCC10020) and R. radiobacter (LMG196) strains (natural producers of bioproducts), which certified the feasibility of the proposal. The production of fermentable sugars from leftover biomass should encourage a search for new bioconversion routes, which can result in economic and environmental benefits and a spread of knowledge.

Short Communication

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Identification of Stable Quantitative Trait Loci for Sheath Blight Resistance Using Recombinant Inbred Line Yuan Chen, Yuxiang Zeng, Zhijuan Ji, Yan Liang, Zhihua Wen, Changdeng Yang 2019, 26(5): 331-338.  DOI: 10.1016/j.rsci.2019.08.007 Abstract ( )   HTML ( )   PDF (1670KB) ( )   To identify stable quantitative trait loci (QTLs) responsible for sheath blight resistance, a recombinant inbred line mapping population consisting of 219 lines was developed by crossing Lemont and Yangdao 4. Average disease rating, average lesion length, maximum disease rating and maximum lesion length were assayed in six different environments. A total of 128 minor effect QTLs were detected by multiple interval mapping. These QTLs explained less than 11.2% of the phenotypic variations individually, and 106 QTLs were clustered in 20 QTL-rich regions/putative loci. Significant QTL × environment interactions were detected at three putative loci (qSBR11.1, qSBR11.2 and qSBR11.3), indicating that these three loci were not stable. The other 17 stable loci (qSBR1.1, qSBR1.2, qSBR2.1, qSBR2.3, qSBR3.1, qSBR3.2, qSBR3.5, qSBR3.6, qSBR5.1, qSBR7.1, qSBR8.1, qSBR9.1, qSBR9.2, qSBR9.3, qSBR12.1, qSBR12.2 and qSBR12.4) provided a foundation for marker-assisted selection in breeding. Analysis of allelic effect on the 20 putative loci identified 7 highly stable loci, including qSBR3.2, qSBR7.1, qSBR8.1, qSBR9.2, qSBR9.3, qSBR12.1 and qSBR12.2.