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Zhang P, Chen Z, Wang F, Wu H, Hao L, Jiang X, Yu Z, Zou L, Jiang H. Response and inversion of skewness parameters to meteorological factors based on RGB model of leaf color digital image. PLoS One 2023; 18:e0288818. [PMID: 37967130 PMCID: PMC10650994 DOI: 10.1371/journal.pone.0288818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 07/04/2023] [Indexed: 11/17/2023] Open
Abstract
In the natural environment, complex and changeable meteorological factors can influence changes in the internal physiology and phenotype of crops. It is important to learn how to convert complex meteorological factor stimuli into plant perception phenotypes when analyzing the biological data obtained under the natural field condition. We restored the true gradation distribution of leaf color, which is also known as the skewed distribution of color scale, and obtained 20 multi-dimensional color gradation skewness-distribution (CGSD) parameters based on the leaf color skewness parameter system. Furthermore, we analyzed the correlation between the five corresponding meteorological factors and canopy CGSD parameters of peppers growing in a greenhouse and cabbages growing in an open air environment, built response model and inversion mode of leaf color to meteorological factors. Based on the analysis, we find a new method for correlating complex environmental problems with multi-dimensional parameters. This study provides a new idea for building a correlation model that uses leaf color as a bridge between meteorological factors and plants internal physiological state.
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Affiliation(s)
- Pei Zhang
- Jiangsu Meteorological Bureau, Nanjing, China
| | - Zhengmeng Chen
- Longyan Company of Fujian Provincial Tobacco Corporation, Longyan, China
| | - Fuzheng Wang
- QinGengRen Modern Agricultural Science and Technology Development (Huai’an) Co., Ltd., Huai’an, China
| | - Hongyan Wu
- Jiangsu Meteorological Bureau, Nanjing, China
| | - Ling Hao
- Lianyungang Meteorological Bureau, Lianyungang, China
| | - Xu Jiang
- Tufts University, Boston, MA, United States of America
| | - Zhiming Yu
- Key Laboratory of Crop Physiology and Ecology in Southern China, Ministry of Agriculture, Jiangsu Collaborative Innovation Center for Modern Crop Prodution, National Engineering and Technology Center for Information Agriculture, Nanjing Agricultural University, Nanjing, People’s Republic of China
| | - Lina Zou
- Longyan Company of Fujian Provincial Tobacco Corporation, Longyan, China
| | - Haidong Jiang
- Key Laboratory of Crop Physiology and Ecology in Southern China, Ministry of Agriculture, Jiangsu Collaborative Innovation Center for Modern Crop Prodution, National Engineering and Technology Center for Information Agriculture, Nanjing Agricultural University, Nanjing, People’s Republic of China
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Ren R, Ji Z, Guo J, Yang X. Cryopreservation of herbaceous Asteraceae seeds: Effects of seed reserves on seed germination and seedling regrowth. Cryobiology 2023; 112:104562. [PMID: 37494976 DOI: 10.1016/j.cryobiol.2023.104562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 07/21/2023] [Accepted: 07/23/2023] [Indexed: 07/28/2023]
Abstract
Carbohydrate, lipid and protein, the three main storage reserves of seeds, are the main sources of raw materials and energy for seed germination and early growth stage of seedlings. In this study, the seed of 16 Asteraceae herbaceous ornamentals were used to compare the changes in seed germination, seedling growth indexes and four major storage reserves of seeds before and after cryopreservation. After cryopreservation, seed germination and seedling growth were preserved in most species (11/16), while one species showed significantly improved post-thaw germination and four had decreased germination. In seeds with preserved germination, no clear variation was noted with regards to the four kinds of storage reserves, or only a slight change in one. However, significantly reduced soluble protein, soluble sugar and fat content and increased starch content were detected in seeds showing reduced germination after cryopreservation. The correlation study further showed that the changes in seed germination were positively correlated with soluble protein, soluble sugar and fat, and negatively correlated with starch. In seedling growth indexes, only cotyledon area was correlated to the content of soluble protein, starch, fat, and seed germination after cryopreservation. These results support the use of soluble protein, soluble sugar, starch and fat as indicators of seed germination after cryopreservation, but not for predicting the seedling growth indexes.
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Affiliation(s)
- Ruifen Ren
- College of Forestry, Shanxi Agricultural University, Taigu, 030801, China.
| | - Zhe Ji
- College of Forestry, Shanxi Agricultural University, Taigu, 030801, China.
| | - Jiayi Guo
- College of Forestry, Shanxi Agricultural University, Taigu, 030801, China.
| | - Xiuyun Yang
- College of Forestry, Shanxi Agricultural University, Taigu, 030801, China.
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3
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Frisk CA, Apangu GP, Petch GM, Creer S, Hanson M, Adams-Groom B, Skjøth CA. Microscale pollen release and dispersal patterns in flowering grass populations. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 880:163345. [PMID: 37028666 DOI: 10.1016/j.scitotenv.2023.163345] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 03/17/2023] [Accepted: 04/03/2023] [Indexed: 05/27/2023]
Abstract
Characterizing pollen release and dispersion processes is fundamental for knowledge advancement in ecological, agricultural and public health disciplines. Understanding pollen dispersion from grass communities is especially relevant due to their high species-specific allergenicity and heterogeneously distributed source areas. Here, we aimed to address questions concerning fine level heterogeneity in grass pollen release and dispersion processes, with a focus on characterizing the taxonomic composition of airborne grass pollen over the grass flowering season using eDNA and molecular ecology methods. High resolution grass pollen concentrations were compared between three microscale sites (<300 m apart) in a rural area in Worcestershire, UK. The grass pollen was modelled with local meteorology in a MANOVA (Multivariate ANOVA) approach to investigate factors relevant to pollen release and dispersion. Simultaneously, airborne pollen was sequenced using Illumina MySeq for metabarcoding, analysed against a reference database with all UK grasses using the R packages DADA2 and phyloseq to calculate Shannon's Diversity Index (α-diversity). The flowering phenology of a local Festuca rubra population was observed. We found that grass pollen concentrations varied on a microscale level, likely attributed to local topography and the dispersion distance of pollen from flowering grasses in local source areas. Six genera (Agrostis, Alopecurus, Arrhenatherum, Holcus, Lolium and Poa) dominated the pollen season, comprising on average 77 % of the relative abundance of grass species reads. Temperature, solar radiation, relative humidity, turbulence and wind speeds were found to be relevant for grass pollen release and dispersion processes. An isolated flowering Festuca rubra population contributed almost 40 % of the relative pollen abundance adjacent to the nearby sampler, but only contributed 1 % to samplers situated 300 m away. This suggests that most emitted grass pollen has limited dispersion distance and our results show substantial variation in airborne grass species composition over short geographical scales.
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Affiliation(s)
- Carl A Frisk
- School of Science and the Environment, University of Worcester, Henwick Grove, WR2 6AJ Worcester, UK.
| | - Godfrey P Apangu
- School of Science and the Environment, University of Worcester, Henwick Grove, WR2 6AJ Worcester, UK
| | - Geoffrey M Petch
- School of Science and the Environment, University of Worcester, Henwick Grove, WR2 6AJ Worcester, UK
| | - Simon Creer
- Molecular Ecology and Evolution Group, School of Natural Sciences, Bangor University, LL57 2UW Bangor, UK
| | - Mary Hanson
- School of Science and the Environment, University of Worcester, Henwick Grove, WR2 6AJ Worcester, UK
| | - Beverley Adams-Groom
- School of Science and the Environment, University of Worcester, Henwick Grove, WR2 6AJ Worcester, UK
| | - Carsten A Skjøth
- School of Science and the Environment, University of Worcester, Henwick Grove, WR2 6AJ Worcester, UK
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4
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Dorvlo IK, Amenorpe G, Amoatey HM, Amiteye S, Kutufam JT, Afutu E, Asare-Bediako E, Darkwa AA. Improvement in cowpea variety Videza for traits of extra earliness and higher seed yield. Heliyon 2022; 8:e12059. [PMID: 36561698 PMCID: PMC9763773 DOI: 10.1016/j.heliyon.2022.e12059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 06/20/2022] [Accepted: 11/24/2022] [Indexed: 12/04/2022] Open
Abstract
The cowpea variety Videza, which was used as the control, matures early (70 days after planting), although it produces low yields. Gamma irradiation mutagenesis was used to induce Videza into extra-early maturing and higher yielding mutant genotypes. A single seed descend population was developed for radio-sensitivity test, and a Lethal Dose 50 (LD50) of 240.5 Gy was determined, and applied from a cobalt-60 (60Co) source, to acutely mass irradiate 1800 Videza seeds, at the Ghana Atomic Energy Commission. The irradiated seeds (M1) were planted to produce M2 seeds bearing plants and subsequently advanced to M3 plants for selection of nine induced plants based on extra earliness and significantly higher seed yields than the parental control. It took 48 days after planting (DAP) for the genotype coded P1N02#1 to reach 50 % maturity followed by 52 DAP for genotypes with codes P4N03#3; P3N01#5; P5N05#6, P4N14#7, P5N07#8, P5N05#10 and 54 DAP for genotype P4N14#11. P1N06#9 had the highest yield (97.38 g/plant), followed by P5N05#10 (95.97 g/plant), P1N08#13 (81.24 g/plant), P2N09#12 (73.94 g/plant), P6N10#19 (70.83 g/plant), P1N06#20 (65.36 kg/plant), P5N07#14 (61.23 g/plant), P4N14# (58.05 g/plant) and P1N08#17 (56.23 g/plant). M3 seeds were advanced to M4 plants for a Preliminary Yield Trial which revealed that induced plants P5N05#10 (1235 kg/ha), P2N09#12 (1206 kg/ha), P5N07#14 (1185 kg/ha), P1N06#20 (1171 kg/ha), P1N06#9 (1051 kg/ha), P1N08#13 (1041 kg/ha), and P6N10#19 (999 kg/ha) outperformed the control (517 kg/ha) and two other commercial varieties. Overall, the two highest performing candidates for further evaluation for varietal release were P5N05#10 and P2N09#12.
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Affiliation(s)
- Innocent Kwaku Dorvlo
- Department of Nuclear Agriculture and Radiation Processing. School of Nuclear and Allied Sciences, College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
| | - Godwin Amenorpe
- Biotechnology and Nuclear Agricultural Research Institute (BNARI), Ghana Atomic Energy Commission (GAEC), Accra, Ghana,Department of Nuclear Agriculture and Radiation Processing. School of Nuclear and Allied Sciences, College of Basic and Applied Sciences, University of Ghana, Accra, Ghana,Corresponding author.
| | - Harry Mensah Amoatey
- Department of Nuclear Agriculture and Radiation Processing. School of Nuclear and Allied Sciences, College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
| | - Samuel Amiteye
- Department of Nuclear Agriculture and Radiation Processing. School of Nuclear and Allied Sciences, College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
| | - Jacob Teye Kutufam
- Biotechnology and Nuclear Agricultural Research Institute (BNARI), Ghana Atomic Energy Commission (GAEC), Accra, Ghana
| | - Emmanuel Afutu
- Department of Crop Science, School of Agriculture, College of Agriculture and Natural Sciences, University of Cape Coast, Cape Coast, Ghana
| | - Elvis Asare-Bediako
- Department of Crop Science, School of Agriculture, College of Agriculture and Natural Sciences, University of Cape Coast, Cape Coast, Ghana
| | - Alfred Anthony Darkwa
- Department of Crop Science, School of Agriculture, College of Agriculture and Natural Sciences, University of Cape Coast, Cape Coast, Ghana
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Riaz A, Kanwal F, Ahmad I, Ahmad S, Farooq A, Madsen CK, Brinch-Pedersen H, Bekalu ZE, Dai F, Zhang G, Alqudah AM. New Hope for Genome Editing in Cultivated Grasses: CRISPR Variants and Application. Front Genet 2022; 13:866121. [PMID: 35923689 PMCID: PMC9340155 DOI: 10.3389/fgene.2022.866121] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 06/23/2022] [Indexed: 12/24/2022] Open
Abstract
With the advent of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and CRISPR-associated protein (Cas) mediated genome editing, crop improvement has progressed significantly in recent years. In this genome editing tool, CRISPR-associated Cas nucleases are restricted to their target of DNA by their preferred protospacer adjacent motifs (PAMs). A number of CRISPR-Cas variants have been developed e.g. CRISPR-Cas9, -Cas12a and -Cas12b, with different PAM requirements. In this mini-review, we briefly explain the components of the CRISPR-based genome editing tool for crop improvement. Moreover, we intend to highlight the information on the latest development and breakthrough in CRISPR technology, with a focus on a comparison of major variants (CRISPR-Cas9, -Cas12a, and -Cas12b) to the newly developed CRISPR-SpRY that have nearly PAM-less genome editing ability. Additionally, we briefly explain the application of CRISPR technology in the improvement of cultivated grasses with regard to biotic and abiotic stress tolerance as well as improving the quality and yield.
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Affiliation(s)
- Asad Riaz
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Farah Kanwal
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Iqrar Ahmad
- Centre for Advanced Studies in Agriculture and Food Security, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Shakeel Ahmad
- Centre for Advanced Studies in Agriculture and Food Security, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Ayesha Farooq
- Centre for Advanced Studies in Agriculture and Food Security, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Claus Krogh Madsen
- Department of Agroecology, Research Center Flakkebjerg, Aarhus University, Slagelse, Denmark
| | - Henrik Brinch-Pedersen
- Department of Agroecology, Research Center Flakkebjerg, Aarhus University, Slagelse, Denmark
| | - Zelalem Eshetu Bekalu
- Department of Agroecology, Research Center Flakkebjerg, Aarhus University, Slagelse, Denmark
| | - Fei Dai
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Guoping Zhang
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- *Correspondence: Guoping Zhang, ; Ahmad M. Alqudah, ,
| | - Ahmad M. Alqudah
- Department of Agroecology, Research Center Flakkebjerg, Aarhus University, Slagelse, Denmark
- *Correspondence: Guoping Zhang, ; Ahmad M. Alqudah, ,
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Reddy B, Mehta S, Prakash G, Sheoran N, Kumar A. Structured Framework and Genome Analysis of Magnaporthe grisea Inciting Pearl Millet Blast Disease Reveals Versatile Metabolic Pathways, Protein Families, and Virulence Factors. J Fungi (Basel) 2022; 8:jof8060614. [PMID: 35736098 PMCID: PMC9225118 DOI: 10.3390/jof8060614] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 04/10/2022] [Accepted: 05/06/2022] [Indexed: 12/19/2022] Open
Abstract
Magnaporthe grisea (T.T. Herbert) M.E. Barr is a major fungal phytopathogen that causes blast disease in cereals, resulting in economic losses worldwide. An in-depth understanding of the basis of virulence and ecological adaptation of M. grisea is vital for devising effective disease management strategies. Here, we aimed to determine the genomic basis of the pathogenicity and underlying biochemical pathways in Magnaporthe using the genome sequence of a pearl millet-infecting M. grisea PMg_Dl generated by dual NGS techniques, Illumina NextSeq 500 and PacBio RS II. The short and long nucleotide reads could be draft assembled in 341 contigs and showed a genome size of 47.89 Mb with the N50 value of 765.4 Kb. Magnaporthe grisea PMg_Dl showed an average nucleotide identity (ANI) of 86% and 98% with M. oryzae and Pyricularia pennisetigena, respectively. The gene-calling method revealed a total of 10,218 genes and 10,184 protein-coding sequences in the genome of PMg_Dl. InterProScan of predicted protein showed a distinct 3637 protein families and 695 superfamilies in the PMg_Dl genome. In silico virulence analysis revealed the presence of 51VFs and 539 CAZymes in the genome. The genomic regions for the biosynthesis of cellulolytic endo-glucanase and beta-glucosidase, as well as pectinolytic endo-polygalacturonase, pectin-esterase, and pectate-lyases (pectinolytic) were detected. Signaling pathways modulated by MAPK, PI3K-Akt, AMPK, and mTOR were also deciphered. Multicopy sequences suggestive of transposable elements such as Type LTR, LTR/Copia, LTR/Gypsy, DNA/TcMar-Fot1, and Type LINE were recorded. The genomic resource presented here will be of use in the development of molecular marker and diagnosis, population genetics, disease management, and molecular taxonomy, and also provide a genomic reference for ascomycetous genome investigations in the future.
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Affiliation(s)
- Bhaskar Reddy
- Division of Plant Pathology, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi 110012, India; (G.P.); (N.S.)
- Correspondence: (B.R.); (A.K.)
| | - Sahil Mehta
- Crop Improvement Group, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India;
| | - Ganesan Prakash
- Division of Plant Pathology, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi 110012, India; (G.P.); (N.S.)
| | - Neelam Sheoran
- Division of Plant Pathology, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi 110012, India; (G.P.); (N.S.)
| | - Aundy Kumar
- Division of Plant Pathology, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi 110012, India; (G.P.); (N.S.)
- Correspondence: (B.R.); (A.K.)
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7
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Keiper F, Atanassova A. Enabling Genome Editing for Enhanced Agricultural Sustainability. Front Genome Ed 2022; 4:898950. [PMID: 35663796 PMCID: PMC9157430 DOI: 10.3389/fgeed.2022.898950] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 04/20/2022] [Indexed: 11/13/2022] Open
Abstract
Agricultural sustainability encompasses environmental, social, and economic aspects, all of which are continually shifting due changing environmental pressures and societal expectations. A range of strategies are required to address these challenges, and these include the use of innovation and adoption of the best available practices and technologies. Advances in biotechnologies, including genome editing, and their application in plant breeding and research are expected to provide a range of benefits that contribute to all aspects of agricultural sustainability. However, adoption of these technologies needs to be supported by proportionate, coherent, forward-looking, and adaptable policies and regulatory approaches. In this Perspective, we reflect on the regulatory challenges associated with commercialising a transgenic crop, and developments thus far in providing regulatory clarity for genome edited crops. We aim to demonstrate that much remains to be done to shift towards a more proportionate and enabling approach before the potential benefits of genome edited crops can be realised. The implications of precautionary and disproportionate regulation are also discussed.
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Affiliation(s)
- Felicity Keiper
- BASF Australia Ltd., Southbank, VIC, Australia
- *Correspondence: Felicity Keiper,
| | - Ana Atanassova
- BASF Belgium Coordination Center, Technologiepark-Zwijnaarde, Ghent, Belgium
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Nakei MD, Venkataramana PB, Ndakidemi PA. Soybean-Nodulating Rhizobia: Ecology, Characterization, Diversity, and Growth Promoting Functions. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2022. [DOI: 10.3389/fsufs.2022.824444] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The worldwide increase in population continues to threaten the sustainability of agricultural systems since agricultural output must be optimized to meet the global rise in food demand. Sub-Saharan Africa (SSA) is among the regions with a fast-growing population but decreasing crop productivity. Pests and diseases, as well as inadequate nitrogen (N) levels in soils, are some of the biggest restrictions to agricultural production in SSA. N is one of the most important plant-limiting elements in agricultural soils, and its deficit is usually remedied by using nitrogenous fertilizers. However, indiscriminate use of these artificial N fertilizers has been linked to environmental pollution calling for alternative N fertilization mechanisms. Soybean (Glycine max) is one of the most important legumes in the world. Several species of rhizobia from the four genera, Bardyrhizobium, Rhizobium, Mesorhizobium, and Ensifer (formerly Sinorhizobium), are observed to effectively fix N with soybean as well as perform various plant-growth promoting (PGP) functions. The efficiency of the symbiosis differs with the type of rhizobia species, soybean cultivar, and biotic factors. Therefore, a complete understanding of the ecology of indigenous soybean-nodulating rhizobia concerning their genetic diversity and the environmental factors associated with their localization and dominance in the soil is important. This review aimed to understand the potential of indigenous soybean-nodulating rhizobia through a synthesis of the literature regarding their characterization using different approaches, genetic diversity, symbiotic effectiveness, as well as their functions in biological N fixation (BNF) and biocontrol of soybean soil-borne pathogens.
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Khan Q, Qin Y, Guo DJ, Zeng XP, Chen JY, Huang YY, Ta QK, Yang LT, Liang Q, Song XP, Xing YX, Li YR. Morphological, agronomical, physiological and molecular characterization of a high sugar mutant of sugarcane in comparison to mother variety. PLoS One 2022; 17:e0264990. [PMID: 35271640 PMCID: PMC8912205 DOI: 10.1371/journal.pone.0264990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 02/22/2022] [Indexed: 11/20/2022] Open
Abstract
Sugarcane is a significant crop plant with the capability of accumulating higher amount of sucrose. In the present study, a high sucrose content sugarcane mutant clone, GXB9, has been studied in comparison to the low sucrose mother clone B9 on morphological, agronomical and physiological level in order to scrutinize the variation because of mutation in GXB9 in field under normal environmental condition. The results showed that GXB9 has less germination, tillering rate, stalk height, leaf length, leaf width, leaf area, number of internodes, internode length and internode diameter than B9. Qualitative traits of leaf and stalk displayed significant variation between GXB9 and B9. Endogenous hormones quantity was also showed variation between the two clones. The relative SPAD reading and chlorophyll a, b concentrations also showed variation between GXB9 and B9. The photosynthetic parameter analysis indicated that the GXB9 has significantly higher net photosynthetic rate (Pn), stomatal conductance (gs) and transpiration rate (Tr) than B9. The qRT-PCR analysis of genes encoding enzymes like SPS, SuSy, CWIN, and CeS showed upregulation in GXB9 and downregulation in B9. However, these genes were significantly differentially expressed between the immature and maturing internodes of GXB9. The cane quality trait analysis showed that GXB9 had higher juice rate, juice gravity purity, brix, juice sucrose content and cane sucrose content than B9. The yield and component investigation results indicated that GXB9 had lower single stalk weight, however higher number of millable stalks per hectare than B9, and GXB9 had lower theoretical cane yield than B9. SSR marker analysis showed genetic variation between GXB9 and B9. This study has shown significant variation in the traits of GXB9 in comparison to B9 which advocates that GXB9 is a high sugar mutant clone of B9 and an elite source for future breeding.
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Affiliation(s)
- Qaisar Khan
- College of Agriculture, Guangxi University, Nanning, China
| | - Ying Qin
- College of Agriculture, Guangxi University, Nanning, China
| | - Dao-Jun Guo
- College of Agriculture, Guangxi University, Nanning, China
| | - Xiu-Peng Zeng
- College of Agriculture, Guangxi University, Nanning, China
| | - Jiao-Yun Chen
- College of Agriculture, Guangxi University, Nanning, China
| | - Yu-Yan Huang
- College of Agriculture, Guangxi University, Nanning, China
| | - Quang-Kiet Ta
- College of Agriculture, Guangxi University, Nanning, China
| | - Li-Tao Yang
- College of Agriculture, Guangxi University, Nanning, China
| | - Qiang Liang
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs, Sugarcane Research Institute of Guangxi Academy of Agricultural Sciences, Sugarcane Research Center of Chinese Academy of Agricultural Sciences, Nanning, China
| | - Xiu-Peng Song
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs, Sugarcane Research Institute of Guangxi Academy of Agricultural Sciences, Sugarcane Research Center of Chinese Academy of Agricultural Sciences, Nanning, China
- * E-mail: (XPS); (YXX); (YRL)
| | - Yong-Xiu Xing
- College of Agriculture, Guangxi University, Nanning, China
- * E-mail: (XPS); (YXX); (YRL)
| | - Yang-Rui Li
- College of Agriculture, Guangxi University, Nanning, China
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs, Sugarcane Research Institute of Guangxi Academy of Agricultural Sciences, Sugarcane Research Center of Chinese Academy of Agricultural Sciences, Nanning, China
- * E-mail: (XPS); (YXX); (YRL)
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10
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Scaling up interactive argumentation by providing counterarguments with a chatbot. Nat Hum Behav 2022; 6:579-592. [DOI: 10.1038/s41562-021-01271-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Accepted: 12/06/2021] [Indexed: 11/08/2022]
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11
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Reddy B, Kumar A, Mehta S, Sheoran N, Chinnusamy V, Prakash G. Hybrid de novo genome-reassembly reveals new insights on pathways and pathogenicity determinants in rice blast pathogen Magnaporthe oryzae RMg_Dl. Sci Rep 2021; 11:22922. [PMID: 34824307 PMCID: PMC8616942 DOI: 10.1038/s41598-021-01980-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 11/01/2021] [Indexed: 01/20/2023] Open
Abstract
Blast disease incited by Magnaporthe oryzae is a major threat to sustain rice production in all rice growing nations. The pathogen is widely distributed in all rice paddies and displays rapid aerial transmissions, and seed-borne latent infection. In order to understand the genetic variability, host specificity, and molecular basis of the pathogenicity-associated traits, the whole genome of rice infecting Magnaporthe oryzae (Strain RMg_Dl) was sequenced using the Illumina and PacBio (RSII compatible) platforms. The high-throughput hybrid assembly of short and long reads resulted in a total of 375 scaffolds with a genome size of 42.43 Mb. Furthermore, comparative genome analysis revealed 99% average nucleotide identity (ANI) with other oryzae genomes and 83% against M. grisea, and 73% against M. poe genomes. The gene calling identified 10,553 genes with 10,539 protein-coding sequences. Among the detected transposable elements, the LTR/Gypsy and Type LINE showed high occurrence. The InterProScan of predicted protein sequences revealed that 97% protein family (PFAM), 98% superfamily, and 95% CDD were shared among RMg_Dl and reference 70-15 genome, respectively. Additionally, 550 CAZymes with high GH family content/distribution and cell wall degrading enzymes (CWDE) such endoglucanase, beta-glucosidase, and pectate lyase were also deciphered in RMg_Dl. The prevalence of virulence factors determination revealed that 51 different VFs were found in the genome. The biochemical pathway such as starch and sucrose metabolism, mTOR signaling, cAMP signaling, MAPK signaling pathways related genes were identified in the genome. The 49,065 SNPs, 3267 insertions and 3611 deletions were detected, and majority of these varinats were located on downstream and upstream region. Taken together, the generated information will be useful to develop a specific marker for diagnosis, pathogen surveillance and tracking, molecular taxonomy, and species delineation which ultimately leads to device improved management strategies for blast disease.
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Affiliation(s)
- Bhaskar Reddy
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Aundy Kumar
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.
| | - Sahil Mehta
- Crop Improvement Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067, India
| | - Neelam Sheoran
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Viswanathan Chinnusamy
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Ganesan Prakash
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
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Deciphering variation of 239 elite japonica rice genomes for whole genome sequences-enabled breeding. Genomics 2021; 113:3083-3091. [PMID: 34237377 DOI: 10.1016/j.ygeno.2021.07.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 07/01/2021] [Accepted: 07/02/2021] [Indexed: 11/23/2022]
Abstract
Revealing genomic variation of representative and diverse germplasm is the cornerstone of deploying genomics information into genetic improvement programs of species of agricultural importance. Here we report the re-sequencing of 239 japonica rice elites representing the genetic diversity of japonica germplasm in China, Japan and Korea. A total of 4.8 million SNPs and PAV of 35,634 genes were identified. The elites from Japan and Korea are closely related and relatively less diverse than those from China. A japonica rice pan-genome was constructed, and 35 Mb non-redundant novel sequences were identified, from which 1131 novel genes were predicted. Strong selection signals of genomic regions were detected on most of the chromosomes. The heading date genes Hd1 and Hd3a have been artificially selected during the breeding process. The results from this study lay the foundation for future whole genome sequences-enabled breeding in rice and provide a paradigm for other species.
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Abstract
In keeping with the directive in Executive Order 13874 (Modernizing the Regulatory Framework for Agricultural Biotechnology Products) to adopt regulatory approaches that are proportionate to risk and avoid arbitrary distinctions across like products, the US Department of Agriculture (USDA) revised its biotechnology regulations by promulgating the Sustainable, Ecological, Consistent, Uniform, Responsible, and Efficient (SECURE) rule. Specifically, the SECURE rule 1) establishes exemptions for plants modified by genetic engineering where the modification could otherwise have been made through conventional breeding, 2) uses risk posed by the introduced trait to determine whether an organism is regulated, rather than relying on whether the organism was developed using a plant pest, and 3) provides a mechanism for a rapid initial review to efficiently distinguish plants developed using genetic engineering that do not pose plausible pathways to increased plant pest risk from those that do. As a result of the focused oversight on potentially riskier crops developed using genetic engineering, USDA is expected to improve the efficiency and effectiveness of its oversight program. The reduced regulatory burden is expected to promote innovation by expanding the number and diversity of developers to include smaller businesses and academics and to increase the number and variety of traits being developed through biotechnology.
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Khodaee L, Azizinezhad R, Etminan AR, Khosroshahi M. Assessment of genetic diversity among Iranian Aegilops triuncialis accessions using ISSR, SCoT, and CBDP markers. J Genet Eng Biotechnol 2021; 19:5. [PMID: 33428012 PMCID: PMC7801538 DOI: 10.1186/s43141-020-00107-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 12/21/2020] [Indexed: 11/17/2022]
Abstract
BACKGROUND Crop wild relatives (CWRs) are commonly used as a suitable genetic reservoir for plant breeding. They can be used for enhancing the tolerance of plant varieties to biotic and abiotic stresses. Studying the genetic diversity of related wheat species in Iran could be useful to improve different traits of bread wheat, since the country is one of the major centers of genetic diversity and distribution of Aegilops species. Therefore, the aim of the present study was to determine the relationship among 48 Aegilops triuncialis accessions using three DNA marker systems, including start codon targeted (SCoT), CAAT box-derived polymorphism (CBDP), and inter-simple sequence repeat (ISSR) markers. RESULTS A total of 359 amplified DNA fragments were generated using 13 CBDP, 14 SCoT, and 16 ISSR primers that produced 96, 147, and 152 bands, respectively. The discriminating power of the three markers was assessed using polymorphism information content (PIC), marker index (MI), and resolving power (Rp). The mean values of PIC for ISSR, SCoT, and CBDP markers were 0.3, 0.26, and 0.34, respectively, indicating the efficiency of the three markers in detecting polymorphism among the studied accessions. ISSR markers had the highest values of MI, Rp, and polymorphism percentage as compared to SCoT and CBDP markers. Based on the Shannon index and heterozygosity values, genetic diversity in the Alborz population was more than in other populations. The accessions were classified into six, five, and five groups based on ISSR, SCoT, and CBDP using the UPGMA method. According to the results of cluster and PCoA analyses, the variation patterns corresponded with the geographical distribution of the Ae. triuncialis accessions. CONCLUSIONS The three markers provided a comprehensive pattern of the genetic diversity among the Iranian Ae. triuncialis accessions. This information could allow for a future insight into wheat breeding programs.
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Affiliation(s)
- Lavin Khodaee
- Department of Biotechnology and Plant Breeding, Islamic Azad University Science and Research Branch, Tehran, Iran
| | - Reza Azizinezhad
- Department of Biotechnology and Plant Breeding, Islamic Azad University Science and Research Branch, Tehran, Iran.
| | - Ali Reza Etminan
- Department of Plant Breeding and Biotechnology, Kermanshah Branch, Islamic Azad University, Kermanshah, Iran
| | - Mahmoud Khosroshahi
- Department of Biotechnology and Plant Breeding, Islamic Azad University Science and Research Branch, Tehran, Iran
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Ahumada-Flores S, Gómez Pando LR, Parra Cota FI, de la Cruz Torres E, Sarsu F, de Los Santos Villalobos S. Technical note: Gamma irradiation induces changes of phenotypic and agronomic traits in wheat (Triticum turgidum ssp. durum). Appl Radiat Isot 2020; 167:109490. [PMID: 33121892 DOI: 10.1016/j.apradiso.2020.109490] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 10/15/2020] [Accepted: 10/21/2020] [Indexed: 10/23/2022]
Abstract
WHEAT VAR CIRNO C2008 was irradiated with gamma rays at 100, 200, and 300 Gy. The irradiated plants obtained at 300 Gy (M1) showed a significant reduction (compared to M0 plants) in germination (i.e. 3.8% at day 5), survival percentage (48%), and plant height (63.3%). Thus, the Probit analysis showed an LD50 of 287.80 Gy. Besides, these irradiated plants, in the field, showed a significant increase (compared to M0 plants) in days to spike initiation (16 days), and maturation (14 days). On the other hand, in the field, fourteen chlorophyll mutants were found (at a different frequency) in the M2 generation, such as Albina, Anthocyanin, Chlorina, Maculata, Tigrina, Striata, Viridis, Viridoalbina, Alboviridis, Xantha, Xanthviridis, Xanthalba, Viridoxantha, and Orange stem. In addition, mutants with changes in agronomic and morphological traits were observed. This nuclear technique is an alternative to obtain promising mutant lines that can be used directly as a variety and/or as parental to transfer these traits to other varieties.
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Affiliation(s)
- Sergio Ahumada-Flores
- -Instituto Tecnológico de Sonora, 5 de Febrero 818 sur, 85000, Cd. Obregón, Sonora, Mexico
| | | | - Fannie Isela Parra Cota
- -Campo Experimental Norman E. Borlaug, Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Norman E. Borlaug Km 12, 85000, Cd. Obregón, Sonora, Mexico
| | - Eulogio de la Cruz Torres
- -Instituto Nacional de Investigaciones Nucleares, Carretera México-Toluca S/N, La Marquesa, Ocoyoacac, Edo. México, C.P, 52750, Mexico
| | - Fatma Sarsu
- - Plant Breeding and Genetic Section, Joint FAO/IAEA Division, International Atomic Energy Agency, Vienna, Austria
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Wijewardene I, Mishra N, Sun L, Smith J, Zhu X, Payton P, Shen G, Zhang H. Improving drought-, salinity-, and heat-tolerance in transgenic plants by co-overexpressing Arabidopsis vacuolar pyrophosphatase gene AVP1 and Larrea Rubisco activase gene RCA. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 296:110499. [PMID: 32540017 DOI: 10.1016/j.plantsci.2020.110499] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Revised: 03/31/2020] [Accepted: 04/06/2020] [Indexed: 05/25/2023]
Abstract
The severity and frequency of many abiotic stresses such as drought, salinity and heat, cause substantial crop losses worldwide, which poses a serious challenge in food security. To increase crop production, new approaches are needed. Previous research has shown that overexpression of the tonoplast H+ pyrophosphatase gene AVP1 leads to improved drought and salt tolerance in transgenic plants. Other research showed that overexpression of thermotolerant ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) activase gene could maintain photosynthesis at higher temperatures, which contributes to higher heat tolerance in transgenic plants. In nature, abiotic stresses rarely come alone, instead these stresses often occur in various combinations. Therefore, it is desirable to make crops more tolerant to multiple stresses, which will likely lead to higher crop yield under various stress conditions. It is shown here that co-overexpression of the Arabidopsis gene AVP1 and the Larrea Rubisco activase gene RCA significantly increases drought, salinity and heat tolerance, resulting in higher biomass and seed yield than wild-type plants. AVP1/RCA co-overexpressing plants are as more drought- and salt-tolerant as AVP1-overexpressing plants, and as more heat-tolerant as RCA-overexpressing plants. More importantly, they produce higher seed yields than AVP1-overexpressing, RCA-overexpressing, and wild-type plants under combined drought and heat conditions.
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Affiliation(s)
- Inosha Wijewardene
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, 79409, USA
| | - Neelam Mishra
- St. Joseph's College Autonomous, Bengaluru, Karnataka, 560027, India
| | - Li Sun
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, 79409, USA
| | - Jennifer Smith
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, 79409, USA
| | - Xunlu Zhu
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, 79409, USA
| | - Paxton Payton
- USDA-ARS Cropping Systems Research Laboratory, Lubbock, TX, USA
| | - Guoxin Shen
- Zhejiang Academy of Agricultural Sciences, Hangzhou, China.
| | - Hong Zhang
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, 79409, USA.
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Stubbington R, Acreman M, Acuña V, Boon PJ, Boulton AJ, England J, Gilvear D, Sykes T, Wood PJ. Ecosystem services of temporary streams differ between wet and dry phases in regions with contrasting climates and economies. PEOPLE AND NATURE 2020. [DOI: 10.1002/pan3.10113] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Affiliation(s)
- Rachel Stubbington
- School of Science and Technology Nottingham Trent University Nottingham UK
| | | | - Vicenç Acuña
- Catalan Institute for Water Research (ICRA) Girona Spain
- University of Girona Girona Spain
| | | | - Andrew J. Boulton
- School of Environmental and Rural Science University of New England Armidale NSW Australia
| | - Judy England
- Research, Analysis and Evaluation Environment Agency Wallingford UK
| | - David Gilvear
- School of Geography, Earth and Environmental Sciences University of Plymouth Plymouth UK
| | - Tim Sykes
- Romsey District Office Environment Agency Romsey UK
| | - Paul J. Wood
- Geography and Environment Loughborough University Loughborough UK
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Idris SH, Abdul Majeed AB, Chang LW. Beyond Halal: Maqasid al-Shari'ah to Assess Bioethical Issues Arising from Genetically Modified Crops. SCIENCE AND ENGINEERING ETHICS 2020; 26:1463-1476. [PMID: 31933118 DOI: 10.1007/s11948-020-00177-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 01/08/2020] [Indexed: 06/10/2023]
Abstract
Genetically modified organisms (GMOs) have increasingly dominated commodity crop production in the world in the endeavour to address issues related to food security. However, this technology is not without problems, and can give rise to bioethical issues for consumers, particularly Muslims. The Islamic perspective on GMOs is complex and goes beyond just the determination of whether food is halal or not. If the food is halal, but the process to obtain it is not thoyibban, as it is unethical, then the food cannot be permitted under the Maqasid al-Shari'ah. This paper examines ethical issues pertaining to GM crops and how the related ethical issues contradict with Islamic principles beyond the binary distinction between the contaminated and uncontaminated food. Since GM technology is a contemporary issue that may not be directly addressed in the al-Quran and Sunnah, other Islamic sources should also be referred to when drawing up this code of ethics to achieve the objective of Syariah (Maqasid al-Shari'ah). Maqasid al-Shari'ah can be applied to frame the Islamic bioethics guideline as it is comprehensive and encompasses moral principles directly applicable to modern biotechnology. The paper subsequently explores how the principles of Maqasid al-Shari'ah are applied in addressing these ethical issues.
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Affiliation(s)
| | | | - Lee Wei Chang
- Centre for Research Services, University of Malaya, Level 2, Research Management and Innovation Complex, 50603, Kuala Lumpur, Malaysia.
- Centre for Civilisational Dialogue, University of Malaya, Kuala Lumpur, Malaysia.
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Exploring Factors Affecting the Acceptance of Genetically Edited Food Among Youth in Japan. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:ijerph17082935. [PMID: 32340355 PMCID: PMC7216076 DOI: 10.3390/ijerph17082935] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 04/06/2020] [Accepted: 04/17/2020] [Indexed: 01/09/2023]
Abstract
Genetically edited food utilizes new techniques that may decrease all of the risks associated with genetically modified food, or "GMO" food. Safety and labeling regulations for genetically edited food are still new, and it is challenging for the consumer to differentiate it from conventional food. Although genetically edited food has the potential for reducing the risks associated with the gene introduction process, consumer perceptions toward it are still unclear. The research has compared the regulations governing GMO food and genetically edited food in Japan, Europe, and the United States. We found that the genetically edited food regulations in Japan are the most science-based, in the meaning that genetically edited food products are allowed to be sold without any safety evaluation. Based on the difference among regions, we further studied the potential acceptance level for such products among Japanese consumers, where regulation seemed science-based as policy. To understand the factors that may affect the adoption of genetically edited food among youth in Japan, we utilized the structural equation modeling (SEM) method with 180 surveys of Japanese university students to measure six factors: Knowledge, Attitude Towards Technology, Perceived Benefits, Perceived Risks, Trust, and Willingness to Purchase. The survey was conducted twice with an intervention in the middle to measure the effect of science communication, and we found significant differences when comparing the two datasets. The results of this survey indicate the importance of increasing knowledge and the positive role of science communication in increasing the adoption and trust of biotechnology products, such as genetically edited food.
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Khanam M, Ara G, Rahman AS, Islam Z, Farhad S, Khan SS, Sanin KI, Rahman MM, Majoor H, Ahmed T. Factors Affecting Food Security in Women Enrolled in a Program for Vulnerable Group Development. Curr Dev Nutr 2020; 4:nzaa037. [PMID: 32296741 PMCID: PMC7144907 DOI: 10.1093/cdn/nzaa037] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 02/03/2020] [Accepted: 03/09/2020] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Food security is defined as physical and economic access to sufficient food to meet the dietary requirements for a productive and healthy life. Evidence from the literature suggests that >800 million people worldwide are food insecure. Vulnerable Group Development (VGD) is the largest social safety net of the Government of Bangladesh targeting ultra-poor women to end hunger, achieve food security, improve nutrition, and promote sustainable agriculture. OBJECTIVES The objective of this study is to explore the factors associated with food security among VGD women in Bangladesh. METHODS A total of 870 women (435/group) participated in the baseline survey and another 800 women (400/group) participated in the endline survey. Participants in the intervention group received monthly rations of 30 kg fortified rice (FFR) and the control group received 30 kg of non-FFR for 12 mo. Multiple logistic regression analysis was used to establish both crude and confounder-adjusted relations between the primary outcome and response variables. Written consent was proved by study participants. This study (PR-14091) was approved by the Research Review Committee and Ethical Review Committee. RESULTS Severe food insecurity in the endline survey decreased from ∼50% to 6.3% in both groups. The hunger scale also improved between the baseline and endline survey. More than 97% of respondents at endline reported no hunger compared with 80% at baseline; only 3% of women in both groups reported moderate hunger at endline. Multivariable regression model showed that ownership of a house and land for agriculture, wealth index (richest quintile), and absence of fever were significantly associated with food security (P < 0.05). CONCLUSIONS Our analysis shows that the VGD rice distribution program significantly improves the food security status of vulnerable women; however, ownership of a house and land for agriculture were the most significant factors associated with household food security in VGD program areas of Bangladesh.
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Affiliation(s)
- Mansura Khanam
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Gulshan Ara
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Ahmed Shafiqur Rahman
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Zhahirul Islam
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Shahriar Farhad
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Sihan Sadat Khan
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Kazi Istiaque Sanin
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Mohammad Mahbobor Rahman
- World Food Programme, IDB Bhaban, IDB Bhaban 14th, 16th and 17th Floor E/8-A, Rokeya Sharani Agargaon, Sher-e-Bangla Nagar, Dhaka-1207, Bangladesh
| | - Herma Majoor
- World Food Programme, IDB Bhaban, IDB Bhaban 14th, 16th and 17th Floor E/8-A, Rokeya Sharani Agargaon, Sher-e-Bangla Nagar, Dhaka-1207, Bangladesh
| | - Tahmeed Ahmed
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
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Ezzat A, Adly M, El-Fiki A. Morphological, agronomical and molecular characterization in irradiated Cowpea (Vignaunguiculata (L.) Walp.) and detection by start codon target markers. JOURNAL OF RADIATION RESEARCH AND APPLIED SCIENCES 2019. [DOI: 10.1080/16878507.2019.1686578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Asmaa Ezzat
- Horticulture Department, Faculty of Agriculture, Minia University, Minia, Egypt
| | - Mohamed Adly
- National Centre for Radiation Research and TechnologyAtomic Energy Authority, Cairo, Egypt
| | - Ayman El-Fiki
- National Centre for Radiation Research and TechnologyAtomic Energy Authority, Cairo, Egypt
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Rodriguez M, Parola R, Andreola S, Pereyra C, Martínez-Noël G. TOR and SnRK1 signaling pathways in plant response to abiotic stresses: Do they always act according to the "yin-yang" model? PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 288:110220. [PMID: 31521220 DOI: 10.1016/j.plantsci.2019.110220] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 08/05/2019] [Accepted: 08/13/2019] [Indexed: 05/20/2023]
Abstract
Plants are sessile photo-autotrophic organisms continuously exposed to a variety of environmental stresses. Monitoring the sugar level and energy status is essential, since this knowledge allows the integration of external and internal cues required for plant physiological and developmental plasticity. Most abiotic stresses induce severe metabolic alterations and entail a great energy cost, restricting plant growth and producing important crop losses. Therefore, balancing energy requirements with supplies is a major challenge for plants under unfavorable conditions. The conserved kinases target of rapamycin (TOR) and sucrose-non-fermenting-related protein kinase-1 (SnRK1) play central roles during plant growth and development, and in response to environmental stresses; these kinases affect cellular processes and metabolic reprogramming, which has physiological and phenotypic consequences. The "yin-yang" model postulates that TOR and SnRK1 act in opposite ways in the regulation of metabolic-driven processes. In this review, we describe and discuss the current knowledge about the complex and intricate regulation of TOR and SnRK1 under abiotic stresses. We especially focus on the physiological perspective that, under certain circumstances during the plant stress response, the TOR and SnRK1 kinases could be modulated differently from what is postulated by the "yin-yang" concept.
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Affiliation(s)
- Marianela Rodriguez
- Instituto de Fisiología y Recursos Genéticos Vegetales (IFRGV), Centro de Investigaciones Agropecuarias (CIAP), Instituto Nacional de Tecnología Agropecuaria (INTA), Camino 60 Cuadras km 5.5, X5020ICA, Córdoba, Argentina; Unidad de Estudios Agropecuarios (UDEA- CONICET), Camino 60 Cuadras km 5.5 X5020ICA, Córdoba, Argentina.
| | - Rodrigo Parola
- Instituto de Fisiología y Recursos Genéticos Vegetales (IFRGV), Centro de Investigaciones Agropecuarias (CIAP), Instituto Nacional de Tecnología Agropecuaria (INTA), Camino 60 Cuadras km 5.5, X5020ICA, Córdoba, Argentina; Unidad de Estudios Agropecuarios (UDEA- CONICET), Camino 60 Cuadras km 5.5 X5020ICA, Córdoba, Argentina.
| | - Sofia Andreola
- Instituto de Fisiología y Recursos Genéticos Vegetales (IFRGV), Centro de Investigaciones Agropecuarias (CIAP), Instituto Nacional de Tecnología Agropecuaria (INTA), Camino 60 Cuadras km 5.5, X5020ICA, Córdoba, Argentina; Unidad de Estudios Agropecuarios (UDEA- CONICET), Camino 60 Cuadras km 5.5 X5020ICA, Córdoba, Argentina.
| | - Cintia Pereyra
- Instituto de Investigaciones en Biodiversidad y Biotecnología (INBIOTEC-CONICET), y Fundación para Investigaciones Biológicas Aplicadas (FIBA), Vieytes 3103, 7600, Mar del Plata, Argentina.
| | - Giselle Martínez-Noël
- Instituto de Investigaciones en Biodiversidad y Biotecnología (INBIOTEC-CONICET), y Fundación para Investigaciones Biológicas Aplicadas (FIBA), Vieytes 3103, 7600, Mar del Plata, Argentina.
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Koeppel I, Hertig C, Hoffie R, Kumlehn J. Cas Endonuclease Technology-A Quantum Leap in the Advancement of Barley and Wheat Genetic Engineering. Int J Mol Sci 2019; 20:ijms20112647. [PMID: 31146387 PMCID: PMC6600890 DOI: 10.3390/ijms20112647] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 05/24/2019] [Accepted: 05/24/2019] [Indexed: 12/21/2022] Open
Abstract
Domestication and breeding have created productive crops that are adapted to the climatic conditions of their growing regions. Initially, this process solely relied on the frequent occurrence of spontaneous mutations and the recombination of resultant gene variants. Later, treatments with ionizing radiation or mutagenic chemicals facilitated dramatically increased mutation rates, which remarkably extended the genetic diversity of crop plants. However, a major drawback of conventionally induced mutagenesis is that genetic alterations occur simultaneously across the whole genome and at very high numbers per individual plant. By contrast, the newly emerging Cas endonuclease technology allows for the induction of mutations at user-defined positions in the plant genome. In fundamental and breeding-oriented research, this opens up unprecedented opportunities for the elucidation of gene functions and the targeted improvement of plant performance. This review covers historical aspects of the development of customizable endonucleases, information on the mechanisms of targeted genome modification, as well as hitherto reported applications of Cas endonuclease technology in barley and wheat that are the agronomically most important members of the temperate cereals. Finally, current trends in the further development of this technology and some ensuing future opportunities for research and biotechnological application are presented.
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Affiliation(s)
- Iris Koeppel
- Plant Reproductive Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, Germany.
| | - Christian Hertig
- Plant Reproductive Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, Germany.
| | - Robert Hoffie
- Plant Reproductive Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, Germany.
| | - Jochen Kumlehn
- Plant Reproductive Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, Germany.
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Dong C, He F, Berkowitz O, Liu J, Cao P, Tang M, Shi H, Wang W, Li Q, Shen Z, Whelan J, Zheng L. Alternative Splicing Plays a Critical Role in Maintaining Mineral Nutrient Homeostasis in Rice ( Oryza sativa). THE PLANT CELL 2018; 30:2267-2285. [PMID: 30254029 PMCID: PMC6241280 DOI: 10.1105/tpc.18.00051] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 07/26/2018] [Accepted: 09/20/2018] [Indexed: 05/19/2023]
Abstract
Alternative splicing (AS) of pre-mRNAs promotes transcriptome and proteome diversity and plays important roles in a wide range of biological processes. However, the role of AS in maintaining mineral nutrient homeostasis in plants is largely unknown. To clarify this role, we obtained whole transcriptome RNA sequencing data from rice (Oryza sativa) roots grown in the presence or absence of several mineral nutrients (Fe, Zn, Cu, Mn, and P). Our systematic analysis revealed 13,291 alternatively spliced genes, representing ∼53.3% of the multiexon genes in the rice genome. As the overlap between differentially expressed genes and differentially alternatively spliced genes is small, a molecular understanding of the plant's response to mineral deficiency is limited by analyzing differentially expressed genes alone. We found that the targets of AS are highly nutrient-specific. To verify the role of AS in mineral nutrition, we characterized mutants in genes encoding Ser/Arg (SR) proteins that function in AS. We identified several SR proteins as critical regulators of Zn, Mn, and P nutrition and showed that three SR protein-encoding genes regulate P uptake and remobilization between leaves and shoots of rice, demonstrating that AS has a key role in regulating mineral nutrient homeostasis in rice.
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Affiliation(s)
- Chunlan Dong
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, P.R. China
| | - Fei He
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, P.R. China
| | - Oliver Berkowitz
- ARC Centre of Excellence in Plant Energy Biology, Department of Animal, Plant, and Soil Sciences, School of Life Sciences, La Trobe University, Victoria 3086, Australia
| | - Jingxian Liu
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, P.R. China
| | - Pengfei Cao
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, P.R. China
| | - Min Tang
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, P.R. China
| | - Huichao Shi
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, P.R. China
| | - Wujian Wang
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, P.R. China
| | - Qiaolu Li
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, P.R. China
| | - Zhenguo Shen
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, P.R. China
- Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, Jiangsu 210095, P.R. China
| | - James Whelan
- ARC Centre of Excellence in Plant Energy Biology, Department of Animal, Plant, and Soil Sciences, School of Life Sciences, La Trobe University, Victoria 3086, Australia
| | - Luqing Zheng
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, P.R. China
- Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, Jiangsu 210095, P.R. China
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25
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Singer SD, Hannoufa A, Acharya S. Molecular improvement of alfalfa for enhanced productivity and adaptability in a changing environment. PLANT, CELL & ENVIRONMENT 2018; 41:1955-1971. [PMID: 29044610 DOI: 10.1111/pce.13090] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 09/29/2017] [Accepted: 10/04/2017] [Indexed: 05/09/2023]
Abstract
Due to an expanding world population and increased buying power, the demand for ruminant products such as meat and milk is expected to grow substantially in coming years, and high levels of forage crop production will therefore be a necessity. Unfortunately, urbanization of agricultural land, intensive agricultural practices, and climate change are all predicted to limit crop production in the future, which means that the development of forage cultivars with improved productivity and adaptability will be essential. Because alfalfa (Medicago sativa L.) is one of the most widely cultivated perennial forage crops, it has been the target of much research in this field. In this review, we discuss progress that has been made towards the improvement of productivity, abiotic stress tolerance, and nutrient-use efficiency, as well as disease and pest resistance, in alfalfa using biotechnological techniques. Furthermore, we consider possible future priorities and avenues for attaining further enhancements in this crop as a means of contributing to the realization of food security in a changing environment.
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Affiliation(s)
- Stacy D Singer
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, Alberta, T1J 4B1, Canada
| | - Abdelali Hannoufa
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, N5V 4T3, Canada
| | - Surya Acharya
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, Alberta, T1J 4B1, Canada
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26
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Song J, Niu B, Wang D, Zhang F. Comparison of the Monte Carlo and guide to uncertainty in measurement methods in estimating measurement uncertainty: Indirect measurement of the CaMV35S promoter in mixed samples of genetically modified soybean. Food Control 2018. [DOI: 10.1016/j.foodcont.2018.02.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Anjago WM, Zhou T, Zhang H, Shi M, Yang T, Zheng H, Wang Z. Regulatory network of genes associated with stimuli sensing, signal transduction and physiological transformation of appressorium in Magnaporthe oryzae. Mycology 2018; 9:211-222. [PMID: 30181927 PMCID: PMC6115909 DOI: 10.1080/21501203.2018.1492981] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 06/21/2018] [Indexed: 02/02/2023] Open
Abstract
Rice blast caused by Magnaporthe oryzae is the most destructive disease affecting the rice production (Oryza sativa), with an average global loss of 10-30% per annum. Recent reports have indicated that the fungus also inflicts blast disease on wheat (Triticum aestivum) posing a serious threat to the wheat production. Due to its easily detected infectious process and manoeuvrable genetic manipulation, M. oryzae is considered a model organism for exploring the molecular mechanism underlying fungal pathogenicity during the pathogen-host interaction. M. oryzae utilises an infectious structure called appressorium to breach the host surface by generating high turgor pressure. The appressorium development is induced by physical and chemical cues which are coordinated by the highly conserved cAMP/PKA, MAPK and calcium signalling cascades. Genes involved in the appressorium development have been identified and well studied in M. oryzae, a summary of the working gene network linking stimuli sensing and physiological transformation of appressorium is needed. This review provides a comprehensive discussion regarding the regulatory networks underlying appressorium development with particular emphasis on sensing of appressorium inducing stimuli, signal transduction, transcriptional regulation and the corresponding developmental and physiological responses. We also discussed the crosstalk and interaction of various pathways during the appressorium development.
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Affiliation(s)
- Wilfred Mabeche Anjago
- Fujian University Key Laboratory for Plant-Microbe interaction, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Tengshen Zhou
- Institute of oceanography, Minjian University, FuzhouChina
| | - Honghong Zhang
- Plant Protection College, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Mingyue Shi
- Plant Protection College, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Tao Yang
- Fujian University Key Laboratory for Plant-Microbe interaction, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Huakun Zheng
- Fujian University Key Laboratory for Plant-Microbe interaction, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zonghua Wang
- Fujian University Key Laboratory for Plant-Microbe interaction, Fujian Agriculture and Forestry University, Fuzhou, China
- Institute of oceanography, Minjian University, FuzhouChina
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28
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Ullah A, Sun H, Yang X, Zhang X. A novel cotton WRKY gene, GhWRKY6-like, improves salt tolerance by activating the ABA signaling pathway and scavenging of reactive oxygen species. PHYSIOLOGIA PLANTARUM 2018; 162:439-454. [PMID: 29027659 DOI: 10.1111/ppl.12651] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 10/03/2017] [Accepted: 10/04/2017] [Indexed: 05/17/2023]
Abstract
WRKY transcription factors are transcriptional regulators of signaling pathways involved in biotic and abiotic stress responses. In this study, we report that ectopic expression of the GhWRKY6-like gene significantly improved salt tolerance in Arabidopsis thaliana while silencing the GhWRKY6-like increase the sensitivity to abiotic stresses in cotton. GhWRKY6-like was localized to the nucleus. Expression of GhWRKY6-like was remarkably induced by salt, polyethylene glycol (PEG) and abscisic acid (ABA) treatments. For further characterization, the GhWRKY6-like gene was cloned and transformed into Arabidopsis. Our findings showed that the germination rate and root length were significantly improved in plants overexpressing GhWRKY6-like vs wild type (WT) under salt, mannitol and ABA treatments. Additionally, the overexpressing lines showed greater salt tolerance than WT plants in soil. In addition, overexpressing plants accumulated less H2 O2 and malondialdehyde (MDA), while higher proline content, superoxide dismutase (SOD) and peroxidase (POD) activities were detected under salt and osmotic stresses. In contrast, virus-induced gene silencing (VIGS) of GhWRKY6-like in cotton showed enhanced sensitivity compared to WT plants during salt and drought stresses. Additionally, expression analysis of stress-responsive genes in GhWRKY6-like Arabidopsis revealed that there was increased expression of genes involved in the ABA signaling pathway (AtABF4, AtABI5 and AtMYC2) and osmotic stress (AtSOS2, AtRD29a and AtRD29b). Our results revealed that GhWRKY6-like enhanced salt tolerance in Arabidopsis by scavenging reactive oxygen species and regulating the ABA signaling pathway. We suggest that overexpression of the GhWRKY6-like gene in cotton will enhance tolerance against salt, drought and osmotic stresses.
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Affiliation(s)
- Abid Ullah
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, P. R. China
| | - Heng Sun
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, P. R. China
| | - Xiyan Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, P. R. China
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, P. R. China
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Datta S, Jankowicz‐Cieslak J, Nielen S, Ingelbrecht I, Till BJ. Induction and recovery of copy number variation in banana through gamma irradiation and low-coverage whole-genome sequencing. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:1644-1653. [PMID: 29476650 PMCID: PMC6097122 DOI: 10.1111/pbi.12901] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 02/02/2018] [Accepted: 02/07/2018] [Indexed: 06/08/2023]
Abstract
Traditional breeding methods are hindered in bananas due to the fact that major cultivars are sterile, parthenocarpic, triploid and thus clonally propagated. This has resulted in a narrow genetic base and limited resilience to biotic and abiotic stresses. Mutagenesis of in vitro propagated bananas is one method to introduce novel alleles and broaden genetic diversity. We previously established a method for the induction and recovery of single nucleotide mutations generated with the chemical mutagen EMS. However, officially released mutant banana varieties have been created using gamma rays, a mutagen that can produce large genomic insertions and deletions (indels). Such dosage mutations may be important for generating observable phenotypes in polyploids. In this study, we establish a low-coverage whole-genome sequencing approach in triploid bananas to recover large genomic indels caused by treatment with gamma irradiation. We first evaluated the commercially released mutant cultivar 'Novaria' and found that it harbours multiple predicted deletions, ranging from 0.3 to 3.8 million base pairs (Mbp). In total, predicted deletions span 189 coding regions. To evaluate the feasibility of generating and maintaining new mutations, we developed a pipeline for mutagenesis and screening for copy number variation in Cavendish bananas using the cultivar 'Williams'. Putative mutations were recovered in 70% of lines treated with 20 Gy and 60% of the lines treated with 40 Gy. While deletion events predominate, insertions were identified in 20 Gy-treated material. Based on these results, we believe this approach can be scaled up to support large breeding projects.
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Affiliation(s)
- Sneha Datta
- Plant Breeding and Genetics LaboratoryJoint FAO/IAEA Division of Nuclear Techniques in Food and AgricultureIAEA Laboratories SeibersdorfInternational Atomic Energy AgencyVienna International CentreViennaAustria
| | - Joanna Jankowicz‐Cieslak
- Plant Breeding and Genetics LaboratoryJoint FAO/IAEA Division of Nuclear Techniques in Food and AgricultureIAEA Laboratories SeibersdorfInternational Atomic Energy AgencyVienna International CentreViennaAustria
| | - Stephan Nielen
- Plant Breeding and Genetics LaboratoryJoint FAO/IAEA Division of Nuclear Techniques in Food and AgricultureIAEA Laboratories SeibersdorfInternational Atomic Energy AgencyVienna International CentreViennaAustria
| | - Ivan Ingelbrecht
- Plant Breeding and Genetics LaboratoryJoint FAO/IAEA Division of Nuclear Techniques in Food and AgricultureIAEA Laboratories SeibersdorfInternational Atomic Energy AgencyVienna International CentreViennaAustria
| | - Bradley J. Till
- Plant Breeding and Genetics LaboratoryJoint FAO/IAEA Division of Nuclear Techniques in Food and AgricultureIAEA Laboratories SeibersdorfInternational Atomic Energy AgencyVienna International CentreViennaAustria
- Present address:
Department of Chromosome BiologyUniversity of ViennaA‐1030ViennaAustria
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30
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Shen PC, Hour AL, Liu LYD. Microarray meta-analysis to explore abiotic stress-specific gene expression patterns in Arabidopsis. BOTANICAL STUDIES 2017; 58:22. [PMID: 28510204 PMCID: PMC5432924 DOI: 10.1186/s40529-017-0176-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 05/05/2017] [Indexed: 05/26/2023]
Abstract
BACKGROUND Abiotic stresses are the major limiting factors that affect plant growth, development, yield and final quality. Deciphering the underlying mechanisms of plants' adaptations to stresses using few datasets might overlook the different aspects of stress tolerance in plants, which might be simultaneously and consequently operated in the system. Fortunately, the accumulated microarray expression data offer an opportunity to infer abiotic stress-specific gene expression patterns through meta-analysis. In this study, we propose to combine microarray gene expression data under control, cold, drought, heat, and salt conditions and determined modules (gene sets) of genes highly associated with each other according to the observed expression data. RESULTS By analyzing the expression variations of the Eigen genes from different conditions, we had identified two, three, and five gene modules as cold-, heat-, and salt-specific modules, respectively. Most of the cold- or heat-specific modules were differentially expressed to a particular degree in shoot samples, while most of the salt-specific modules were differentially expressed to a particular degree in root samples. A gene ontology (GO) analysis on the stress-specific modules suggested that the gene modules exclusively enriched stress-related GO terms and that different genes under the same GO terms may be alternatively disturbed in different conditions. The gene regulatory events for two genes, DREB1A and DEAR1, in the cold-specific gene module had also been validated, as evidenced through the literature search. CONCLUSIONS Our protocols study the specificity of the gene modules that were specifically activated under a particular type of abiotic stress. The biplot can also assist to visualize the stress-specific gene modules. In conclusion, our approach has the potential to further elucidate mechanisms in plants and beneficial for future experiments design under different abiotic stresses.
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Affiliation(s)
- Po-chih Shen
- Biometrics Division, Department of Agronomy, National Taiwan University, Taipei, Taiwan
| | - Ai-ling Hour
- Department of Life Science, Fu-Jen Catholic University, Xinbei, Taiwan
| | - Li-yu Daisy Liu
- Biometrics Division, Department of Agronomy, National Taiwan University, Taipei, Taiwan
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31
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Ståhl T, Zaal MP, Skitka LJ. Moralized Rationality: Relying on Logic and Evidence in the Formation and Evaluation of Belief Can Be Seen as a Moral Issue. PLoS One 2016; 11:e0166332. [PMID: 27851777 PMCID: PMC5112873 DOI: 10.1371/journal.pone.0166332] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 10/26/2016] [Indexed: 11/18/2022] Open
Abstract
In the present article we demonstrate stable individual differences in the extent to which a reliance on logic and evidence in the formation and evaluation of beliefs is perceived as a moral virtue, and a reliance on less rational processes is perceived as a vice. We refer to this individual difference variable as moralized rationality. Eight studies are reported in which an instrument to measure individual differences in moralized rationality is validated. Results show that the Moralized Rationality Scale (MRS) is internally consistent, and captures something distinct from the personal importance people attach to being rational (Studies 1–3). Furthermore, the MRS has high test-retest reliability (Study 4), is conceptually distinct from frequently used measures of individual differences in moral values, and it is negatively related to common beliefs that are not supported by scientific evidence (Study 5). We further demonstrate that the MRS predicts morally laden reactions, such as a desire for punishment, of people who rely on irrational (vs. rational) ways of forming and evaluating beliefs (Studies 6 and 7). Finally, we show that the MRS uniquely predicts motivation to contribute to a charity that works to prevent the spread of irrational beliefs (Study 8). We conclude that (1) there are stable individual differences in the extent to which people moralize a reliance on rationality in the formation and evaluation of beliefs, (2) that these individual differences do not reduce to the personal importance attached to rationality, and (3) that individual differences in moralized rationality have important motivational and interpersonal consequences.
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Affiliation(s)
- Tomas Ståhl
- Department of Psychology, University of Illinois at Chicago, Chicago, Illinois, United States of America
- * E-mail:
| | - Maarten P. Zaal
- Department of Psychology, University of Exeter, Exeter, United Kingdom
| | - Linda J. Skitka
- Department of Psychology, University of Illinois at Chicago, Chicago, Illinois, United States of America
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32
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Should Organic Agriculture Maintain Its Opposition to GM? New Techniques Writing the Same Old Story. SUSTAINABILITY 2016. [DOI: 10.3390/su8111105] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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33
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Effects of labeling a product eco-friendly and genetically modified: A cross-cultural comparison for estimates of taste, willingness to pay and health consequences. Food Qual Prefer 2016. [DOI: 10.1016/j.foodqual.2016.01.007] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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34
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Kibue GW, Liu X, Zheng J, Zhang X, Pan G, Li L, Han X. Farmers' Perceptions of Climate Variability and Factors Influencing Adaptation: Evidence from Anhui and Jiangsu, China. ENVIRONMENTAL MANAGEMENT 2016; 57:976-986. [PMID: 26796698 DOI: 10.1007/s00267-016-0661-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2014] [Accepted: 01/09/2016] [Indexed: 06/05/2023]
Abstract
Impacts of climate variability and climate change are on the rise in China posing great threat to agriculture and rural livelihoods. Consequently, China is undertaking research to find solutions of confronting climate change and variability. However, most studies of climate change and variability in China largely fail to address farmers' perceptions of climate variability and adaptation. Yet, without an understanding of farmers' perceptions, strategies are unlikely to be effective. We conducted questionnaire surveys of farmers in two farming regions, Yifeng, Jiangsu and Qinxi, Anhui achieving 280 and 293 responses, respectively. Additionally, we used climatological data to corroborate the farmers' perceptions of climate variability. We found that farmers' were aware of climate variability such that were consistent with climate records. However, perceived impacts of climate variability differed between the two regions and were influenced by farmers' characteristics. In addition, the vast majorities of farmers were yet to make adjustments in their farming practices as a result of numerous challenges. These challenges included socioeconomic and socio-cultural barriers. Results of logit modeling showed that farmers are more likely to adapt to climate variability if contact with extension services, frequency of seeking information, household heads' education, and climate variability perceptions are improved. These results suggest the need for policy makers to understand farmers' perceptions of climate variability and change in order to formulate policies that foster adaptation, and ultimately protect China's agricultural assets.
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Affiliation(s)
- Grace Wanjiru Kibue
- Center for Climate Change and Agriculture, Nanjing Agricultural University, 1 Weigang, Nanjing , 210095, China.
- Faculty of Environment and Resources Development, Egerton University, 536, Nakuru, Kenya.
| | - Xiaoyu Liu
- Center for Climate Change and Agriculture, Nanjing Agricultural University, 1 Weigang, Nanjing , 210095, China
| | - Jufeng Zheng
- Center for Climate Change and Agriculture, Nanjing Agricultural University, 1 Weigang, Nanjing , 210095, China
| | - Xuhui Zhang
- Center for Climate Change and Agriculture, Nanjing Agricultural University, 1 Weigang, Nanjing , 210095, China
| | - Genxing Pan
- Center for Climate Change and Agriculture, Nanjing Agricultural University, 1 Weigang, Nanjing , 210095, China
| | - Lianqing Li
- Center for Climate Change and Agriculture, Nanjing Agricultural University, 1 Weigang, Nanjing , 210095, China
| | - Xiaojun Han
- Center for Climate Change and Agriculture, Nanjing Agricultural University, 1 Weigang, Nanjing , 210095, China
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35
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Yang YT, Chen B. Governing GMOs in the USA: science, law and public health. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2016; 96:1851-1855. [PMID: 26536836 DOI: 10.1002/jsfa.7523] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Revised: 11/01/2015] [Accepted: 11/01/2015] [Indexed: 06/05/2023]
Abstract
Controversy surrounds the production and consumption of genetically modified organisms (GMOs). Proponents argue that GMO food sources represent the only viable solution to food shortages in an ever-growing global population. Science reports no harm from GMO use and consumption so far. Opponents fear the potentially negative impact that GMO development and use could have on the environment and consumers, and are concerned about the lack of data on the long-term effects of GMO use. We discuss the development of GMO food sources, the history of legislation and policy for the labeling requirements of GMO food products, and the health, environmental, and legal rationale for and against GMO food labeling. The Food and Drug Administration regulates food with GMOs within a coordinated framework of federal agencies. Despite mounting scientific evidence that GMO foods are substantially equivalent to traditionally bred food sources, debate remains over the appropriateness of GMO food labeling. In fact, food manufacturers have mounted a First Amendment challenge against Vermont's passage of a law that requires GMO labeling. Mandatory GMO labeling is not supported by science. Compulsory GMO labels may not only hinder the development of agricultural biotechnology, but may also exacerbate the misconception that GMOs endanger people's health.
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Affiliation(s)
- Y Tony Yang
- College of Health and Human Services, George Mason University, Fairfax, VA, 22020, USA
| | - Brian Chen
- Department of Health Services Policy and Management, Arnold School of Public Health, University of South Carolina, Columbia, SC, 29208, USA
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36
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Ghanian M, Ghoochani OM, Kitterlin M, Jahangiry S, Zarafshani K, Van Passel S, Azadi H. Attitudes of Agricultural Experts Toward Genetically Modified Crops: A Case Study in Southwest Iran. SCIENCE AND ENGINEERING ETHICS 2016; 22:509-524. [PMID: 26045394 DOI: 10.1007/s11948-015-9653-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2014] [Accepted: 05/14/2015] [Indexed: 06/04/2023]
Abstract
The production of genetically modified (GM) crops is growing around the world, and with it possible opportunities to combat food insecurity and hunger, as well as solutions to current problems facing conventional agriculture. In this regard the use of GMOs in food and agricultural applications has increased greatly over the past decade. However, the development of GM crops has been a matter of considerable interest and worldwide public controversy. This, in addition to skepticism, has stifled the use of this practice on a large scale in many areas, including Iran. It stands to reason that a greater understanding of this practice could be formed after a review of the existing expert opinions surrounding GM crops. Therefore, the purpose of this study was to analyze the predictors that influence agricultural experts' attitudes toward the development of and policies related to GM crops. Using a descriptive correlational research method, questionnaire data was collected from 65 experts from the Agricultural Organization in the Gotvand district in Southwest Iran. Results indicated that agricultural experts were aware of the environmental benefits and possible risks associated with GM crops. The majority of participants agreed that GM crops could improve food security and accelerate rural development, and were proponents of labeling practices for GM crops. Finally, there was a positive correlation between the perception of benefits and attitudes towards GM crops.
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Affiliation(s)
- Mansour Ghanian
- Department of Agricultural Extension and Education, Khuzestan Ramin Agriculture and Natural Resources University, Ahvaz, Iran
| | - Omid M Ghoochani
- Department of Agricultural Extension and Education, Khuzestan Ramin Agriculture and Natural Resources University, Ahvaz, Iran.
| | - Miranda Kitterlin
- Chaplin School of Hospitality and Tourism Management, Florida International University, Miami, FL, USA.
| | - Sheida Jahangiry
- Department of Agricultural Extension and Education, Khuzestan Ramin Agriculture and Natural Resources University, Ahvaz, Iran
| | - Kiumars Zarafshani
- Department of Agricultural Extension and Education, Razi University, Kermanshah, Iran
| | - Steven Van Passel
- Centre for Environmental Sciences, Hasselt University, Hasselt, Belgium
| | - Hossein Azadi
- Centre for Environmental Sciences, Hasselt University, Hasselt, Belgium
- Department of Geography, Ghent University, Ghent, Belgium
- Economics and Rural Development, Gembloux Agro-Bio Tech, University of Liège, Liège, Belgium
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37
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Burlakovskiy MS, Yemelyanov VV, Lutova LA. Plant Based Bioreactors of Recombinant Cytokines (Review). APPL BIOCHEM MICRO+ 2016; 52:121-137. [PMID: 32214409 PMCID: PMC7087682 DOI: 10.1134/s0003683816020034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Indexed: 01/16/2023]
Abstract
Cytokines are a family of signaling polypeptides involved in intercellular interactions in the process of the immune response, as well as in the regulation of a number of normal physiological functions. Cytokines are used in medicine for the treatment of cancer, immune disorders, viral infections, and other socially significant diseases, but the extent of their use is limited by the high production cost of the active agent. The development of this area of pharmacology is associated with the success of genetic engineering, which allows the production of significant amounts of protein by transgenic organisms. The review discusses the latest advances in the production of various cytokines with the use of genetically modified plants.
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Affiliation(s)
- M. S. Burlakovskiy
- Biology Faculty, St. Petersburg State University, St. Petersburg, 199034 Russia
| | - V. V. Yemelyanov
- Biology Faculty, St. Petersburg State University, St. Petersburg, 199034 Russia
| | - L. A. Lutova
- Biology Faculty, St. Petersburg State University, St. Petersburg, 199034 Russia
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38
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Ye S, Gao X. Excavating abiotic stress-related gene resources of terrestrial macroscopic cyanobacteria for crop genetic engineering: dawn and challenge. Bioengineered 2015; 6:313-5. [PMID: 26418632 DOI: 10.1080/21655979.2015.1091907] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
Genetically engineered (GE) crops with resistance to environmental stresses are one of the most important solutions for future food security. Numerous genes associated to plant stress resistance have been identified and characterized. However, the current reality is that only a few transgenic crops expressing prokaryotic genes are successfully applied in field conditions. These few prokaryotic genes include Agrobacterium strain CP4 EPSPS gene, Bacillus thuringiensis Cry1Ab gene and a bacterial chaperonin gene. Thus, the excavation of potentially critical genes still remains an arduous task for crop engineering. Terrestrial macroscopic cyanobacteria, Nostoc commune and Nostoc flagelliforme, which exhibit extreme resistance to desiccation stress, may serve as new prokaryotic bioresources for excavating critical genes. Recently, their marker gene wspA was heterologously expressed in Arabidopsis plant and the transgenics exhibited more flourishing root systems than wild-type plants under osmotic stress condition. In addition, some new genes associated with drought response and adaptation in N. flagelliforme are being uncovered by our ongoing RNA-seq analysis. Although the relevant work about the terrestrial macroscopic cyanobacteria is still underway, we believe that the prospect of excavating their critical genes for application in GE crops is quite optimistic.
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Affiliation(s)
- Shuifeng Ye
- a Shanghai Agrobiological Gene Center ; Shanghai , China
| | - Xiang Gao
- b School of Life Sciences; Central China Normal University ; Wuhan , China
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39
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Growth trend of scientific literature on genetic improvement through the database Scopus. Scientometrics 2015. [DOI: 10.1007/s11192-015-1733-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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40
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Hicks DJ. Epistemological depth in a GM crops controversy. STUDIES IN HISTORY AND PHILOSOPHY OF BIOLOGICAL AND BIOMEDICAL SCIENCES 2015; 50:1-12. [PMID: 25768981 DOI: 10.1016/j.shpsc.2015.02.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Revised: 01/01/2015] [Accepted: 02/07/2015] [Indexed: 06/04/2023]
Abstract
This paper examines the scientific controversy over the yields of genetically modified [GM] crops as a case study in epistemologically deep disagreements. Appeals to "the evidence" are inadequate to resolve such disagreements; not because the interlocutors have radically different metaphysical views (as in cases of incommensurability), but instead because they assume rival epistemological frameworks and so have incompatible views about what kinds of research methods and claims count as evidence. Specifically, I show that, in the yield debate, proponents and opponents of GM crops cite two different sets of claims as evidence, which correspond to two rival epistemological frameworks, classical experimental epistemology and Nancy Cartwright's evidence for use. I go on to argue that, even if both sides of the debate accepted Cartwright's view, they might still disagree over what counts as evidence, because evidence for use ties standards of evidence to what is sometimes called the "context of application."
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Affiliation(s)
- Daniel J Hicks
- Rotman Institute of Philosophy, University of Western Ontario, London, Ontario, N6A 5B8, Canada.
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Azadi H, Ghanian M, Ghoochani OM, Rafiaani P, Taning CNT, Hajivand RY, Dogot T. Genetically Modified Crops: Towards Agricultural Growth, Agricultural Development, or Agricultural Sustainability? FOOD REVIEWS INTERNATIONAL 2015. [DOI: 10.1080/87559129.2014.994816] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Dong F, Mitchell PD, Colquhoun J. Measuring farm sustainability using data envelope analysis with principal components: the case of Wisconsin cranberry. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2015; 147:175-183. [PMID: 25277860 DOI: 10.1016/j.jenvman.2014.08.025] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Revised: 03/12/2014] [Accepted: 08/18/2014] [Indexed: 06/03/2023]
Abstract
Measuring farm sustainability performance is a crucial component for improving agricultural sustainability. While extensive assessments and indicators exist that reflect the different facets of agricultural sustainability, because of the relatively large number of measures and interactions among them, a composite indicator that integrates and aggregates over all variables is particularly useful. This paper describes and empirically evaluates a method for constructing a composite sustainability indicator that individually scores and ranks farm sustainability performance. The method first uses non-negative polychoric principal component analysis to reduce the number of variables, to remove correlation among variables and to transform categorical variables to continuous variables. Next the method applies common-weight data envelope analysis to these principal components to individually score each farm. The method solves weights endogenously and allows identifying important practices in sustainability evaluation. An empirical application to Wisconsin cranberry farms finds heterogeneity in sustainability practice adoption, implying that some farms could adopt relevant practices to improve the overall sustainability performance of the industry.
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Affiliation(s)
- Fengxia Dong
- Department of Agricultural and Applied Economics, University of Wisconsin-Madison, 427 Lorch Street, Madison, WI 53706, USA.
| | - Paul D Mitchell
- Department of Agricultural and Applied Economics, University of Wisconsin-Madison, 427 Lorch Street, Madison, WI 53706, USA.
| | - Jed Colquhoun
- Department of Horticulture, University of Wisconsin-Madison, 1575 Linden Drive, Madison, WI 53706, USA.
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Oliver MJ. Why we need GMO crops in agriculture. MISSOURI MEDICINE 2014; 111:492-507. [PMID: 25665234 PMCID: PMC6173531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Within 35 years (2049) the global population will reach an estimated nine billion people. This presents a massive challenge to agriculture: how do we feed all of these people with nutritious food in a sustainable way? Presently the yields of most major crops are stagnating while the demand for food, both grain and animal protein, is growing. To meet the challenge of improving yields requires a constant commitment to generating a steady supply of improved cultivars and lines for all major crops. Conventional breeding cannot keep pace with what is required; to meet the targets biotechnology and the production of genetically-modified (GM) crops is filling the gap. However, there are still concerns as to the safety of GM crops for human consumption and the environment. In this review I explore the need for GM crops, the way they are produced, and their impact and safety. The future is very promising for GM technologies to meet the future global needs for food feed and fiber in a sustainable and responsible way. GM crops are only one part of the solution. To meet the targeted yields, nutritional quality, and sustainable production, we need all of the tools at our disposal including conventional and organic food production systems.
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Soto CM. Protein engineering and other bio-synthetic routes for bio-based materials: current uses and potential applications. Front Chem 2014; 2:83. [PMID: 25353016 PMCID: PMC4195369 DOI: 10.3389/fchem.2014.00083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Accepted: 09/19/2014] [Indexed: 11/13/2022] Open
Affiliation(s)
- Carissa M Soto
- U. S. Naval Research Laboratory, Center for Bio/Molecular Science and Engineering Washington, DC, USA
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Mattoo AK. Translational research in agricultural biology-enhancing crop resistivity against environmental stress alongside nutritional quality. Front Chem 2014; 2:30. [PMID: 24926479 PMCID: PMC4046571 DOI: 10.3389/fchem.2014.00030] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Accepted: 05/05/2014] [Indexed: 01/24/2023] Open
Affiliation(s)
- Autar K. Mattoo
- Sustainable Agricultural Systems Laboratory, United States Department of Agriculture, The Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research ServiceBeltsville, MD, USA
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Wang B, Wang RR, Cui ZH, Bi WL, Li JW, Li BQ, Ozudogru EA, Volk GM, Wang QC. Potential applications of cryogenic technologies to plant genetic improvement and pathogen eradication. Biotechnol Adv 2014; 32:583-95. [DOI: 10.1016/j.biotechadv.2014.03.003] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Revised: 01/27/2014] [Accepted: 03/13/2014] [Indexed: 01/08/2023]
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Yu H, Li Y, Li X, Romeis J, Wu K. Expression of Cry1Ac in transgenic Bt soybean lines and their efficiency in controlling lepidopteran pests. PEST MANAGEMENT SCIENCE 2013; 69:1326-33. [PMID: 23564718 DOI: 10.1002/ps.3508] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2012] [Revised: 12/02/2012] [Accepted: 02/08/2013] [Indexed: 05/10/2023]
Abstract
BACKGROUND Two transgenic lines of the soybean Glycine max, MON87701 expressing the Cry1Ac protein and MON87701RR2Y expressing Cry1Ac + EPSPS proteins, were evaluated for their resistance to four lepidopteran pests in the laboratory using detached-leaf bioassays throughout the soybean growth seasons (before anthesis, during anthesis and after anthesis) in China. Enzyme-linked immunosorbent assays (ELISAs) were used to monitor the Cry1Ac expression in soybean leaves. RESULTS The bioassay results revealed that both transgenic soybean lines exhibited significantly high resistance against Helicoverpa armigera (Hübner) throughout the soybean growing seasons. The survival rates of H. armigera larvae ranged from 5.4 to 24.4% when feeding on the transgenic soybean leaves, significantly lower than the survival rates when feeding on control leaves (71.1-94.9%). Limited resistance was found for both transgenic soybean lines against Spodoptera litura (Fabricius), although the survival rates and weight of S. litura larvae as well as female fecundity were significantly decreased when feeding on Bt soybean leaves compared with feeding on control leaves. In contrast, both transgenic soybean lines provided almost no resistance to Spodoptera exigua (Hübner) and Agrotis ypsilon (Rottemberg). Cry1Ac expression in the leaves of both transgenic soybean lines was relatively stable throughout the soybean growing season, with a peak occurring at V6 -8 and V11 -12 before anthesis. The ELISA results were positively correlated with the results from the insect bioassays. CONCLUSIONS The results show that, while Cry1Ac-expressing Bt soybeans may provide good protection against H. armigera, alternative control measures are required to manage S. exigua, S. litura and A. ypsilon.
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Affiliation(s)
- Huilin Yu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
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Clarke JD, Alexander DC, Ward DP, Ryals JA, Mitchell MW, Wulff JE, Guo L. Assessment of genetically modified soybean in relation to natural variation in the soybean seed metabolome. Sci Rep 2013; 3:3082. [PMID: 24170158 PMCID: PMC3812653 DOI: 10.1038/srep03082] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Accepted: 10/11/2013] [Indexed: 11/09/2022] Open
Abstract
Genetically modified (GM) crops currently constitute a significant and growing part of agriculture.An important aspect of GM crop adoption is to demonstrate safety; identifying differences in end points with respect to conventional crops is a part of the safety assessment process [corrected]. Untargeted metabolomics has the ability to profile diverse classes of metabolites and thus could be an adjunct for identification of differences between the GM crop and its conventional counterpart [corrected].To account for environmental effects and introgression of GM traits into diverse genetic backgrounds, we propose that the assessment for GM crop metabolic composition should be understood within the context of the natural variation for the crop. Using a non-targeted metabolomics platform, we profiled 169 metabolites and established their dynamic ranges from the seeds of 49 conventional soybean lines representing the current commercial genetic diversity. We further demonstrated that the metabolome of a GM line had no significant deviation from natural variation within the soybean metabolome, with the exception of changes in the targeted engineered pathway.
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Affiliation(s)
- Joseph D. Clarke
- Syngenta Biotechnology, Inc., 3504 Cornwallis Road, Research Triangle Park, NC 27709, USA
- These authors contributed equally to this work
| | - Danny C. Alexander
- Metabolon Inc., 617 Davis Drive, Suite 400, Durham, NC 27713, USA
- These authors contributed equally to this work
| | - Dennis P. Ward
- Syngenta Biotechnology, Inc., 3504 Cornwallis Road, Research Triangle Park, NC 27709, USA
| | - John A. Ryals
- Metabolon Inc., 617 Davis Drive, Suite 400, Durham, NC 27713, USA
| | | | - Jacob E. Wulff
- Metabolon Inc., 617 Davis Drive, Suite 400, Durham, NC 27713, USA
| | - Lining Guo
- Metabolon Inc., 617 Davis Drive, Suite 400, Durham, NC 27713, USA
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Genomic misconception: a fresh look at the biosafety of transgenic and conventional crops. A plea for a process agnostic regulation. N Biotechnol 2013; 31:1-17. [PMID: 23684919 DOI: 10.1016/j.nbt.2013.04.008] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2012] [Revised: 09/01/2012] [Accepted: 04/15/2013] [Indexed: 12/17/2022]
Abstract
The regulation of genetically engineered crops, in Europe and within the legislation of the Cartagena biosafety protocol is built on false premises: The claim was (and unfortunately still is) that there is a basic difference between conventional and transgenic crops, this despite the fact that this has been rejected on scientifically solid grounds since many years. This contribution collects some major arguments for a fresh look at regulation of transgenic crops, they are in their molecular processes of creation not basically different from conventional crops, which are based in their breeding methods on natural, sometimes enhanced mutation. But the fascination and euphoria of the discoveries in molecular biology and the new perspectives in plant breeding in the sixties and seventies led to the wrong focus on transgenic plants alone. In a collective framing process the initial biosafety debates focused on the novelty of the process of transgenesis. When early debates on the risk assessment merged into legislative decisions, this wrong focus on transgenesis alone seemed uncontested. The process-focused view was also fostered by a conglomerate of concerned scientists and biotechnology companies, both with a vested interest to at least tolerate the rise of the safety threshold to secure research money and to discourage competitors of all kinds. Policy minded people and opponent activists without deeper insight in the molecular science agreed to those efforts without much resistance. It is interesting to realize, that the focus on processes was uncontested by a majority of regulators, this despite of serious early warnings from important authorities in science, mainly of US origin. It is time to change the regulation of genetically modified (GM) crops toward a more science based process-agnostic legislation. Although this article concentrates on the critique of the process-oriented regulation, including some details about the history behind, there should be no misunderstanding that there are other important factors responsible for the failure of this kind of process-oriented regulation, most importantly: the predominance of politics in the decision making processes combined with the lack of serious scientific debates on regulatory matters within the European Union and also in the Cartagena system, the obscure and much too complex decision making structures within the EU, and the active, professional, negative and intimidating role of fundamental opposition against GM crops on all levels dealing with flawed science, often declared as better parallel science published by 'independent' scientists.
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