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Ji R, Zhou Y, Cai J, Chu K, Zeng Y, Cheng H. Release characteristics of hydrochar-derived dissolved organic matter: Effects of hydrothermal temperature and environmental conditions. CHEMOSPHERE 2023; 321:138138. [PMID: 36791817 DOI: 10.1016/j.chemosphere.2023.138138] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 01/10/2023] [Accepted: 02/11/2023] [Indexed: 06/18/2023]
Abstract
Much research has been done on the preparation and application of hydrochars, but research on the release characteristics of hydrochar-derived dissolved organic matter (HDOM) is very limited; clarifying the release characteristics of HDOM is important for understanding and adjusting the environmental behaviour of hydrochar. Herein, the potential release of HDOM from rice straw-derived hydrochars prepared at different hydrothermal temperatures was investigated under various potential environmental conditions for the first time. The total release quantity and humification degree of HDOM decreased with increasing hydrothermal temperature. The critical dividing line for various hydrothermal reactions, decomposition and polymerization, was in the range of 240 °C-260 °C. Alkaline condition increased the HDOM release amount (up to 299 mg g-1), molecular weight (as high as 423 Da) and molecular diversity (8857 compounds) from rice straw-derived hydrochars. The unique substances of HDOM released under alkaline condition were mainly distributed in lipids-like substances, CRAM/lignins-like substances, aromatic structures, and tannins-like substances, while few unique substances were found under acidic condition. Additionally, CRAM/lignins-like substances were the most abundant in all HDOM samples, reaching 82%, which were relatively stable and could achieve carbon sequestration in different environments. The findings provided a new insight on understanding the potential environment behaviors of hydrochar.
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Affiliation(s)
- Rongting Ji
- Nanjing Institute of Environmental Science, Ministry of Ecology and Environment of the People's Republic of China, Nanjing, 210042, PR China
| | - Yue Zhou
- Nanjing Institute of Environmental Science, Ministry of Ecology and Environment of the People's Republic of China, Nanjing, 210042, PR China; Co-Innovation Center for the Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, PR China; College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Jinbang Cai
- Nanjing Institute of Environmental Science, Ministry of Ecology and Environment of the People's Republic of China, Nanjing, 210042, PR China
| | - Kejian Chu
- College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Yuan Zeng
- Nanjing Institute of Environmental Science, Ministry of Ecology and Environment of the People's Republic of China, Nanjing, 210042, PR China.
| | - Hu Cheng
- Co-Innovation Center for the Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, PR China.
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2
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Zhang G, Hu Y, Pan X, Cao R, Hu Q, Fu R, Risalat H, Shang B. Effects of increased ozone on rice panicle morphology. iScience 2023; 26:106471. [PMID: 37096034 PMCID: PMC10122049 DOI: 10.1016/j.isci.2023.106471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 01/10/2023] [Accepted: 03/20/2023] [Indexed: 04/08/2023] Open
Abstract
Ground-level ozone threatens rice production, which provides staple food for more than half of the world's population. Improving the adaptability of rice crops to ozone pollution is essential to ending global hunger. Rice panicles not only affect grain yield and grain quality but also the adaptability of plants to environmental changes, but the effects of ozone on rice panicles are not well understood. Through an open top chamber experiment, we investigated the effects of long-term and short-term ozone on the traits of rice panicles, finding that both long-term and short-term ozone significantly reduced the number of panicle branches and spikelets in rice, and especially the fertility of spikelets in hybrid cultivar. The reduction in spikelet quantity and fertility because of ozone exposure is caused by changes in secondary branches and attached spikelet. These results suggest the potential for effective adaptation to ozone by altering breeding targets and developing growth stage-specific agricultural techniques.
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3
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Platani M, Sokefun O, Bassil E, Apidianakis Y. Genetic engineering and genome editing in plants, animals and humans: Facts and myths. Gene 2023; 856:147141. [PMID: 36574935 DOI: 10.1016/j.gene.2022.147141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 12/17/2022] [Accepted: 12/21/2022] [Indexed: 12/25/2022]
Abstract
Human history is inextricably linked to the introduction of desirable heritable traits in plants and animals. Selective breeding (SB) predates our historical period and has been practiced since the advent of agriculture and farming more than ten thousand years ago. Since the 1970s, methods of direct plant and animal genome manipulation are constantly being developed. These are collectively described as "genetic engineering" (GE). Plant GE aims to improve nutritional value, insect resistance and weed control. Animal GE has focused on livestock improvement and disease control. GE applications also involve medical improvements intended to treat human disease. The scientific consensus built around marketed products of GE organisms (GEOs) is usually well established, noting significant benefits and low risks. GEOs are exhaustively scrutinized in the EU and many non-EU countries for their effects on human health and the environment, but scrutiny should be equally applied to all previously untested organisms derived directly from nature or through selective breeding. In fact, there is no evidence to suggest that natural or selectively bred plants and animals are in principle safer to humans than GEOs. Natural and selectively bred strains evolve over time via genetic mutations that can be as risky to humans and the environment as the mutations found in GEOs. Thus, previously untested plant and animal strains aimed for marketing should be proven useful or harmful to humans only upon comparative testing, regardless of their origin. Highlighting the scientific consensus declaring significant benefits and rather manageable risks provided by equitably accessed GEOs, can mitigate negative predispositions by policy makers and the public. Accordingly, we provide an overview of the underlying technologies and the scientific consensus to help resolve popular myths about the safety and usefulness of GEOs.
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Affiliation(s)
- Maria Platani
- Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | - Owolabi Sokefun
- Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | - Elias Bassil
- Horticultural Sciences Department, University of Florida, Gainesville, USA
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Impacts of Climate Change on Rice Grain: A Literature Review on What Is Happening, and How Should We Proceed? Foods 2023; 12:foods12030536. [PMID: 36766065 PMCID: PMC9914188 DOI: 10.3390/foods12030536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 01/19/2023] [Accepted: 01/20/2023] [Indexed: 01/27/2023] Open
Abstract
More than half of the people on Earth get their calories, proteins, and minerals from rice grains. Staple increases in the quantity and quality of rice grains are key to ending hunger and malnutrition. Rice production, however, is vulnerable to climate change, and the climate on Earth is becoming more fluctuating with the atmospheric change induced by human activities. As a result, the impacts of climate change on rice grain (ICCRG) have sparked widespread concern. In order to reveal the development and the trend in the study on the ICCRG, a bibliometric analysis was conducted. The results showed that both the model simulations and the field experiment-based observations, as reflected by APSIM (the Agricultural Production Systems sIMulator) and free-air carbon dioxide (CO2) enrichment, are of concern to researchers worldwide, especially in China, India, the United States, and Japan. Different types of warming include short-term, nighttime, soil and water, and canopy, and their interactions with other climate factors, such as CO2, or agronomic factors, such as nitrogen level, are also of concern to researchers. Spatiotemporal variations in changing weather and regional adaptations from developed and developing countries are challenging the evaluation of ICCRG from an economic perspective. In order to improve the efficacy of breeding adaptable cultivars and developing agronomic management, interdisciplinary studies integrating molecular biology, plant physiology, agronomy, food chemistry, ecology, and socioeconomics are needed.
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5
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Assessment of allelic and genetic diversity, and population structure among farmers' rice varieties using microsatellite markers and morphological traits. GENE REPORTS 2022. [DOI: 10.1016/j.genrep.2022.101719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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6
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Discovery of the Earliest Rice Paddy in the Mixed Rice–Millet Farming Area of China. LAND 2022. [DOI: 10.3390/land11060831] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Neolithic rice remains were recovered from a mixed rice–millet farming area in China outside the original centers of rice farming. Whether the rice remains were the result of local cultivation or obtained through trade remains unclear. Rice paddy fields are direct evidence of local cultivation. In this study, phytolith samples from the Zhangwangzhuang site were analyzed. The discriminant function distinguished 17 of 30 samples in the suspected paddy field area as rice paddy fields with an average probability of 74%; The proportion of rice bulliform phytoliths with ≥9 scales indicated that rice (Oryza sativa) was still being domesticated and, moreover, six η-type phytoliths from broomcorn millet (Panicum miliaceum) were identified. These results suggested that the suspected paddy field at Zhangwangzhuang might be the earliest rice paddy field (ca. 6000 cal. BP) in northern China and that mixed farming was practiced here since the early Yangshao period. This study adopted discriminant analysis methods to discover ancient rice paddy fields, observed rice paddy fields outside the core rice origin area, and provided the earliest evidence regarding the development of mixed rice–millet farming in the upper Huai River region.
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Toyoizumi T, Ikegaya A, Kosugi T. Surface disinfection influences the antioxidant capacity and GABA content of saline‐treated brown rice (
Oryza sativa
L.). Cereal Chem 2022. [DOI: 10.1002/cche.10544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Tomoyasu Toyoizumi
- Shizuoka Prefectural Research Institute of Agriculture and Forestry, 678‐1 Tomigaoka Iwata, Shizuoka 438‐0803 Japan
| | - Atsushi Ikegaya
- Shizuoka Prefectural Research Institute of Agriculture and Forestry, 678‐1 Tomigaoka Iwata, Shizuoka 438‐0803 Japan
- Shizuoka Professional University Junior College of Agriculture, 678‐1 Tomigaoka Iwata, Shizuoka 438‐0803 Japan
| | - Toru Kosugi
- Shizuoka Prefectural Research Institute of Agriculture and Forestry, 678‐1 Tomigaoka Iwata, Shizuoka 438‐0803 Japan
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Toyoizumi T, Kosugi T, Toyama Y, Nakajima T. Effects of high-temperature cooking on the gamma-aminobutyric acid content and antioxidant capacity of germinated brown rice ( Oryza sativa L.). CYTA - JOURNAL OF FOOD 2021. [DOI: 10.1080/19476337.2021.1905721] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Tomoyasu Toyoizumi
- Shizuoka Prefectural Research Institute of Agriculture and Forestry, Iwata, Japan
| | - Toru Kosugi
- Shizuoka Prefectural Research Institute of Agriculture and Forestry, Iwata, Japan
| | - Yusuke Toyama
- Shizuoka Prefectural Research Institute of Agriculture and Forestry, Iwata, Japan
| | - Teruko Nakajima
- Shizuoka Prefectural Research Institute of Agriculture and Forestry, Iwata, Japan
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de Oliveira BHN, Wairich A, Turchetto-Zolet AC, Fett JP, Ricachenevsky FK. The Mitochondrial Iron-Regulated (MIR) gene is Oryza genus specific and evolved before speciation within the Oryza sativa complex. PLANTA 2020; 251:94. [PMID: 32253515 DOI: 10.1007/s00425-020-03386-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Accepted: 03/28/2020] [Indexed: 05/07/2023]
Abstract
The MIR gene is not an Oryza sativa orphan gene, but an Oryza genus-specific gene that evolved before AA lineage speciation by a complex origination process. Rice (Oryza sativa L.) is a model species and an economically relevant crop. The Oryza genus comprises 25 species, with genomic data available for several Oryza species, making it a model for genetics and evolution. The Mitochondrial Iron-Regulated (MIR) gene was previously implicated in the O. sativa Fe deficiency response, and was considered an orphan gene present only in rice. Here we show that MIR is also found in other Oryza species that belong to the Oryza sativa complex, which have AA genome type and constitute the primary gene pool for O. sativa breeding. Our data suggest that MIR originated in a stepwise process, in which sequences derived from an exon fragment of the raffinose synthase gene were pseudogenized into non-coding, which in turn originated the MIR gene de novo. All species with a putative functional MIR gene conserve their regulation by Fe deficiency, with the exception of Oryza barthii. In O. barthii, the MIR coding sequence was translocated to a different chromosomal position and separated from its regulatory region, leading to a lack of Fe deficiency responsiveness. Moreover, the MIR co-expression subnetwork cluster in O. sativa is responsive to Fe deficiency, evidencing the importance of the newly originated gene in Fe uptake. This work establishes that MIR is not an orphan gene as previously proposed, but a de novo originated gene within the genus Oryza. We also showed that MIR is undergoing genomic changes in one species (O. barthii), with an impact on Fe deficiency response.
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Affiliation(s)
- Ben Hur Neves de Oliveira
- Centro de Biotecnologia e Programa de Pós-Graduação em Biologia Celular e Molecular, Universidade Federal Do Rio Grande Do Sul, Av. Bento Gonçalves 9500, Building 43.421 CEP, Porto Alegre, Rio Grande do Sul, 91509-900, Brazil
| | - Andriele Wairich
- Centro de Biotecnologia e Programa de Pós-Graduação em Biologia Celular e Molecular, Universidade Federal Do Rio Grande Do Sul, Av. Bento Gonçalves 9500, Building 43.421 CEP, Porto Alegre, Rio Grande do Sul, 91509-900, Brazil
| | - Andreia Carina Turchetto-Zolet
- Departamento de Genética e Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal Do Rio Grande Do Sul, Av. Bento Gonçalves 9500, Building 43.323, CEP, Porto Alegre, Rio Grande do Sul, 91509-900, Brazil
| | - Janette Palma Fett
- Centro de Biotecnologia e Programa de Pós-Graduação em Biologia Celular e Molecular, Universidade Federal Do Rio Grande Do Sul, Av. Bento Gonçalves 9500, Building 43.421 CEP, Porto Alegre, Rio Grande do Sul, 91509-900, Brazil
- Departamento de Botânica, Universidade Federal Do Rio Grande Do Sul, Av. Bento Gonçalves 9500, Building 43.423, CEP, Porto Alegre, Rio Grande do Sul, 91509-900, Brazil
| | - Felipe Klein Ricachenevsky
- Centro de Biotecnologia e Programa de Pós-Graduação em Biologia Celular e Molecular, Universidade Federal Do Rio Grande Do Sul, Av. Bento Gonçalves 9500, Building 43.421 CEP, Porto Alegre, Rio Grande do Sul, 91509-900, Brazil.
- Departamento de Botânica, Universidade Federal Do Rio Grande Do Sul, Av. Bento Gonçalves 9500, Building 43.423, CEP, Porto Alegre, Rio Grande do Sul, 91509-900, Brazil.
- Departamento de Biologia, Universidade Federal de Santa Maria, Av. Roraima 1000, Building 16, Room 3254, CEP, Santa Maria, Rio Grande do Sul, 97105-900, Brazil.
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10
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Scherm B, Balmas V, Infantino A, Aragona M, Valente MT, Desiderio F, Marcello A, Phanthavong S, Burgess LW, Rau D. Clonality, spatial structure, and pathogenic variation in Fusarium fujikuroi from rain-fed rice in southern Laos. PLoS One 2019; 14:e0226556. [PMID: 31869352 PMCID: PMC6927642 DOI: 10.1371/journal.pone.0226556] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Accepted: 11/29/2019] [Indexed: 11/18/2022] Open
Abstract
Bakanae disease, caused by the fungal phytopathogen Fusarium fujikuroi, can be detected in most rice (Oryza sativa L.) growing areas worldwide. In this study, we investigated the population structure of this fungus in southern Lao PDR, a country located near the geographic origin of rice domestication. Microsatellites (SSRs) and mating type (MAT) analyses, pathogenicity and fungicide sensitivity tests were integrated in the study. The first key finding is that the population genetic structure of F. fujikuroi in Lao PDR is consistent with high clonal reproduction. Indeed, (i) “true” clones were identified; (ii) within populations, MAT types were frequently skewed from 1:1 ratio, (iii) linkage disequilibrium (among SSRs as also among SSRs and MAT) was present, and (iv) gene-flow between opposite MAT types within the same population is restricted. The presence of genetic divergence among areas and populations and the occurrence of positive spatial autocorrelation of genetic variation, indicate that migration is restricted, and that genetic drift plays an important role in the evolution of this fungus. Two main well-defined groups of isolates were detected (FST = 0.213) that display a non-random spatial distribution. They differ in the ability to induce seedlings death but not seedlings elongation (the typical Bakanae symptom) suggesting that the pathogen’s ability to induce the two symptoms is under different genetic control. Finally, we compared two agroecosystems with contrasting characteristics: low-input and traditional (Lao PDR) vs high-input and modern (Italy). We found differences in the level of population structuring and of spatial autocorrelation. This suggests that the evolutionary potential of the fungus not only depends on its intrinsic characteristics, but is strongly influenced by other external factors, most likely by the dynamics of infested seed exchange. Thus, quarantine and chemical treatments are a way to reduce population connectivity and hence the evolutionary potential of this pathogen.
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Affiliation(s)
- Barbara Scherm
- Dipartimento di Agraria, Sezione di Patologia ed Entomologia, Università degli Studi di Sassari, Sassari, Italy
| | - Virgilio Balmas
- Dipartimento di Agraria, Sezione di Patologia ed Entomologia, Università degli Studi di Sassari, Sassari, Italy
| | - Alessandro Infantino
- Council for Agricultural Research and Economics (CREA), Research Centre for Plant Protection and Certification, Rome, Italy
| | - Maria Aragona
- Council for Agricultural Research and Economics (CREA), Research Centre for Plant Protection and Certification, Rome, Italy
| | - Maria Teresa Valente
- Council for Agricultural Research and Economics (CREA), Research Centre for Plant Protection and Certification, Rome, Italy
| | - Francesca Desiderio
- Council for Agricultural Research and Economics, Research Centre for Genomics and Bioinformatics, Fiorenzuola d’Arda (PC), Italy
| | - Angela Marcello
- Dipartimento di Agraria, Sezione di Patologia ed Entomologia, Università degli Studi di Sassari, Sassari, Italy
| | - Sengphet Phanthavong
- Provincial Agriculture and Forestry, Thaluang Village, Pakse, Champasak, Lao PDR
| | - Lester W. Burgess
- Sydney Insitute of Agriculture, Faculty of Science, University of Sydney, New South Wales, Australia
| | - Domenico Rau
- Dipartimento di Agraria, Sezione di Patologia ed Entomologia, Università degli Studi di Sassari, Sassari, Italy
- * E-mail:
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11
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Chai Q, Li Y, Li X, Wu W, Peng H, Jia R, Sun Q. Assessment of variation in paddy microbial communities under different storage temperatures and relative humidity by Illumina sequencing analysis. Food Res Int 2019; 126:108581. [DOI: 10.1016/j.foodres.2019.108581] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 07/04/2019] [Accepted: 07/24/2019] [Indexed: 02/07/2023]
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12
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Wairich A, de Oliveira BHN, Arend EB, Duarte GL, Ponte LR, Sperotto RA, Ricachenevsky FK, Fett JP. The Combined Strategy for iron uptake is not exclusive to domesticated rice (Oryza sativa). Sci Rep 2019; 9:16144. [PMID: 31695138 PMCID: PMC6834603 DOI: 10.1038/s41598-019-52502-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 10/14/2019] [Indexed: 01/12/2023] Open
Abstract
Iron (Fe) is an essential micronutrient that is frequently inaccessible to plants. Rice (Oryza sativa L.) plants employ the Combined Strategy for Fe uptake, which is composed by all features of Strategy II, common to all Poaceae species, and some features of Strategy I, common to non-Poaceae species. To understand the evolution of Fe uptake mechanisms, we analyzed the root transcriptomic response to Fe deficiency in O. sativa and its wild progenitor O. rufipogon. We identified 622 and 2,017 differentially expressed genes in O. sativa and O. rufipogon, respectively. Among the genes up-regulated in both species, we found Fe transporters associated with Strategy I, such as IRT1, IRT2 and NRAMP1; and genes associated with Strategy II, such as YSL15 and IRO2. In order to evaluate the conservation of these Strategies among other Poaceae, we identified the orthologs of these genes in nine species from the Oryza genus, maize and sorghum, and evaluated their expression profile in response to low Fe condition. Our results indicate that the Combined Strategy is not specific to O. sativa as previously proposed, but also present in species of the Oryza genus closely related to domesticated rice, and originated around the same time the AA genome lineage within Oryza diversified. Therefore, adaptation to Fe2+ acquisition via IRT1 in flooded soils precedes O. sativa domestication.
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Affiliation(s)
- Andriele Wairich
- Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Ben Hur Neves de Oliveira
- Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Ezequiel Barth Arend
- Faculdade de Agronomia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Guilherme Leitão Duarte
- Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Lucas Roani Ponte
- Departamento de Biologia, Centro de Ciências Naturais e Exatas, Universidade Federal de Santa Maria, Santa Maria, Brazil
| | - Raul Antonio Sperotto
- Programa de Pós-Graduação em Biotecnologia, Universidade do Vale do Taquari - Univates, Lajeado, Brazil
| | - Felipe Klein Ricachenevsky
- Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.
- Departamento de Biologia, Centro de Ciências Naturais e Exatas, Universidade Federal de Santa Maria, Santa Maria, Brazil.
| | - Janette Palma Fett
- Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.
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13
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Wu X, Heffelfinger C, Zhao H, Dellaporta SL. Benchmarking variant identification tools for plant diversity discovery. BMC Genomics 2019; 20:701. [PMID: 31500583 PMCID: PMC6734213 DOI: 10.1186/s12864-019-6057-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 08/22/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The ability to accurately and comprehensively identify genomic variations is critical for plant studies utilizing high-throughput sequencing. Most bioinformatics tools for processing next-generation sequencing data were originally developed and tested in human studies, raising questions as to their efficacy for plant research. A detailed evaluation of the entire variant calling pipeline, including alignment, variant calling, variant filtering, and imputation was performed on different programs using both simulated and real plant genomic datasets. RESULTS A comparison of SOAP2, Bowtie2, and BWA-MEM found that BWA-MEM was consistently able to align the most reads with high accuracy, whereas Bowtie2 had the highest overall accuracy. Comparative results of GATK HaplotypCaller versus SAMtools mpileup indicated that the choice of variant caller affected precision and recall differentially depending on the levels of diversity, sequence coverage and genome complexity. A cross-reference experiment of S. lycopersicum and S. pennellii reference genomes revealed the inadequacy of single reference genome for variant discovery that includes distantly-related plant individuals. Machine-learning-based variant filtering strategy outperformed the traditional hard-cutoff strategy resulting in higher number of true positive variants and fewer false positive variants. A 2-step imputation method, which utilized a set of high-confidence SNPs as the reference panel, showed up to 60% higher accuracy than direct LD-based imputation. CONCLUSIONS Programs in the variant discovery pipeline have different performance on plant genomic dataset. Choice of the programs is subjected to the goal of the study and available resources. This study serves as an important guiding information for plant biologists utilizing next-generation sequencing data for diversity characterization and crop improvement.
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Affiliation(s)
- Xing Wu
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, 06520-8104, USA
| | - Christopher Heffelfinger
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, 06520-8104, USA
| | - Hongyu Zhao
- Department of Biostatistics, Yale School of Public Health, Yale University, New Haven, CT, 06520-8034, USA
| | - Stephen L Dellaporta
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, 06520-8104, USA.
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14
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Wang X, Sun W, Ma X. Differential impacts of copper oxide nanoparticles and Copper(II) ions on the uptake and accumulation of arsenic in rice (Oryza sativa). ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 252:967-973. [PMID: 31252135 DOI: 10.1016/j.envpol.2019.06.052] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 05/13/2019] [Accepted: 06/11/2019] [Indexed: 05/27/2023]
Abstract
Arsenic (As) in rice grains is a serious food safety concern. Some coexisting engineered nanoparticles (ENPs) were shown to alter the accumulation and speciation of As in rice grains. However, investigation on the effects of copper oxide nanoparticles (CuO NPs), a popular ingredient in pesticides, on the uptake and accumulation of As is rare. We explored the potentially different impact of CuO NPs and corresponding Cu(II) ions on the accumulation of two As species in rice seedlings in a hydroponic system. Rice seedlings were treated with a combinations of 1 mg/L of arsenite (As(III)) or arsenate (As(V)) and 100 mg/L of CuO NPs or Cu(II) for 6 days. Both forms of Cu significantly reduced the accumulation of total As in rice tissues, with Cu(II) exhibiting significantly greater effect than CuO NPs. As speciation in rice roots was markedly affected by both forms of Cu, and the impacts were Cu-form dependent. For example, the co-existence of As(V) with CuO NPs led to a 45% decrease of As(V) in rice roots, while the co-existence of As(V) with Cu(II) caused a 47% increase in As(V) in rice roots. As speciation in rice shoots was less affected by co-present Cu than in rice roots. Co-occurring As(III) or As(V) lowered Cu concentration in rice roots by 40% and 50% in treatments with CuO NPs, but did not affect Cu content in rice roots co-exposed to Cu(II). The study confirmed the reciprocal effect of co-occurring CuO NPs or Cu(II) and As in rice paddies and highlighted the unique "nano-effect" of CuO NPs. The results alsos showed that the initial oxidation state of As plays an important role in the interactions between As and Cu. The results shed light on the current debate on the safe applications of nano-enabled agrichemicals vs. conventional metal salts in agriculture.
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Affiliation(s)
- Xiaoxuan Wang
- Zachry Department of Civil Engineering, Texas A&M University, TAMU 3136, College Station, TX, 77843-3136, USA
| | - Wenjie Sun
- Department of Civil and Environmental Engineering, Southern Methodist University, 3101 Dyer Street, Dallas, TX, 75205, USA
| | - Xingmao Ma
- Zachry Department of Civil Engineering, Texas A&M University, TAMU 3136, College Station, TX, 77843-3136, USA.
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15
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New clues into the mechanisms of rice domestication. J Biosci 2019. [DOI: 10.1007/s12038-019-9844-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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16
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Liu J, Simms M, Song S, King RS, Cobb GP. Physiological Effects of Copper Oxide Nanoparticles and Arsenic on the Growth and Life Cycle of Rice ( Oryza sativa japonica 'Koshihikari'). ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:13728-13737. [PMID: 30403853 DOI: 10.1021/acs.est.8b03731] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
A factorial study was conducted to evaluate the phytotoxicity of copper oxide nanoparticles (nCuO, 0.1-100 mg/L), arsenic (As, 0 and 10 mg/kg), and their interaction to rice plants ( Oryza sativa japonica 'Koshihikari') during the life cycle. No significant effect was observed on seed germination. The main effects of nCuO and As were observed on lengths and biomasses of seedling shoots and roots and on root branching. The interaction between nCuO and As also significantly influenced these parameters. nCuO addition increased Cu uptake in seedlings and generally improved seedling growth. With As addition, As was highly concentrated in roots and increased in shoots, and seedling growth was also inhibited. Additionally, nCuO and As had significant main and interaction effects on mature plant dry biomass, panicle number, total grain weight, average grain weight, and several other panicle parameters. Moreover, nCuO and As interacted to affect panicle emergence. nCuO also decreased As accumulation in dehusked grains. The accelerated heading stage by nCuO may help shorten the life cycle of rice plants, thereby reducing As accumulation in grains. This study is the first to examine the influence of nCuO in combination with As on the life cycle of rice plants.
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Affiliation(s)
- Jing Liu
- Department of Environmental Science , Baylor University , One Bear Place No. 97266 , Waco , Texas 76798-7266 , United States
| | - Madie Simms
- Department of Environmental Science , Baylor University , One Bear Place No. 97266 , Waco , Texas 76798-7266 , United States
| | - Shuai Song
- Department of Civil Engineering , Taiyuan University of Technology , Yingze West Street No. 79 , Taiyuan , Shanxi , China 030024
| | - Ryan S King
- Department of Environmental Science , Baylor University , One Bear Place No. 97266 , Waco , Texas 76798-7266 , United States
| | - George P Cobb
- Department of Environmental Science , Baylor University , One Bear Place No. 97266 , Waco , Texas 76798-7266 , United States
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17
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Bell E, Nakai S, Burzio LA. Stacked Genetically Engineered Trait Products Produced by Conventional Breeding Reflect the Compositional Profiles of Their Component Single Trait Products. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:7794-7804. [PMID: 29953223 DOI: 10.1021/acs.jafc.8b02317] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
An expanding trend for genetically engineered (GE) crops is to cultivate varieties in which two or more single trait products have been combined using conventional breeding to produce a stacked trait product that provides a useful grouping of traits. Here, we report results from compositional analysis of several GE stacked trait products from maize and soybean. The results demonstrate that these products are each compositionally equivalent to a relevant non-GE comparator variety, except for predictable shifts in the fatty acid profile in the case of stacked trait products that contain a trait, MON 87705, that confers a high-oleic-acid phenotype in soybean. In each case, the conclusion on compositional equivalence for the stacked trait product reflects the conclusions obtained for the single trait products. These results provide strong support for conducting a reassessment of those regulatory guidelines that mandate explicit characterization of stacked trait products produced through conventional breeding.
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Affiliation(s)
- Erin Bell
- Monsanto Company , 700 Chesterfield Parkway West , Chesterfield , Missouri 63017 , United States
| | - Shuichi Nakai
- Monsanto Japan, Limited , 2-5-18 Kyobashi , Chuo-ku, Tokyo 104-0031 , Japan
| | - Luis A Burzio
- Monsanto Company , 700 Chesterfield Parkway West , Chesterfield , Missouri 63017 , United States
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18
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Liu J, Dhungana B, Cobb GP. Environmental behavior, potential phytotoxicity, and accumulation of copper oxide nanoparticles and arsenic in rice plants. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2018; 37:11-20. [PMID: 28796373 DOI: 10.1002/etc.3945] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Revised: 05/22/2017] [Accepted: 08/08/2017] [Indexed: 05/27/2023]
Abstract
Copper oxide nanoparticles (CuO NPs) are widely used in many industries. The increasing release of CuO NPs from both intentional and unintentional sources into the environment may pose risks to rice plants, thereby reducing the quality or quantity of this staple grain in the human diet. Not only has arsenic (As) contamination decreased rice yield, but As accumulation in rice has also been a great human health concern for a few decades. New technologies have succeeded in removing As from water by nanomaterials. By all accounts, few studies have addressed CuO NP phytotoxicity to rice, and the interactions of CuO NPs with As are poorly described. The present study 1) reviews studies about the environmental behavior and phytotoxicity of CuO NPs and As and research about the interaction of CuO NPs with As in the environment, 2) discusses critically the potential mechanisms of CuO NP and As toxicity in plants and their interaction, and 3) proposes future research directions for solving the As problem in rice. Environ Toxicol Chem 2018;37:11-20. © 2017 SETAC.
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Affiliation(s)
- Jing Liu
- Department of Environmental Science, Baylor University, Waco, Texas, USA
| | - Birendra Dhungana
- Department of Environmental Science, Baylor University, Waco, Texas, USA
| | - George P Cobb
- Department of Environmental Science, Baylor University, Waco, Texas, USA
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19
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Ding J, Ulanov AV, Dong M, Yang T, Nemzer BV, Xiong S, Zhao S, Feng H. Enhancement of gama-aminobutyric acid (GABA) and other health-related metabolites in germinated red rice (Oryza sativa L.) by ultrasonication. ULTRASONICS SONOCHEMISTRY 2018; 40:791-797. [PMID: 28946487 DOI: 10.1016/j.ultsonch.2017.08.029] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 08/13/2017] [Accepted: 08/27/2017] [Indexed: 05/23/2023]
Abstract
Red rice (Oryza sativa L.) that has a red (reddish brown) bran layer in de-hulled rice is known to contain rich biofunctional components. Germination is an effective technique to improve the nutritional quality, digestibility, and flavor of de-hulled rice. Ultrasonication, a form of physical stimulation, has been documented as a novel approach to improve the nutritional quality of plant-based food. This study was undertaken to test the use of ultrasound to enhance the nutritional value of red rice. Ultrasonication (5min, 16W/L) was applied to rice during soaking or after 66h germination. Changes of metabolites (amino acids, sugars, and organic acids) in red rice treated by ultrasonication were determined using a GC/MS plant primary metabolomics analysis platform. Differential expressed metabolites were identified through multivariate statistical analysis. Results showed that γ-aminobutyric acid (GABA) and riboflavin (vitamin B2) in red rice significantly increased after germination for 72h, and then experienced a further increase after treatment by ultrasound at different stages during germination. The metabolomics analysis showed that some plant metabolites, i.e. GABA, O-phosphoethanolamine, and glucose-6-phosphate were significantly increased after the ultrasonic treatment (VIP>1.5) in comparison with the untreated germinated rice. The findings of this study showed that controlled germination with ultrasonic stress is an effective method to enhance GABA and other health-promoted components in de-hulled rice.
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Affiliation(s)
- Junzhou Ding
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; College of Food Sciences and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Alexander V Ulanov
- Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Mengyi Dong
- Department of Nutrition and Food Studies, George Mason University, Fairfax, VA 22030, USA
| | - Tewu Yang
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Sciences and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | | | - Shanbai Xiong
- College of Food Sciences and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Siming Zhao
- College of Food Sciences and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Hao Feng
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
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20
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Evidence for mid-Holocene rice domestication in the Americas. Nat Ecol Evol 2017; 1:1693-1698. [PMID: 28993622 DOI: 10.1038/s41559-017-0322-4] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 08/22/2017] [Indexed: 11/09/2022]
Abstract
The development of agriculture is one of humankind's most pivotal achievements. Questions about plant domestication and the origins of agriculture have engaged scholars for well over a century, with implications for understanding its legacy on global subsistence strategies, plant distribution, population health and the global methane budget. Rice is one of the most important crops to be domesticated globally, with both Asia (Oryza sativa L.) and Africa (Oryza glaberrima Steud.) discussed as primary centres of domestication. However, until now the pre-Columbian domestication of rice in the Americas has not been documented. Here we document the domestication of Oryza sp. wild rice by the mid-Holocene residents of the Monte Castelo shell mound starting at approximately 4,000 cal. yr BP, evidenced by increasingly larger rice husk phytoliths. Our data provide evidence for the domestication of wild rice in a region of the Amazon that was also probably the cradle of domestication of other major crops such as cassava (Manihot esculenta), peanut (Arachis hypogaea) and chilli pepper (Capsicum sp.). These results underline the role of wetlands as prime habitats for plant domestication worldwide.
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21
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Chronosequencing methanogenic archaea in ancient Longji rice Terraces in China. Sci Bull (Beijing) 2017; 62:879-887. [PMID: 36659324 DOI: 10.1016/j.scib.2017.05.024] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 05/22/2017] [Accepted: 05/22/2017] [Indexed: 01/21/2023]
Abstract
Chronosequences of ancient rice terraces serve as an invaluable archive for reconstructions of historical human-environment interactions. Presently, however, these reconstructions are based on traditional soil physico-chemical properties. The microorganisms in palaeosols have been unexplored. We hypothesized that microbial information can be used as an additional proxy to complement and consolidate archaeological interpretations. To test this hypothesis, the palaeoenvironmental methanogenic archaeal DNA in Longji Terraces, one of the famous ancient terraces in China, dating back to the late Yuan Dynasty (CE 1361-1406), was chronosequenced by high-throughput sequencing. It was found that the methanogenic archaeal abundance, diversity and community composition were closely associated with the 630years of rice cultivation and in line with changes in multi-proxy data. Particularly, the centennial- and decadal-scale influences of known historical events, including social turbulences (The Taiping Rebellion, CE 1850-1865), palaeoclimate changes (the Little Ice Age) and recorded natural disasters (earthquakes and inundation), on ancient agricultural society were clearly echoed in the microbial archives as variations in alpha and beta diversity. This striking correlation suggests that the microorganisms archived in palaeosols can be quantitatively and qualitatively analyzed to provide an additional proxy, and palaeo-microbial information could be routinely incorporated in the toolkit for archaeological interpretation.
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22
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Fragoso CA, Moreno M, Wang Z, Heffelfinger C, Arbelaez LJ, Aguirre JA, Franco N, Romero LE, Labadie K, Zhao H, Dellaporta SL, Lorieux M. Genetic Architecture of a Rice Nested Association Mapping Population. G3 (BETHESDA, MD.) 2017; 7:1913-1926. [PMID: 28450374 PMCID: PMC5473768 DOI: 10.1534/g3.117.041608] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 04/14/2017] [Indexed: 12/21/2022]
Abstract
Describing the genetic diversity in the gene pool of crops will provide breeders with novel resources for varietal improvement. Nested Association Mapping (NAM) populations are uniquely suited for characterizing parental diversity through the shuffling and fixation of parental haplotypes. Here, we describe a set of 1879 rice NAM lines created through the selfing and single-seed descent of F1 hybrids derived from elite IR64 indica crossed with 10 diverse tropical japonica lines. Genotyping data indicated tropical japonica alleles were captured at every queried locus despite the presence of segregation distortion factors. Several distortion loci were mapped, both shared and unique, among the 10 populations. Using two-point and multi-point genetic map calculations, our datasets achieved the ∼1500 cM expected map size in rice. Finally, we highlighted the utility of the NAM lines for QTL mapping, including joint analysis across the 10 populations, by confirming known QTL locations for the trait days to heading.
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Affiliation(s)
- Christopher A Fragoso
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06511
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06511
| | - Maria Moreno
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06511
| | - Zuoheng Wang
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06511
- Department of Biostatistics, Yale University, New Haven, Connecticut 06511
| | - Christopher Heffelfinger
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06511
| | - Lady J Arbelaez
- Rice Genetics and Genomics Laboratory, International Center for Tropical Agriculture, Cali 6713, Colombia
| | - John A Aguirre
- Rice Genetics and Genomics Laboratory, International Center for Tropical Agriculture, Cali 6713, Colombia
| | - Natalia Franco
- Rice Genetics and Genomics Laboratory, International Center for Tropical Agriculture, Cali 6713, Colombia
| | - Luz E Romero
- Rice Genetics and Genomics Laboratory, International Center for Tropical Agriculture, Cali 6713, Colombia
| | - Karine Labadie
- Commissariat à L'énergie Atomique et aux Énergies Alternatives, Institut de Génomique, Genoscope, 91000 Evry, France
| | - Hongyu Zhao
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06511
- Department of Biostatistics, Yale University, New Haven, Connecticut 06511
| | - Stephen L Dellaporta
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06511
| | - Mathias Lorieux
- Rice Genetics and Genomics Laboratory, International Center for Tropical Agriculture, Cali 6713, Colombia
- Diversité, Adaptation, Développement des Plantes Research Unit, Institut de Recherche pour le Développement, F-34394 Montpellier, France
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23
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Anthropogenic Landscapes, Human Action and the Process of Co-Construction with other Species: Making Anthromes in the Anthropocene. LAND 2017. [DOI: 10.3390/land6010015] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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24
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Chin HS, Wu YP, Hour AL, Hong CY, Lin YR. Genetic and Evolutionary Analysis of Purple Leaf Sheath in Rice. RICE (NEW YORK, N.Y.) 2016; 9:8. [PMID: 26922355 PMCID: PMC4769704 DOI: 10.1186/s12284-016-0080-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 02/19/2016] [Indexed: 05/11/2023]
Abstract
BACKGROUND Anthocyanin accumulates in many plant tissues or organs, in rice for example leading to red, purple red and purple phenotypes for protection from damage by biotic and abiotic stresses and for reproduction. Purple leaf, leaf sheath, stigma, pericarp, and apiculus are common in wild rice and landraces and occasionally found in modern cultivars. No gene directly conferring anthocyanin deposited in a purple leaf sheath has yet been isolated by using natural variants. An F2 population derived from ssp. japonica cv. Tainung 72 (TNG72) with purple leaf sheath (PSH) crossed with ssp. indica cv. Taichung Sen 17 (TCS17) with green leaf sheath (GSH) was utilized to isolate a gene conferring leaf sheath color. RESULTS By positional cloning, 10-and 3-bp deletions in the R2R3 Myb domain of OsC1 were uncovered in GSH varieties TCS17 and Nipponbare, respectively. Allelic diversity, rather than gene expression levels of OsC1, might be responsible for anthocyanin accumulation. Parsimony-based analysis of genetic diversity in 50 accessions, including cultivars, landraces, and A-genome wild rice, suggests that independent mutation occurred in Asian, African, South American, and Australian species, while O. meridionalis had a divergent sequence. OsC1 was thought of as a domestication related gene, with up to 90 % reduction of genetic diversity in GSH; however, no values from three tests showed significant differences from neutral expectations, implying that OsC1 had not been subjected to recent selection. Haplotype network analysis revealed that species from different continents formed unique haplotypes with no gene flow. Two major groups of haplotypes corresponding to 10-bp deletion and other sequences were formed in Asian rice, including O. rufipogon, O. nivara and O. sativa. Introgressions of OsC1 between subspecies through natural and artificial hybridization were not rare. Because artificial and natural selection imposed admixture on rice germplasm in Taiwan, the genealogy of OsC1 might not be congruent with the current distribution of alleles through lineage diversification. CONCLUSION OsC1 is responsible for purple leaf sheath, and much new information about OsC1 is provided e.g., new alleles, non-domestication syndrome, and incongruence of genealogy with geographic distribution.
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Affiliation(s)
- Han-shiuan Chin
- />Department of Agronomy, National Taiwan University, Taipei, Taiwan
| | - Yong-pei Wu
- />Department of Agronomy, Chiayi Agricultural Experiment Station, Taiwan Agricultural Research Institute, Chiayi, Taiwan
| | - Ai-ling Hour
- />Department of Life Science, Fu-Jen Catholic University, Xinbei, Taiwan
| | - Chwan-yang Hong
- />Department of Agricultural Chemistry, National Taiwan University, Taipei, Taiwan
| | - Yann-rong Lin
- />Department of Agronomy, National Taiwan University, Taipei, Taiwan
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25
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Porcel R, Aroca R, Azcon R, Ruiz-Lozano JM. Regulation of cation transporter genes by the arbuscular mycorrhizal symbiosis in rice plants subjected to salinity suggests improved salt tolerance due to reduced Na(+) root-to-shoot distribution. MYCORRHIZA 2016; 26:673-84. [PMID: 27113587 DOI: 10.1007/s00572-016-0704-5] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 04/18/2016] [Indexed: 05/18/2023]
Abstract
Rice is a salt-sensitive crop whose productivity is strongly reduced by salinity around the world. Plants growing in saline soils are subjected to the toxicity of specific ions such as sodium, which damage cell organelles and disrupt metabolism. Plants have evolved biochemical and molecular mechanisms to cope with the negative effects of salinity. These include the regulation of genes with a role in the uptake, transport or compartmentation of Na(+) and/or K(+). Studies have shown that the arbuscular mycorrhizal (AM) symbiosis alleviates salt stress in several host plant species. However, despite the abundant literature showing mitigation of ionic imbalance by the AM symbiosis, the molecular mechanisms involved are barely explored. The objective of this study was to elucidate the effects of the AM symbiosis on the expression of several well-known rice transporters involved in Na(+)/K(+) homeostasis and measure Na(+) and K(+) contents and their ratios in different plant tissues. Results showed that OsNHX3, OsSOS1, OsHKT2;1 and OsHKT1;5 genes were considerably upregulated in AM plants under saline conditions as compared to non-AM plants. Results suggest that the AM symbiosis favours Na(+) extrusion from the cytoplasm, its sequestration into the vacuole, the unloading of Na(+) from the xylem and its recirculation from photosynthetic organs to roots. As a result, there is a decrease of Na(+) root-to-shoot distribution and an increase of Na(+) accumulation in rice roots which seems to enhance the plant tolerance to salinity and allows AM rice plants to maintain their growing processes under salt conditions.
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Affiliation(s)
- Rosa Porcel
- Departamento de Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín (CSIC), Profesor Albareda n° 1, 18008, Granada, Spain
| | - Ricardo Aroca
- Departamento de Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín (CSIC), Profesor Albareda n° 1, 18008, Granada, Spain
| | - Rosario Azcon
- Departamento de Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín (CSIC), Profesor Albareda n° 1, 18008, Granada, Spain
| | - Juan Manuel Ruiz-Lozano
- Departamento de Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín (CSIC), Profesor Albareda n° 1, 18008, Granada, Spain.
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26
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Kumagai M, Kanehara M, Shoda S, Fujita S, Onuki S, Ueda S, Wang L. Rice Varieties in Archaic East Asia: Reduction of Its Diversity from Past to Present Times. Mol Biol Evol 2016; 33:2496-505. [PMID: 27461246 DOI: 10.1093/molbev/msw142] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The Asian cultivated rice, Oryza sativa, is one of the most important crops feeding more than a third of global population. In spite of the studies for several decades, the origin and domestication history of rice varietal groups, japonica and indica, have not been fully unveiled. Genetic information of ancient rice remains is essential for direct and exclusive insight into the domestication history of rice. We performed ancient DNA analysis of 950- to 2,800-year-old rice remains excavated from Japan and Korea. We found the presence of both japonica- and indica-type varieties in the Yayoi period and the middle ages of Japan and the middle part of Korea Peninsula 2,000 years ago. It is popularly considered that japonica has been exclusively cultivated in northern part of East Asia including Japan and Korea. Our result disclosed unexpectedly wide diversity of rice varieties in archaic East Asia. The present results from ancient rice DNA reveal an exclusive insight for the domestication history of rice which is not provided as far as contemporary rice.
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Affiliation(s)
- Masahiko Kumagai
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Masaaki Kanehara
- Department of Teacher Training and School Education, Nara University of Education, Nara, Japan
| | - Shin'ya Shoda
- Nara National Research Institute for Cultural Properties, Nara, Japan
| | | | - Shizuo Onuki
- Department of Archaeology, Graduate School of Humanities and Sociology, The University of Tokyo, Tokyo, Japan
| | - Shintaroh Ueda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Li Wang
- School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang, China
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27
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Yin M, Zheng HX, Su J, Feng Z, McManus DP, Zhou XN, Jin L, Hu W. Co-dispersal of the blood fluke Schistosoma japonicum and Homo sapiens in the Neolithic Age. Sci Rep 2015; 5:18058. [PMID: 26686813 PMCID: PMC4685303 DOI: 10.1038/srep18058] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 11/03/2015] [Indexed: 11/09/2022] Open
Abstract
The global spread of human infectious diseases is of considerable public health and biomedical interest. Little is known about the relationship between the distribution of ancient parasites and that of their human hosts. Schistosoma japonicum is one of the three major species of schistosome blood flukes causing the disease of schistosomiasis in humans. The parasite is prevalent in East and Southeast Asia, including the People's Republic of China, the Philippines and Indonesia. We studied the co-expansion of S. japonicum and its human definitive host. Phylogenetic reconstruction based on complete mitochondrial genome sequences showed that S. japonicum radiated from the middle and lower reaches of the Yangtze River to the mountainous areas of China, Japan and Southeast Asia. In addition, the parasite experienced two population expansions during the Neolithic agriculture era, coinciding with human migration and population growth. The data indicate that the advent of rice planting likely played a key role in the spread of schistosomiasis in Asia. Moreover, the presence of different subspecies of Oncomelania hupensis intermediate host snails in different localities in Asia allowed S. japonicum to survive in new rice-planting areas, and concurrently drove the intraspecies divergence of the parasite.
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Affiliation(s)
- Mingbo Yin
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Hong-Xiang Zheng
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Jing Su
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Zheng Feng
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Key Laboratory of Parasite and Vector Biology of the Chinese Ministry of Health, WHO Collaborating Center for Malaria, Schistosomiasis and Filariasis, Shanghai, 200025, China
| | - Donald P. McManus
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4006, Australia
| | - Xiao-Nong Zhou
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Key Laboratory of Parasite and Vector Biology of the Chinese Ministry of Health, WHO Collaborating Center for Malaria, Schistosomiasis and Filariasis, Shanghai, 200025, China
| | - Li Jin
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200438, China
- Chinese Academy of Sciences Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, SIBS, CAS, Shanghai, 200021, China
| | - Wei Hu
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200438, China
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Key Laboratory of Parasite and Vector Biology of the Chinese Ministry of Health, WHO Collaborating Center for Malaria, Schistosomiasis and Filariasis, Shanghai, 200025, China
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28
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Gong HY, Li Y, Fang G, Hu DH, Jin WB, Wang ZH, Li YS. Transgenic Rice Expressing Ictb and FBP/Sbpase Derived from Cyanobacteria Exhibits Enhanced Photosynthesis and Mesophyll Conductance to CO2. PLoS One 2015; 10:e0140928. [PMID: 26488581 PMCID: PMC4638112 DOI: 10.1371/journal.pone.0140928] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 10/01/2015] [Indexed: 01/05/2023] Open
Abstract
To find a way to promote the rate of carbon flux and further improve the photosynthetic rate in rice, two CO2-transporting and fixing relevant genes, Ictb and FBP/Sbpase, which were derived from cyanobacteria with the 35SCaMV promotor in the respective constructs, were transformed into rice. Three homologous transgenic groups with Ictb, FBP/Sbpase and the two genes combined were constructed in parallel, and the functional effects of these two genes were investigated by physiological, biochemical and leaf anatomy analyses. The results indicated that the mesophyll conductance and net photosynthetic rate were higher at approximately 10.5-36.8% and 13.5-34.6%, respectively, in the three groups but without any changes in leaf anatomy structure compared with wild type. Other physiological and biochemical parameters increased with the same trend in the three groups, which showed that the effect of FBP/SBPase on improving photosynthetic capacity was better than that of ICTB and that there was an additive effect in ICTB+FBP/SBPase. ICTB localized in the cytoplasm, whereas FBP/SBPase was successfully transported to the chloroplast. The two genes might show a synergistic interaction to promote carbon flow and the assimilation rate as a whole. The multigene transformation engineering and its potential utility for improving the photosynthetic capacity and yield in rice were discussed.
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Affiliation(s)
- Han Yu Gong
- State Key Laboratory for Hybrid Rice, College of Life Sciences, Wuhan
University, Wuhan, China
- Engineering Research Centre for the Protection and Utilization of
Bioresource in Ethnic Area of Southern China, South-Central University for
Nationalities, Wuhan, China
| | - Yang Li
- State Key Laboratory for Hybrid Rice, College of Life Sciences, Wuhan
University, Wuhan, China
| | - Gen Fang
- State Key Laboratory for Hybrid Rice, College of Life Sciences, Wuhan
University, Wuhan, China
| | - Dao Heng Hu
- State Key Laboratory for Hybrid Rice, College of Life Sciences, Wuhan
University, Wuhan, China
| | - Wen Bin Jin
- State Key Laboratory for Hybrid Rice, College of Life Sciences, Wuhan
University, Wuhan, China
| | - Zhao Hai Wang
- State Key Laboratory for Hybrid Rice, College of Life Sciences, Wuhan
University, Wuhan, China
| | - Yang Sheng Li
- State Key Laboratory for Hybrid Rice, College of Life Sciences, Wuhan
University, Wuhan, China
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29
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Huan X, Lu H, Wang C, Tang X, Zuo X, Ge Y, He K. Bulliform Phytolith Research in Wild and Domesticated Rice Paddy Soil in South China. PLoS One 2015; 10:e0141255. [PMID: 26488583 PMCID: PMC4619503 DOI: 10.1371/journal.pone.0141255] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2015] [Accepted: 10/06/2015] [Indexed: 11/18/2022] Open
Abstract
Bulliform phytoliths play an important role in researching rice origins as they can be used to distinguish between wild and domesticated rice. Rice bulliform phytoliths are characterized by numerous small shallow fish-scale decorations on the lateral side. Previous studies have shown that domesticated rice has a larger number of these decorations than wild rice and that the number of decorations ≥9 is a useful feature for identifying domesticated rice. However, this standard was established based on limited samples of modern rice plants. In this study, we analyzed soil samples from both wild and domesticated rice paddies. Results showed that, in wild rice soil samples, the proportion of bulliform phytoliths with ≥9 decorations was 17.46% ± 8.29%, while in domesticated rice soil samples, the corresponding proportion was 63.70% ± 9.22%. This suggests that the proportion of phytoliths with ≥9 decorations can be adopted as a criterion for discriminating between wild and domesticated rice in prehistoric soil. This indicator will be of significance in improving the application of fish-scale decorations to research into rice origins and the rice domestication process.
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Affiliation(s)
- Xiujia Huan
- Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Houyuan Lu
- Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, China
- Center for Excellence in Tibetan Plateau Earth Science, Chinese Academy of Sciences, Beijing, China
| | - Can Wang
- Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiangan Tang
- Soil & Fertilizer and Environmental & Resources Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang, Jiangxi Province, China
| | - Xinxin Zuo
- Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, China
| | - Yong Ge
- Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Keyang He
- Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
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30
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Gardener C, Kumar SV. Hot n' Cold: Molecular Signatures of Domestication Bring Fresh Insights into Environmental Adaptation. MOLECULAR PLANT 2015; 8:1439-1441. [PMID: 26343968 DOI: 10.1016/j.molp.2015.08.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Revised: 08/24/2015] [Accepted: 08/25/2015] [Indexed: 06/05/2023]
Affiliation(s)
- Catherine Gardener
- Cell and Developmental Biology Department, John Innes Centre, Norwich NR4 7UH, UK
| | - S Vinod Kumar
- Cell and Developmental Biology Department, John Innes Centre, Norwich NR4 7UH, UK.
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31
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Bendix C, Marshall CM, Harmon FG. Circadian Clock Genes Universally Control Key Agricultural Traits. MOLECULAR PLANT 2015; 8:1135-52. [PMID: 25772379 DOI: 10.1016/j.molp.2015.03.003] [Citation(s) in RCA: 118] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Revised: 02/26/2015] [Accepted: 03/04/2015] [Indexed: 05/17/2023]
Abstract
Circadian clocks are endogenous timers that enable plants to synchronize biological processes with daily and seasonal environmental conditions in order to allocate resources during the most beneficial times of day and year. The circadian clock regulates a number of central plant activities, including growth, development, and reproduction, primarily through controlling a substantial proportion of transcriptional activity and protein function. This review examines the roles that alleles of circadian clock genes have played in domestication and improvement of crop plants. The focus here is on three groups of circadian clock genes essential to clock function in Arabidopsis thaliana: PSEUDO-RESPONSE REGULATORs, GIGANTEA, and the evening complex genes early flowering 3, early flowering 4, and lux arrhythmo. homologous genes from each group underlie quantitative trait loci that have beneficial influences on key agricultural traits, especially flowering time but also yield, biomass, and biennial growth habit. Emerging insights into circadian clock regulation of other fundamental plant processes, including responses to abiotic and biotic stresses, are discussed to highlight promising avenues for further crop improvement.
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Affiliation(s)
- Claire Bendix
- Plant Gene Expression Center, USDA-ARS, Albany, CA 94710, USA; Department of Plant & Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Carine M Marshall
- Plant Gene Expression Center, USDA-ARS, Albany, CA 94710, USA; Department of Plant & Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Frank G Harmon
- Plant Gene Expression Center, USDA-ARS, Albany, CA 94710, USA; Department of Plant & Microbial Biology, University of California, Berkeley, CA 94720, USA.
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32
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Fuller DQ. From the marshes to your menu. NATURE PLANTS 2015; 1:14015. [PMID: 27246061 DOI: 10.1038/nplants.2014.15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
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33
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Dametto A, Buffon G, Dos Reis Blasi ÉA, Sperotto RA. Ubiquitination pathway as a target to develop abiotic stress tolerance in rice. PLANT SIGNALING & BEHAVIOR 2015; 10:e1057369. [PMID: 26236935 PMCID: PMC4883960 DOI: 10.1080/15592324.2015.1057369] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Revised: 05/26/2015] [Accepted: 05/27/2015] [Indexed: 05/18/2023]
Abstract
Abiotic stresses may result in significant losses in rice grain productivity. Protein regulation by the ubiquitin/proteasome system has been studied as a target mechanism to optimize adaptation and survival strategies of plants to different environmental stresses. This article aimed at highlighting recent discoveries about the roles ubiquitination may play in the exposure of rice plants to different abiotic stresses, enabling the development of modified plants tolerant to stress. Responses provided by the ubiquitination process include the regulation of the stomatal opening, phytohormones levels, protein stabilization, cell membrane integrity, meristematic cell maintenance, as well as the regulation of reactive oxygen species and heavy metals levels. It is noticeable that ubiquitination is a potential means for developing abiotic stress tolerant plants, being an excellent alternative to rice (and other cultures) improvement programs.
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Affiliation(s)
- Andressa Dametto
- Programa de Pós-Graduação em Biotecnologia (PPGBiotec) and Centro Universitário UNIVATES; Lajeado, RS, Brazil
| | - Giseli Buffon
- Programa de Pós-Graduação em Biotecnologia (PPGBiotec) and Centro Universitário UNIVATES; Lajeado, RS, Brazil
| | | | - Raul Antonio Sperotto
- Programa de Pós-Graduação em Biotecnologia (PPGBiotec) and Centro Universitário UNIVATES; Lajeado, RS, Brazil
- Centro de Ciências Biológicas e da Saúde (CCBS); Centro Universitário UNIVATES; Lajeado, RS, Brazil
- Correspondence to: Raul Antonio Sperotto;
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