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Yu G, Sun B, Zhu Z, Mehareb EM, Teng A, Han J, Zhang H, Liu J, Liu X, Raza G, Zhang B, Zhang Y, Wang K. Genome-wide DNase I-hypersensitive site assay reveals distinct genomic distributions and functional features of open chromatin in autopolyploid sugarcane. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:573-589. [PMID: 37897092 DOI: 10.1111/tpj.16513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 09/15/2023] [Accepted: 10/09/2023] [Indexed: 10/29/2023]
Abstract
The characterization of cis-regulatory DNA elements (CREs) is essential for deciphering the regulation of gene expression in eukaryotes. Although there have been endeavors to identify CREs in plants, the properties of CREs in polyploid genomes are still largely unknown. Here, we conducted the genome-wide identification of DNase I-hypersensitive sites (DHSs) in leaf and stem tissues of the auto-octoploid species Saccharum officinarum. We revealed that DHSs showed highly similar distributions in the genomes of these two S. officinarum tissues. Notably, we observed that approximately 74% of DHSs were located in distal intergenic regions, suggesting considerable differences in the abundance of distal CREs between S. officinarum and other plants. Leaf- and stem-dependent transcriptional regulatory networks were also developed by mining the binding motifs of transcription factors (TFs) from tissue-specific DHSs. Four TEOSINTE BRANCHED 1, CYCLOIDEA, and PCF1 (TCP) TFs (TCP2, TCP4, TCP7, and TCP14) and two ethylene-responsive factors (ERFs) (ERF109 and ERF03) showed strong causal connections with short binding distances from each other, pointing to their possible roles in the regulatory networks of leaf and stem development. Through functional validation in transiently transgenic protoplasts, we isolate a set of tissue-specific promoters. Overall, the DHS maps presented here offer a global view of the potential transcriptional regulatory elements in polyploid sugarcane and can be expected to serve as a valuable resource for both transcriptional network elucidation and genome editing in sugarcane breeding.
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Affiliation(s)
- Guangrun Yu
- School of Life Sciences, Nantong University, Nantong, 226019, China
| | - Bo Sun
- School of Life Sciences, Nantong University, Nantong, 226019, China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zhiying Zhu
- School of Life Sciences, Nantong University, Nantong, 226019, China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Eid M Mehareb
- Sugar Crops Research Institute (SRCI), Agricultural Research Center (ARC), Giza, 12619, Egypt
| | - Ailing Teng
- School of Life Sciences, Nantong University, Nantong, 226019, China
| | - Jinlei Han
- School of Life Sciences, Nantong University, Nantong, 226019, China
| | - Hui Zhang
- School of Life Sciences, Nantong University, Nantong, 226019, China
| | - Jiayong Liu
- Sugarcane Institute, Yunnan Academy of Agricultural Sciences, Kaiyuan, 661699, China
| | - Xinlong Liu
- Sugarcane Institute, Yunnan Academy of Agricultural Sciences, Kaiyuan, 661699, China
| | - Ghulam Raza
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, 38000, Pakistan
| | - Baohong Zhang
- Department of Biology, East Carolina University, Greenville, North Carolina, 27858, USA
| | - Yuebin Zhang
- Sugarcane Institute, Yunnan Academy of Agricultural Sciences, Kaiyuan, 661699, China
| | - Kai Wang
- School of Life Sciences, Nantong University, Nantong, 226019, China
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Yang Y, Zhang C, Li H, Yang Z, Xu Z, Tai D, Ni D, Wei P, Yi C, Yang J, Ding Y. An epi-allele of SMS causes Sanming dominant genic male sterility in rice. SCIENCE CHINA. LIFE SCIENCES 2023; 66:2701-2710. [PMID: 37930474 DOI: 10.1007/s11427-023-2457-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Accepted: 09/22/2023] [Indexed: 11/07/2023]
Abstract
Male sterility is an important trait in rice for hybrid rice (Oryza sativa) breeding. However, the factors involved in dominant male sterility are largely unknown. Here, we identified a gene from Sanming dominant genic male sterile rice, named Sanming dominant male sterility (SMS), and reported that an epi-allele of this locus contributes to male sterility. Segregation analysis attributed dominant male sterility to a single locus, SMS, which we characterized using a male-sterile near isogenic line (NIL) of rice cultivar 93-11. The SMS locus was heterozygous in the male-sterile 93-11 NIL, containing an epi-allele identical to that in 93-11, and an epi-allele identical to that in rice cultivar Nipponbare, which we refer to as SMS9 and SMSN, respectively. SMS9 is silent and hyper-methylated, whereas SMSN is expressed and hypo-methylated in the 93-11 NIL. Overexpressing SMSN led to male sterility. Mutations in SMS rescued the male sterility of the 93-11 NIL. Interestingly, we observed the duplication of SMSN in Nipponbare, but did not observe the duplication of SMS9 in 93-11. Together, these findings suggest that the reduced methylation and enhanced expression of the SMSN epi-allele in the 93-11 NIL is responsible for its role in conferring dominant male sterility.
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Affiliation(s)
- Yachun Yang
- Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230036, China
- Institute of Health and Medicine, Hefei Comprehesive National Science Center, Hefei, 230031, China
| | - Cheng Zhang
- Institute of Health and Medicine, Hefei Comprehesive National Science Center, Hefei, 230031, China
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics; School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Hao Li
- Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230036, China
- Institute of Health and Medicine, Hefei Comprehesive National Science Center, Hefei, 230031, China
| | - Zeyuan Yang
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics; School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Zuntao Xu
- Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230036, China
- Institute of Health and Medicine, Hefei Comprehesive National Science Center, Hefei, 230031, China
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics; School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Dewei Tai
- Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230036, China
- Institute of Health and Medicine, Hefei Comprehesive National Science Center, Hefei, 230031, China
| | - Dahu Ni
- Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230036, China
| | - Pengcheng Wei
- Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230036, China
| | - Chengxin Yi
- Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230036, China
| | - Jianbo Yang
- Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230036, China.
| | - Yong Ding
- Institute of Health and Medicine, Hefei Comprehesive National Science Center, Hefei, 230031, China.
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics; School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China.
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3
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Brooks EG, Elorriaga E, Liu Y, Duduit JR, Yuan G, Tsai CJ, Tuskan GA, Ranney TG, Yang X, Liu W. Plant Promoters and Terminators for High-Precision Bioengineering. BIODESIGN RESEARCH 2023; 5:0013. [PMID: 37849460 PMCID: PMC10328392 DOI: 10.34133/bdr.0013] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 06/12/2023] [Indexed: 10/19/2023] Open
Abstract
High-precision bioengineering and synthetic biology require fine-tuning gene expression at both transcriptional and posttranscriptional levels. Gene transcription is tightly regulated by promoters and terminators. Promoters determine the timing, tissues and cells, and levels of the expression of genes. Terminators mediate transcription termination of genes and affect mRNA levels posttranscriptionally, e.g., the 3'-end processing, stability, translation efficiency, and nuclear to cytoplasmic export of mRNAs. The promoter and terminator combination affects gene expression. In the present article, we review the function and features of plant core promoters, proximal and distal promoters, and terminators, and their effects on and benchmarking strategies for regulating gene expression.
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Affiliation(s)
- Emily G. Brooks
- Department of Horticultural Science, North Carolina State University, Raleigh, NC 27607, USA
| | - Estefania Elorriaga
- Department of Horticultural Science, North Carolina State University, Raleigh, NC 27607, USA
| | - Yang Liu
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - James R. Duduit
- Department of Horticultural Science, North Carolina State University, Raleigh, NC 27607, USA
| | - Guoliang Yuan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Chung-Jui Tsai
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Warnell School of Forestry and Natural Resource, University of Georgia, Athens, GA 30602, USA
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - Gerald A. Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Thomas G. Ranney
- Mountain Crop Improvement Lab, Department of Horticultural Science, Mountain Horticultural Crops Research and Extension Center, North Carolina State University, Mills River, NC 28759, USA
| | - Xiaohan Yang
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Warnell School of Forestry and Natural Resource, University of Georgia, Athens, GA 30602, USA
| | - Wusheng Liu
- Department of Horticultural Science, North Carolina State University, Raleigh, NC 27607, USA
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Chang X, Yang M, Li H, Wu J, Zhang J, Yin C, Ma W, Chen H, Zhou F, Lin Y. Cloning of the promoter of rice brown planthopper feeding-inducible gene OsTPS31 and identification of related cis-regulatory elements. PEST MANAGEMENT SCIENCE 2023; 79:1809-1819. [PMID: 36637212 DOI: 10.1002/ps.7356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/15/2022] [Accepted: 01/13/2023] [Indexed: 06/17/2023]
Abstract
BACKGROUND Brown planthopper (BPH; Nilaparvata lugens) is one of the most serious pests of rice in the world. Insect-resistant genetic engineering is a very effective technology to control BPH. The promoters and cis-regulatory elements inducible by plant-feeding insects are critical for genetic engineering of insect-resistant crops. RESULTS In this study, we cloned a promoter Ptps31 and a 7 bp cis-regulatory sequence that up-regulated downstream genes induced by BPH feeding. The promoter of OsTPS31 (Ptps31) unresponsive to physical damage but responsive to BPH feeding was cloned and functionally verified. The results showed that expression of the OsBPH14 gene driven by the promoter region from -510 to -246 bp in rice could significantly improve the resistance to BPH. The promoter region from -376 to -370 bp (TAGTGTC) was identified as a cis-regulatory sequence related to BPH feeding induction of downstream gene expression. CONCLUSION The findings provide a new promoter and a new cis-regulatory sequence tool for the research on and application of rice BPH resistance genes, as well as a new perspective for functional analysis of the OsTPS31 gene. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Xinlei Chang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Mei Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Hanpeng Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jiemin Wu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jianguo Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Changxi Yin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Weihua Ma
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Hao Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Fei Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yongjun Lin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
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Combined Hybridization and Evaluation of High-Lysine Rice: Nutritional and Physicochemical Qualities and Field Performance. Int J Mol Sci 2022; 23:ijms232012166. [PMID: 36293019 PMCID: PMC9603072 DOI: 10.3390/ijms232012166] [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: 09/06/2022] [Revised: 10/07/2022] [Accepted: 10/10/2022] [Indexed: 11/28/2022] Open
Abstract
Rice, as a major food crop, provides necessary energy and nutrition for humans and livestock. However, its nutritional value is affected by lysine. Using point mutation, we previously obtained AK2 (aspartokinase) and DHDPS1 (dihydrodipicolinate synthase) genes insensitive to lysine feedback inhibition and constructed transgenic lines AK2-52 and DHDPS1-22, which show increased lysine synthesis, as well as Ri-12, which shows decreased lysine degradation by inhibiting rice lysine ketoglutarate reductase/saccharopine dehydrogenase (LKR/SDH) activity. In this study, further transgenic lines were hybridized and evaluated. The lysine content of mature seeds from pyramid lines PRD and PRA increased 32.5- and 29.8-fold, respectively, compared with the wild-type, while the three-gene pyramiding line PRDA had a moderate lysine content. The total lysine, total free lysine, and total protein contents of PRD and PRA also increased and had no obvious impact on the physical and chemical quality, seed appearance, and main agronomic traits. Meanwhile, comparative analysis with polygenic polymeric lines GR containing bacterial AK (lysC) and DHDPS (dapA) genes revealed differences in the way bacterial and endogenous rice AK and DHDPS regulate lysine biosynthesis. These results provide a reference for further evaluation and commercialization of high-lysine transgenic rice.
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Lin M, Yan J, Ali MM, Wang S, Tian S, Chen F, Lin Z. Isolation and Functional Characterization of a Green-Tissue Promoter in Japonica Rice (Oryza sativa subsp. Japonica). BIOLOGY 2022; 11:biology11081092. [PMID: 35892948 PMCID: PMC9332004 DOI: 10.3390/biology11081092] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 07/20/2022] [Accepted: 07/21/2022] [Indexed: 11/22/2022]
Abstract
Simple Summary Transgenic applications have largely focused on constitutive promoters in plants. However, strong and continuous over-expression of certain genes may be redundant and even harmful to plant growth. Thus, tissue-specific promoters are the most suitable for regulating target gene expression. Although several tissue-specific promoters have been identified, the regulatory mechanism of tissue-specific gene expression remains unclear. By a series of GUS staining of 5′ and 3′ deletions, we uncover tissue-specific cis-acting elements in GSX7R, including ten light-responsive elements. The results reveal that GSX7R is a reverse green tissue-specific promoter, except in endosperm. In contrast, strong tissue-specific promoters that can be used for rice improvements are limited. In this study, we successfully showed that the GSX7R promoter can drive the Cry1Ab gene to resistant rice yellow stem borer. In addition, our study demonstrates an effective promoter to drive foreign genes for crop improvement. Abstract Plant promoters play a vital role in the initiation and regulation of gene transcription. In this study, a rice protein/gene of unknown expression, named Os8GSX7, was gained from a rice T-DNA capture line. The semi-quantitative RT-PCR analysis showed that the gene was only expressed in root, glume, and flower, but not in stem, leaf, embryo, and endosperm of japonica rice. The GUS activity analysis of the GSX7R promoter showed that it was a reverse green tissue expression promoter, except in endosperm. The forward promoter of GSX7 cannot normally drive the expression of the foreign GUS gene, while the reverse promoter of GSX7 is a green tissue-specific expression promoter, which can drive the expression of the foreign GUS gene. The region from −2097 to −1543 bp was the key region for controlling the green tissue-specific expression. The regulatory sequences with different lengths from the 2097 bp reverse sequence from the upstream region of the Os8GSX7 were fused with the GUS reporter gene and stably expressed in rice. Furthermore, transgenic rice plants carrying Cry1Ab encoding Bacillus thuringiensis endotoxin, regulated by GSX7R, were resistant to yellow stem borer. The analysis suggested that 10 light responsive elements of tissue-specific expression were found, including ACE, Box4, CAT-box, G-Box, G-box, GATA motif, GC motif, I-box, Sp1, and chs-unit1 M1. In addition, the results of 5′ and 3′ deletions further speculated that ACE and I-box may be the key elements for determining the green tissue-specific expression of GSX7R promoter.
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Affiliation(s)
- Mi Lin
- Fujian Academy of Agricultural Sciences Biotechnology Institute, Fuzhou 350003, China; (M.L.); (J.Y.)
| | - Jingwan Yan
- Fujian Academy of Agricultural Sciences Biotechnology Institute, Fuzhou 350003, China; (M.L.); (J.Y.)
| | - Muhammad Moaaz Ali
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.M.A.); (S.W.); (S.T.)
| | - Shaojuan Wang
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.M.A.); (S.W.); (S.T.)
| | - Shengnan Tian
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.M.A.); (S.W.); (S.T.)
| | - Faxing Chen
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.M.A.); (S.W.); (S.T.)
- Correspondence: (F.C.); (Z.L.)
| | - Zhimin Lin
- Fujian Academy of Agricultural Sciences Biotechnology Institute, Fuzhou 350003, China; (M.L.); (J.Y.)
- Correspondence: (F.C.); (Z.L.)
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Park J, Demirer GS, Cheung LS. Toolboxes for plant systems biology research. Curr Opin Biotechnol 2022; 75:102692. [PMID: 35144172 DOI: 10.1016/j.copbio.2022.102692] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 12/22/2021] [Accepted: 01/20/2022] [Indexed: 02/07/2023]
Abstract
The terms 'systems' and 'synthetic biology' are often used together, with most scientists striding between the two fields rather than adhering to a single side. Often too, scientists want to understand a system to inform the design of gene circuits that could endow it with new functions. However, this does not need to be the progression of research, as synthetic constructs can help improve our understanding of a system. Here, we review synthetic biology tool kits with the potential to overcome pleiotropic effects, compensatory mechanisms, and redundancy in plants. Combined with -omics techniques, these tools could reveal novel insights on plant growth and development, an aim that has gained renewed urgency given the impact of climate change on crop productivity.
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Affiliation(s)
- Jihyun Park
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Gozde S Demirer
- Department of Plant Biology and Genome Center, University of California Davis, Davis, CA 95616, USA; Department of Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Lily S Cheung
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA.
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8
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Zagoskin AA, Zakharova MV, Nagornykh MO. Structural Elements of DNA and RNA Eukaryotic Expression Vectors for In Vitro and In Vivo Genome Editor Delivery. Mol Biol 2022; 56:950-962. [PMCID: PMC9735121 DOI: 10.1134/s0026893322060218] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 06/25/2022] [Accepted: 06/28/2022] [Indexed: 12/14/2022]
Abstract
Gene editing with programmable nucleases opens new perspectives in important practice areas, such as healthcare and agriculture. The most challenging problem for the safe and effective therapeutic use of gene editing technologies is the proper delivery and expression of gene editors in cells and tissues of different organisms. Virus-based and nonviral systems can be used for the successful delivery of gene editors. Here we have reviewed structural elements of nonviral DNA- and RNA-based expression vectors for gene editing and delivery methods in vitro and in vivo.
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Affiliation(s)
- A. A. Zagoskin
- Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, 142290 Pushchino, Russia
| | - M. V. Zakharova
- Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, 142290 Pushchino, Russia
| | - M. O. Nagornykh
- Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, 142290 Pushchino, Russia ,Sirius University of Science and Technology, Sirius, 354349 Sochi, Russia
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Wang Z, Wei K, Xiong M, Wang J, Zhang C, Fan X, Huang L, Zhao D, Liu Q, Li Q. Glucan, Water-Dikinase 1 (GWD1), an ideal biotechnological target for potential improving yield and quality in rice. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:2606-2618. [PMID: 34416068 PMCID: PMC8633486 DOI: 10.1111/pbi.13686] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 08/13/2021] [Accepted: 08/15/2021] [Indexed: 05/07/2023]
Abstract
The source-sink relationship determines the overall agronomic performance of rice. Cloning and characterizing key genes involved in the regulation of source and sink dynamics is imperative for improving rice yield. However, few source genes with potential application in rice have been identified. Glucan, Water-Dikinase 1 (GWD1) is an essential enzyme that plays a pivotal role in the first step of transitory starch degradation in source tissues. In the present study, we successfully generated gwd1 weak mutants by promoter editing using CRISPR/Cas9 system, and also leaf-dominant overexpression lines of GWD1 driven by Osl2 promoter. Analysis of the gwd1 plants indicated that promoter editing mediated down-regulation of GWD1 caused no observable effects on rice growth and development, but only mildly modified its grain transparency and seed germination. However, the transgenic pOsl2::GWD1 overexpression lines showed improvements in multiple key traits, including rice yield, grain shape, rice quality, seed germination and stress tolerance. Therefore, our study shows that GWD1 is not only involved in transitory starch degradation in source tissues, but also plays key roles in the seeds, which is a sink tissue. In conclusion, we find that GWD1 is an ideal biotechnological target with promising potential for the breeding of elite rice cultivars via genetic engineering.
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Affiliation(s)
- Zhen Wang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding /Key Laboratory of Plant Functional Genomics of the Ministry of EducationCollege of AgricultureYangzhou UniversityYangzhouJiangsuChina
| | - Ke Wei
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding /Key Laboratory of Plant Functional Genomics of the Ministry of EducationCollege of AgricultureYangzhou UniversityYangzhouJiangsuChina
| | - Min Xiong
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding /Key Laboratory of Plant Functional Genomics of the Ministry of EducationCollege of AgricultureYangzhou UniversityYangzhouJiangsuChina
| | - Jin‐Dong Wang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding /Key Laboratory of Plant Functional Genomics of the Ministry of EducationCollege of AgricultureYangzhou UniversityYangzhouJiangsuChina
| | - Chang‐Quan Zhang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding /Key Laboratory of Plant Functional Genomics of the Ministry of EducationCollege of AgricultureYangzhou UniversityYangzhouJiangsuChina
- Co‐Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province / Jiangsu Key Laboratory of Crop Genetics and PhysiologyYangzhou UniversityYangzhouJiangsuChina
| | - Xiao‐Lei Fan
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding /Key Laboratory of Plant Functional Genomics of the Ministry of EducationCollege of AgricultureYangzhou UniversityYangzhouJiangsuChina
- Co‐Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province / Jiangsu Key Laboratory of Crop Genetics and PhysiologyYangzhou UniversityYangzhouJiangsuChina
| | - Li‐Chun Huang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding /Key Laboratory of Plant Functional Genomics of the Ministry of EducationCollege of AgricultureYangzhou UniversityYangzhouJiangsuChina
- Co‐Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province / Jiangsu Key Laboratory of Crop Genetics and PhysiologyYangzhou UniversityYangzhouJiangsuChina
| | - Dong‐Sheng Zhao
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding /Key Laboratory of Plant Functional Genomics of the Ministry of EducationCollege of AgricultureYangzhou UniversityYangzhouJiangsuChina
- Co‐Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province / Jiangsu Key Laboratory of Crop Genetics and PhysiologyYangzhou UniversityYangzhouJiangsuChina
| | - Qiao‐Quan Liu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding /Key Laboratory of Plant Functional Genomics of the Ministry of EducationCollege of AgricultureYangzhou UniversityYangzhouJiangsuChina
- Co‐Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province / Jiangsu Key Laboratory of Crop Genetics and PhysiologyYangzhou UniversityYangzhouJiangsuChina
| | - Qian‐Feng Li
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding /Key Laboratory of Plant Functional Genomics of the Ministry of EducationCollege of AgricultureYangzhou UniversityYangzhouJiangsuChina
- Co‐Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province / Jiangsu Key Laboratory of Crop Genetics and PhysiologyYangzhou UniversityYangzhouJiangsuChina
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Ben Saad R, Ben Romdhane W, Zouari N, Ben Hsouna A, Harbaoui M, Brini F, Ghneim-Herrera T. Characterization of a novel LmSAP gene promoter from Lobularia maritima: Tissue specificity and environmental stress responsiveness. PLoS One 2020; 15:e0236943. [PMID: 32735612 PMCID: PMC7394455 DOI: 10.1371/journal.pone.0236943] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 07/16/2020] [Indexed: 12/03/2022] Open
Abstract
Halophyte Lobularia maritima LmSAP encodes an A20AN1 zinc-finger stress-associated protein which expression is up-regulated by abiotic stresses and heavy metals in transgenic tobacco. To deepen our understanding of LmSAP function, we isolated a 1,147 bp genomic fragment upstream of LmSAP coding sequence designated as PrLmSAP. In silico analyses of PrLmSAP revealed the presence of consensus CAAT and TATA boxes and cis-regulatory elements required for abiotic stress, phytohormones, pathogen, and wound responses, and also for tissue-specific expression. The PrLmSAP sequence was fused to the β-glucuronidase (gusA) reporter gene and transferred to rice. Histochemical GUS staining showed a pattern of tissue-specific expression in transgenic rice, with staining observed in roots, coleoptiles, leaves, stems and floral organs but not in seeds or in the root elongation zone. Wounding strongly stimulated GUS accumulation in leaves and stems. Interestingly, we observed a high stimulation of the promoter activity when rice seedlings were exposed to NaCl, PEG, ABA, MeJA, GA, cold, and heavy metals (Al3+, Cd2+, Cu2+ and Zn2+). These results suggest that the LmSAP promoter can be a convenient tool for stress-inducible gene expression and is a potential candidate for crop genetic engineering.
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Affiliation(s)
- Rania Ben Saad
- Biotechnology and Plant Improvement Laboratory, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Walid Ben Romdhane
- Biotechnology and Plant Improvement Laboratory, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
- Plant Production Department, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Nabil Zouari
- Biotechnology and Plant Improvement Laboratory, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Anis Ben Hsouna
- Biotechnology and Plant Improvement Laboratory, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
- Departments of Life Sciences, Faculty of Sciences of Gafsa, Gafsa, Tunisia
| | - Marwa Harbaoui
- Biotechnology and Plant Improvement Laboratory, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Faical Brini
- Biotechnology and Plant Improvement Laboratory, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
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11
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Bai J, Wang X, Wu H, Ling F, Zhao Y, Lin Y, Wang R. Comprehensive construction strategy of bidirectional green tissue-specific synthetic promoters. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:668-678. [PMID: 31393049 PMCID: PMC7004895 DOI: 10.1111/pbi.13231] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 07/29/2019] [Accepted: 08/06/2019] [Indexed: 05/03/2023]
Abstract
Bidirectional green tissue-specific promoters have important application prospects in genetic engineering and crop genetic improvement. However, there is no report on the application of them, mainly due to undiscovered natural bidirectional green tissue-specific promoters and the lack of a comprehensive approach for the synthesis of these promoters. In order to compensate for this vacancy, the present study reports a novel strategy for the expression regulatory sequence selection and the bidirectional green tissue-specific synthetic promoter construction. Based on this strategy, seven promoters were synthesized and introduced into rice by agrobacterium-mediated transformation. The functional identification of these synthetic promoters was performed by the expression pattern of GFP and GUS reporter genes in two reverse directions in transgenic rice. The results indicated that all the synthetic promoters possessed bidirectional expression activities in transgenic rice, and four synthetic promoters (BiGSSP2, BiGSSP3, BiGSSP6, BiGSSP7) showed highly bidirectional expression efficiencies specifically in green tissues (leaf, sheath, panicle, stem), which could be widely applied to agricultural biotechnology. Our study provided a feasible strategy for the construction of synthetic promoters, and we successfully created four bidirectional green tissue-specific synthetic promoters. It is the first report on bidirectional green tissue-specific promoters that could be efficiently applied in genetic engineering.
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Affiliation(s)
- Jiuyuan Bai
- Key Laboratory of Bio‐Resource and Eco‐Environment of Ministry of EducationCollege of life sciencesSichuan UniversityChengduChina
| | - Xin Wang
- Key Laboratory of Bio‐Resource and Eco‐Environment of Ministry of EducationCollege of life sciencesSichuan UniversityChengduChina
| | - Hao Wu
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene ResearchHuazhong Agricultural UniversityWuhanChina
| | - Fei Ling
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene ResearchHuazhong Agricultural UniversityWuhanChina
| | - Yun Zhao
- Key Laboratory of Bio‐Resource and Eco‐Environment of Ministry of EducationCollege of life sciencesSichuan UniversityChengduChina
| | - Yongjun Lin
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene ResearchHuazhong Agricultural UniversityWuhanChina
| | - Rui Wang
- Key Laboratory of Bio‐Resource and Eco‐Environment of Ministry of EducationCollege of life sciencesSichuan UniversityChengduChina
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12
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Yoo YH, Kim YJ, Moon S, Gho YS, Hong WJ, Kim EJ, Jiang X, Jung KH. Fast Track to Discover Novel Promoters in Rice. PLANTS 2020; 9:plants9010125. [PMID: 31963727 PMCID: PMC7020180 DOI: 10.3390/plants9010125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 01/13/2020] [Accepted: 01/15/2020] [Indexed: 12/04/2022]
Abstract
Promoters are key components for the application of biotechnological techniques in crop plants. Reporter genes such as GUS or GFP have been used to test the activity of promoters for diverse applications. A huge number of T-DNAs carrying promoterless GUS near their right borders have been inserted into the rice genome, and 105,739 flanking sequence tags from rice lines with this T-DNA insertion have been identified, establishing potential promoter trap lines for 20,899 out of 55,986 genes in the rice genome. Anatomical meta-expression data and information on abiotic stress related to these promoter trap lines enable us to quickly identify new promoters associated with various expression patterns. In the present report, we introduce a strategy to identify new promoters in a very short period of time using a combination of meta-expression analysis and promoter trap lines.
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13
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Gao L, Tian Y, Chen MC, Wei L, Gao TG, Yin HJ, Zhang JL, Kumar T, Liu LB, Wang SM. Cloning and functional characterization of epidermis-specific promoter MtML1 from Medicago truncatula. J Biotechnol 2019; 300:32-39. [PMID: 31085201 DOI: 10.1016/j.jbiotec.2019.05.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 04/23/2019] [Accepted: 05/09/2019] [Indexed: 01/21/2023]
Abstract
Epidermis-specific promoters are necessary for ectopic expression of specific functional genes such as the cuticle-related genes. Previous studies indicated that both ECERIFERUM 6 (AtCER6) and MERISTEM L1 LAYER (ATML1) promoters from Arabidopsis thaliana can drive gene expression specifically in the epidermis of shoot apical meristems (SAMs) and leaves. However, the epidermis-specific promoters from legume plants have not been reported. Here, we cloned a 5' flanking sequence from the upstream -2150 bp to the translational start ATG codon of MtML1 gene of legume model plant Medicago truncatula. PlantCARE analysis indicated that this sequence matches the characteristics of a promoter, having TATA box and CAAT box, as well as contains some conserved elements of epidermis-specific promoters like AtCER6 and ATML1 promoters. The β-glucuronidase (GUS) histochemical analysis showed that MtML1 promoter can drive GUS gene expression in transiently transformed Nicotiana tabacum leaves under non-inducing condition. Furthermore, it can also control GUS expression in leaves and siliques rather than roots of the stably transformed Arabidopsis. More importantly, the leaf cross-section observations indicated that MtML1 exclusively expressed in the epidermis of leaves. These results suggested that MtML1 promoter performed the epidermis-specific in plant shoot. Our study establishes the foundation for driving the cuticle-related gene to express in epidermis, which may be very useful in genetic engineering of legume plants.
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Affiliation(s)
- Li Gao
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, P.R. China
| | - Ye Tian
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, P.R. China
| | - Meng-Ci Chen
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, P.R. China
| | - Li Wei
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, P.R. China
| | - Tian-Ge Gao
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, P.R. China
| | - Hong-Ju Yin
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, P.R. China
| | - Jin-Lin Zhang
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, P.R. China
| | - Tanweer Kumar
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, P.R. China
| | - Lin-Bo Liu
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, P.R. China
| | - Suo-Min Wang
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, P.R. China.
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14
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Hong WJ, Kim YJ, Chandran AKN, Jung KH. Infrastructures of systems biology that facilitate functional genomic study in rice. RICE (NEW YORK, N.Y.) 2019; 12:15. [PMID: 30874968 PMCID: PMC6419666 DOI: 10.1186/s12284-019-0276-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Accepted: 03/06/2019] [Indexed: 05/08/2023]
Abstract
Rice (Oryza sativa L.) is both a major staple food for the worldwide population and a model crop plant for studying the mode of action of agronomically valuable traits, providing information that can be applied to other crop plants. Due to the development of high-throughput technologies such as next generation sequencing and mass spectrometry, a huge mass of multi-omics data in rice has been accumulated. Through the integration of those data, systems biology in rice is becoming more advanced.To facilitate such systemic approaches, we have summarized current resources, such as databases and tools, for systems biology in rice. In this review, we categorize the resources using six omics levels: genomics, transcriptomics, proteomics, metabolomics, integrated omics, and functional genomics. We provide the names, websites, references, working states, and number of citations for each individual database or tool and discuss future prospects for the integrated understanding of rice gene functions.
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Affiliation(s)
- Woo-Jong Hong
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Korea
| | - Yu-Jin Kim
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Korea
| | | | - Ki-Hong Jung
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Korea.
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15
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Apriana A, Sisharmini A, Aswidinnoor H, Trijatmiko KR, Sudarsono S. Promoter deletion analysis reveals root-specific expression of the alkenal reductase gene (OsAER1) in Oryza sativa. FUNCTIONAL PLANT BIOLOGY : FPB 2019; 46:376-391. [PMID: 32172746 DOI: 10.1071/fp18237] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 01/12/2019] [Indexed: 06/10/2023]
Abstract
Root-specific promoters are useful in plant genetic engineering, primarily to improve water and nutrient absorption. The aim of this study was to clone and characterise the promoter of the Oryza sativa L. alkenal reductase (OsAER1) gene encoding 2-alkenal reductase, an NADPH-dependent oxidoreductase. Expression analysis using quantitative real-time PCR confirmed the root-specific expression of the OsAER1 gene. Subsequently, a 3082-bp fragment of the OsAER1 promoter was isolated from a local Indonesian rice cultivar, Awan Kuning. Sequencing and further nucleotide sequence analysis of the 3082-bp promoter fragment (PA-5) revealed the presence of at least 10 root-specific cis-regulatory elements putatively responsible for OsAER1 root-specific expression. Using the 3082-bp promoter fragment to drive the expression of the GUS reporter transgene confirmed that the OsAER1 promoter is root-specific. Further, the analysis indicated that OsAER1 promoter activity was absent in leaves, petioles and shoots during sprouting, vegetative, booting and generative stages of rice development. In contrast, the promoter activity was present in anthers and aleurone layers of immature seeds 7-20 days after anthesis. Moreover, there was no promoter activity observed in the aleurone layers of mature seeds. The OsAER1 promoter activity is induced by Al-toxicity, NaCl and submergence stresses, indicating the OsAER1 promoter activity is induced by those stresses. Exogenous treatments of transgenic plants carrying the PA-5 promoter construct with abscisic acid and indoleacetic acid also induced expression of the GUS reporter transgene, indicating the role of plant growth regulators in controlling OsAER1 promoter activity. Promoter deletion analysis was conducted to identify the cis-acting elements of the promoter responsible for controlling root-specific expression. The GUS reporter gene was fused with various deletion fragments of the OsAER1 promoter and the resulting constructs were transformed in rice plants to generate transgenic plants. The results of this analysis indicated that cis-acting elements controlling root-specific expression are located between -1562 to -1026bp of the OsAER1 CDS. Here we discusses the results of the conducted analyses, the possible role of OsAER1 in rice growth and development, possible contributions and the potential usage of these findings in future plant research.
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Affiliation(s)
- Aniversari Apriana
- PMB Lab, Department of Agronomy and Horticulture, Faculty of Agriculture, Bogor Agricultural University, Jalan Raya Ciampea, Bogor, Indonesia; and Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and Development, Jalan Tentara Pelajar 3A, Bogor, Indonesia
| | - Atmitri Sisharmini
- Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and Development, Jalan Tentara Pelajar 3A, Bogor, Indonesia
| | - Hajrial Aswidinnoor
- PMB Lab, Department of Agronomy and Horticulture, Faculty of Agriculture, Bogor Agricultural University, Jalan Raya Ciampea, Bogor, Indonesia
| | - Kurniawan R Trijatmiko
- Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and Development, Jalan Tentara Pelajar 3A, Bogor, Indonesia; and Corresponding authors. Emails: ;
| | - Sudarsono Sudarsono
- PMB Lab, Department of Agronomy and Horticulture, Faculty of Agriculture, Bogor Agricultural University, Jalan Raya Ciampea, Bogor, Indonesia; and Corresponding authors. Emails: ;
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16
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Zhai X, Kong Q, An P, Ren X. The Function and Mechanism of Pathogenesis-Related 5 Protein Resistance in Cherry Tomato in Response to Alternaria alternata. FOOD BIOTECHNOL 2018. [DOI: 10.1080/08905436.2018.1481088] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Xin Zhai
- College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi’an, Shaanxi, China
| | - Qingjun Kong
- College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi’an, Shaanxi, China
| | - Peipei An
- College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi’an, Shaanxi, China
| | - Xueyan Ren
- College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi’an, Shaanxi, China
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17
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Nuccio ML, Paul M, Bate NJ, Cohn J, Cutler SR. Where are the drought tolerant crops? An assessment of more than two decades of plant biotechnology effort in crop improvement. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 273:110-119. [PMID: 29907303 DOI: 10.1016/j.plantsci.2018.01.020] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 01/29/2018] [Accepted: 01/31/2018] [Indexed: 05/22/2023]
Abstract
Since the dawn of modern biotechnology public and private enterprise have pursued the development of a new breed of drought tolerant crop products. After more than 20 years of research and investment only a few such products have reached the market. This is due to several technical and market constraints. The technical challenges include the difficulty in defining tractable single-gene trait development strategies, the logistics of moving traits from initial to commercial genetic backgrounds, and the disconnect between conditions in farmer's fields and controlled environments. Market constraints include the significant difficulty, and associated costs, in obtaining access to markets around the world. Advances in the biology of plant water management, including response to water deficit reveal new opportunities to improve crop response to water deficit and new genome-based tools promise to usher in the next era of crop improvement. As biotechnology looks to improve crop productivity under drought conditions, the environmental and food security advantages will influence public perception and shift the debate toward benefits rather than risks.
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Affiliation(s)
- Michael L Nuccio
- Syngenta Crop Protection, LLC., 9 Davis Drive, Research Triangle Park, NC, 27709, USA.
| | - Matthew Paul
- Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK.
| | - Nicholas J Bate
- Syngenta Crop Protection, LLC., 9 Davis Drive, Research Triangle Park, NC, 27709, USA.
| | - Jonathan Cohn
- Syngenta Crop Protection, LLC., 9 Davis Drive, Research Triangle Park, NC, 27709, USA.
| | - Sean R Cutler
- Plant Cell Biology and Chemistry, Botany and Plant Sciences Chemistry Genomics Building, University of California Riverside, CA, 92521, USA.
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18
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Gianinetti A, Finocchiaro F, Bagnaresi P, Zechini A, Faccioli P, Cattivelli L, Valè G, Biselli C. Seed Dormancy Involves a Transcriptional Program That Supports Early Plastid Functionality during Imbibition. PLANTS 2018; 7:plants7020035. [PMID: 29671830 PMCID: PMC6026906 DOI: 10.3390/plants7020035] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 04/05/2018] [Accepted: 04/11/2018] [Indexed: 01/18/2023]
Abstract
Red rice fully dormant seeds do not germinate even under favorable germination conditions. In several species, including rice, seed dormancy can be removed by dry-afterripening (warm storage); thus, dormant and non-dormant seeds can be compared for the same genotype. A weedy (red) rice genotype with strong dormancy was used for mRNA expression profiling, by RNA-Seq, of dormant and non-dormant dehulled caryopses (here addressed as seeds) at two temperatures (30 °C and 10 °C) and two durations of incubation in water (8 h and 8 days). Aim of the study was to highlight the differences in the transcriptome of dormant and non-dormant imbibed seeds. Transcript data suggested important differences between these seeds (at least, as inferred by expression-based metabolism reconstruction): dry-afterripening seems to impose a respiratory impairment onto non-dormant seeds, thus glycolysis is deduced to be preferentially directed to alcoholic fermentation in non-dormant seeds but to alanine production in dormant ones; phosphoenolpyruvate carboxykinase, pyruvate phosphate dikinase and alanine aminotransferase pathways appear to have an important gluconeogenetic role associated with the restoration of plastid functions in the dormant seed following imbibition; correspondingly, co-expression analysis pointed out a commitment to guarantee plastid functionality in dormant seeds. At 8 h of imbibition, as inferred by gene expression, dormant seeds appear to preferentially use carbon and nitrogen resources for biosynthetic processes in the plastid, including starch and proanthocyanidins accumulation. Chromatin modification appears to be a possible mechanism involved in the transition from dormancy to germination. Non-dormant seeds show higher expression of genes related to cell wall modification, suggesting they prepare for acrospire/radicle elongation.
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Affiliation(s)
- Alberto Gianinetti
- Council for Agricultural Research and Economics-Research Centre for Genomics and Bioinformatics, via S. Protaso 302, 29017 Fiorenzuola d'Arda (PC), Italy.
| | - Franca Finocchiaro
- Council for Agricultural Research and Economics-Research Centre for Genomics and Bioinformatics, via S. Protaso 302, 29017 Fiorenzuola d'Arda (PC), Italy.
| | - Paolo Bagnaresi
- Council for Agricultural Research and Economics-Research Centre for Genomics and Bioinformatics, via S. Protaso 302, 29017 Fiorenzuola d'Arda (PC), Italy.
| | - Antonella Zechini
- Council for Agricultural Research and Economics-Research Centre for Genomics and Bioinformatics, via S. Protaso 302, 29017 Fiorenzuola d'Arda (PC), Italy.
| | - Primetta Faccioli
- Council for Agricultural Research and Economics-Research Centre for Genomics and Bioinformatics, via S. Protaso 302, 29017 Fiorenzuola d'Arda (PC), Italy.
| | - Luigi Cattivelli
- Council for Agricultural Research and Economics-Research Centre for Genomics and Bioinformatics, via S. Protaso 302, 29017 Fiorenzuola d'Arda (PC), Italy.
| | - Giampiero Valè
- Council for Agricultural Research and Economics-Research Centre for Genomics and Bioinformatics, via S. Protaso 302, 29017 Fiorenzuola d'Arda (PC), Italy.
- Council for Agricultural Research and Economics-Research Centre for Cereal and Industrial Crops, s.s. 11 to Torino, km 2.5, 13100 Vercelli, Italy.
| | - Chiara Biselli
- Council for Agricultural Research and Economics-Research Centre for Genomics and Bioinformatics, via S. Protaso 302, 29017 Fiorenzuola d'Arda (PC), Italy.
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Li QF, Yu JW, Lu J, Fei HY, Luo M, Cao BW, Huang LC, Zhang CQ, Liu QQ. Seed-Specific Expression of OsDWF4, a Rate-Limiting Gene Involved in Brassinosteroids Biosynthesis, Improves Both Grain Yield and Quality in Rice. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:3759-3772. [PMID: 29613784 DOI: 10.1021/acs.jafc.8b00077] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Brassinosteroids (BRs) are essential plant-specific steroidal hormones that regulate diverse growth and developmental processes in plants. We evaluated the effects of OsDWF4, a gene that encodes a rate-limiting enzyme in BR biosynthesis, on both rice yield and quality when driven by the Gt1 or Ubi promoter, which correspond to seed-specific or constitutive expression, respectively. Generally, transgenic plants expressing OsDWF4 showed increased grain yield with more tillers and longer and heavier seeds. Moreover, the starch physicochemical properties of the transgenic rice were also improved. Interestingly, OsDWF4 was found to exert different effects on either rice yield or quality when driven by the different promoters. The overall performance of the pGt1::OsDWF4 lines was better than that of the pUbi::OsDWF4 lines. Our data not only demonstrate the effects of OsDWF4 overexpression on both rice yield and quality but also suggest that a seed-specific promoter is a good choice in BR-mediated rice breeding programs.
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Affiliation(s)
- Qian-Feng Li
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province/Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture , Yangzhou University , Yangzhou 225009 , China
- Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province/Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education , Yangzhou University , Yangzhou 225009 , China
| | - Jia-Wen Yu
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province/Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture , Yangzhou University , Yangzhou 225009 , China
| | - Jun Lu
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province/Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture , Yangzhou University , Yangzhou 225009 , China
| | - Hong-Yuan Fei
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province/Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture , Yangzhou University , Yangzhou 225009 , China
| | - Ming Luo
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden , Chinese Academy of Sciences , Guangzhou 510650 , China
| | - Bu-Wei Cao
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province/Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture , Yangzhou University , Yangzhou 225009 , China
| | - Li-Chun Huang
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province/Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture , Yangzhou University , Yangzhou 225009 , China
| | - Chang-Quan Zhang
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province/Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture , Yangzhou University , Yangzhou 225009 , China
- Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province/Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education , Yangzhou University , Yangzhou 225009 , China
| | - Qiao-Quan Liu
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province/Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture , Yangzhou University , Yangzhou 225009 , China
- Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province/Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education , Yangzhou University , Yangzhou 225009 , China
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20
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Moon S, Chandran AKN, Gho YS, Park SA, Kim SR, Yoo YH, Jung KH. Integrated omics analysis of root-preferred genes across diverse rice varieties including Japonica and indica cultivars. JOURNAL OF PLANT PHYSIOLOGY 2018; 220:11-23. [PMID: 29132026 DOI: 10.1016/j.jplph.2017.10.003] [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] [Received: 04/11/2017] [Revised: 10/02/2017] [Accepted: 10/16/2017] [Indexed: 06/07/2023]
Abstract
Plant root systems play essential roles in developmental processes, such as the absorption of water and inorganic nutrients, and structural support. Gene expression is affected by growth conditions and the genetic background of plants. To identify highly conserved root-preferred genes in rice across diverse growth conditions and varieties, we used two independent meta-anatomical expression profiles based on a large collection of Affymetrix and Agilent 44K microarray data sets available for public use. We then identified 684 loci with root-preferred expression, which were validated with in silico analysis using both meta-expression profiles. The expression patterns of four candidate genes were confirmed in vivo by monitoring expression of β-glucuronidase under control of the candidate-gene promoters, providing new tools to manipulate agronomic traits associated with roots. We also utilized real-time PCR to examine the root-preferential expression of 14 genes across four rice varieties, including japonica and indica cultivars. Using a database of rice genes with known functions, we identified the reported functions of 39 out of the 684 candidate genes. Sixteen genes are directly involved in root development, while the remaining are involved in processes indirectly related to root development (i.e., soil-stress tolerance or growth retardation). This indicates the importance of our candidate genes for studies on root development and function. Gene ontology enrichment analysis in the 'biological processes' category revealed that root-preferred genes in rice are closely associated with nutrient transport-related genes, indicating that the primary role of roots is the uptake of nutrients from soil. In addition, predicted protein-protein interaction analysis suggested a molecular network for root development composed of 215 interactions associated with 44 root-preferred or root development-related genes. Taken together, our data provide an important foundation for future research on root development in rice.
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Affiliation(s)
- Sunok Moon
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Korea
| | | | - Yun-Shil Gho
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Korea
| | - Sun-A Park
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Korea
| | - Sung-Ryul Kim
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Korea
| | - Yo-Han Yoo
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Korea
| | - Ki-Hong Jung
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Korea.
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Kim SW, Lee SK, Jeong HJ, An G, Jeon JS, Jung KH. Crosstalk between diurnal rhythm and water stress reveals an altered primary carbon flux into soluble sugars in drought-treated rice leaves. Sci Rep 2017; 7:8214. [PMID: 28811563 PMCID: PMC5557844 DOI: 10.1038/s41598-017-08473-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Accepted: 06/30/2017] [Indexed: 12/13/2022] Open
Abstract
Plants retain rhythmic physiological responses when adapting to environmental challenges. However, possible integrations between drought conditions and those responses have not received much focus, especially regarding crop plants, and the relationship between abiotic stress and the diurnal cycle is generally not considered. Therefore, we conducted a genome-wide analysis to identify genes showing both diurnal regulation and water-deficiency response in rice (Oryza sativa). Among the 712 drought-responsive genes primary identified, 56.6% are diurnally expressed while 47.6% of the 761 that are down-regulated by drought are also diurnal. Using the β-glucuronidase reporter system and qRT-PCR analyses, we validated expression patterns of two candidate genes, thereby supporting the reliability of our transcriptome data. MapMan analysis indicated that diurnal genes up-regulated by drought are closely associated with the starch-sucrose pathway while those that are down-regulated are involved in photosynthesis. We then confirmed that starch-sucrose contents and chlorophyll fluorescence are altered in a diurnal manner under drought stress, suggesting these metabolic diurnal alterations as a novel indicator to evaluate the drought response in rice leaves. We constructed a functional gene network associated with the starch-sucrose KEGG metabolic pathway for further functional studies, and also developed a regulatory pathway model that includes OsbZIP23 transcription factor.
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Affiliation(s)
- Seo-Woo Kim
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Korea
| | - Sang-Kyu Lee
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Korea
| | - Hee-Jeong Jeong
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Korea
| | - Gynheung An
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Korea
| | - Jong-Seong Jeon
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Korea.
| | - Ki-Hong Jung
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Korea.
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Huang X, Peng X, Sun MX. OsGCD1 is essential for rice fertility and required for embryo dorsal-ventral pattern formation and endosperm development. THE NEW PHYTOLOGIST 2017; 215:1039-1058. [PMID: 28585692 DOI: 10.1111/nph.14625] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 04/25/2017] [Indexed: 05/20/2023]
Abstract
Rice fertility is critical for rice reproduction and is thus a focus of interest. Most studies have addressed male sterility and its relation to rice production. The mechanisms of regulation of embryogenesis and endosperm development are essential for rice reproduction, but remain largely unknown. Here, we report a functional analysis of the rice gene OsGCD1, which encodes a highly conserved homolog of Arabidopsis GCD1 (GAMETE CELLS DEFECTIVE1). OsGCD1 mutants were generated using the CRISPR/Cas9 system and subjected to functional analysis. The homozygote mutants cannot be obtained, whereas heterozygotes showed altered phenotypes. In the majority of aborted seeds, the endosperm nucleus divided a limited number of times. The free nuclei were distributed only at the micropylar end of embryo sacs, and their oriented positioning was blocked. In addition, aleurone differentiation was interrupted. The embryo developed slowly, and pattern formation, particularly the dorsal-ventral pattern and symmetry establishment, of embryos was disturbed. Thus, the embryos showed various morphological and structural dysplasias. Our findings reveal that OsGCD1 is essential for rice fertility and is required for dorsal-ventral pattern formation and endosperm free nucleus positioning, suggesting a critical role in sexual reproduction of both monocotyledon and dicotyledon plants.
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Affiliation(s)
- Xiaorong Huang
- College of Life Science, State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan, 430072, China
| | - Xiongbo Peng
- College of Life Science, State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan, 430072, China
| | - Meng-Xiang Sun
- College of Life Science, State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan, 430072, China
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Yoo YH, Nalini Chandran AK, Park JC, Gho YS, Lee SW, An G, Jung KH. OsPhyB-Mediating Novel Regulatory Pathway for Drought Tolerance in Rice Root Identified by a Global RNA-Seq Transcriptome Analysis of Rice Genes in Response to Water Deficiencies. FRONTIERS IN PLANT SCIENCE 2017; 8:580. [PMID: 28491065 PMCID: PMC5405136 DOI: 10.3389/fpls.2017.00580] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 03/30/2017] [Indexed: 05/18/2023]
Abstract
Water deficiencies are one of the most serious challenges to crop productivity. To improve our understanding of soil moisture stress, we performed RNA-Seq analysis using roots from 4-week-old rice seedlings grown in soil that had been subjected to drought conditions for 2-3 d. In all, 1,098 genes were up-regulated in response to soil moisture stress for 3 d, which causes severe damage in root development after recovery, unlikely that of 2 d. Comparison with previous transcriptome data produced in drought condition indicated that more than 68% of our candidate genes were not previously identified, emphasizing the novelty of our transcriptome analysis for drought response in soil condition. We then validated the expression patterns of two candidate genes using a promoter-GUS reporter system in planta and monitored the stress response with novel molecular markers. An integrating omics tool, MapMan analysis, indicated that RING box E3 ligases in the ubiquitin-proteasome pathways are significantly stimulated by induced drought. We also analyzed the functions of 66 candidate genes that have been functionally investigated previously, suggesting the primary roles of our candidate genes in resistance or tolerance relating traits including drought tolerance (29 genes) through literature searches besides diverse regulatory roles of our candidate genes for morphological traits (15 genes) or physiological traits (22 genes). Of these, we used a T-DNA insertional mutant of rice phytochrome B (OsPhyB) that negatively regulates a plant's degree of tolerance to water deficiencies through the control of total leaf area and stomatal density based on previous finding. Unlike previous result, we found that OsPhyB represses the activity of ascorbate peroxidase and catalase mediating reactive oxygen species (ROS) processing machinery required for drought tolerance of roots in soil condition, suggesting the potential significance of remaining uncharacterized candidate genes for manipulating drought tolerance in rice.
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Kumar M, Gho YS, Jung KH, Kim SR. Genome-Wide Identification and Analysis of Genes, Conserved between japonica and indica Rice Cultivars, that Respond to Low-Temperature Stress at the Vegetative Growth Stage. FRONTIERS IN PLANT SCIENCE 2017; 8:1120. [PMID: 28713404 PMCID: PMC5491850 DOI: 10.3389/fpls.2017.01120] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 06/09/2017] [Indexed: 05/14/2023]
Abstract
Cold stress is very detrimental to crop production. However, only a few genes in rice have been identified with known functions related to cold tolerance. To meet this agronomic challenge more effectively, researchers must take global approaches to select useful candidate genes and find the major regulatory factors. We used five Gene expression omnibus series data series of Affymetrix array data, produced with cold stress-treated samples from the NCBI Gene Expression Omnibus (http://www.ncbi.nlm.nih.gov/geo/), and identified 502 cold-inducible genes common to both japonica and indica rice cultivars. From them, we confirmed that the expression of two randomly chosen genes was increased by cold stress in planta. In addition, overexpression of OsWRKY71 enhanced cold tolerance in 'Dongjin,' the tested japonica cultivar. Comparisons between japonica and indica rice, based on calculations of plant survival rates and chlorophyll fluorescence, confirmed that the japonica rice was more cold-tolerant. Gene Ontology enrichment analysis indicate that the 'L-phenylalanine catabolic process,' within the Biological Process category, was the most highly overrepresented under cold-stress conditions, implying its significance in that response in rice. MapMan analysis classified 'Major Metabolic' processes and 'Regulatory Gene Modules' as two other major determinants of the cold-stress response and suggested several key cis-regulatory elements. Based on these results, we proposed a model that includes a pathway for cold stress-responsive signaling. Results from our functional analysis of the main signal transduction and transcription regulation factors identified in that pathway will provide insight into novel regulatory metabolism(s), as well as a foundation by which we can develop crop plants with enhanced cold tolerance.
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Affiliation(s)
- Manu Kumar
- Department of Life Sciences, Sogang UniversitySeoul, South Korea
| | - Yun-Shil Gho
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee UniversityYongin, South Korea
| | - Ki-Hong Jung
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee UniversityYongin, South Korea
- *Correspondence: Seong-Ryong Kim, Ki-Hong Jung,
| | - Seong-Ryong Kim
- Department of Life Sciences, Sogang UniversitySeoul, South Korea
- *Correspondence: Seong-Ryong Kim, Ki-Hong Jung,
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25
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Nguyen TD, Moon S, Nguyen VNT, Gho Y, Chandran AKN, Soh MS, Song JT, An G, Oh SA, Park SK, Jung KH. Genome-wide identification and analysis of rice genes preferentially expressed in pollen at an early developmental stage. PLANT MOLECULAR BIOLOGY 2016; 92:71-88. [PMID: 27356912 DOI: 10.1007/s11103-016-0496-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 05/23/2016] [Indexed: 06/06/2023]
Abstract
Microspore production using endogenous developmental programs has not been well studied. The main limitation is the difficulty in identifying genes preferentially expressed in pollen grains at early stages. To overcome this limitation, we collected transcriptome data from anthers and microspore/pollen and performed meta-expression analysis. Subsequently, we identified 410 genes showing preferential expression patterns in early developing pollen samples of both japonica and indica cultivars. The expression patterns of these genes are distinguishable from genes showing pollen mother cell or tapetum-preferred expression patterns. Gene Ontology enrichment and MapMan analyses indicated that microspores in rice are closely linked with protein degradation, nucleotide metabolism, and DNA biosynthesis and regulation, while the pollen mother cell or tapetum are strongly associated with cell wall metabolism, lipid metabolism, secondary metabolism, and RNA biosynthesis and regulation. We also generated transgenic lines under the control of the promoters of eight microspore-preferred genes and confirmed the preferred expression patterns in plants using the GUS reporting system. Furthermore, cis-regulatory element analysis revealed that pollen specific elements such as POLLEN1LELAT52, and 5659BOXLELAT5659 were commonly identified in the promoter regions of eight rice genes with more frequency than estimation. Our study will provide new sights on early pollen development in rice, a model crop plant.
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Affiliation(s)
- Tien Dung Nguyen
- School of Applied Biosciences, Kyungpook National University, Daegu, 702-701, Republic of Korea
| | - Sunok Moon
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, 446-701, Republic of Korea
| | - Van Ngoc Tuyet Nguyen
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, 446-701, Republic of Korea
| | - Yunsil Gho
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, 446-701, Republic of Korea
| | - Anil Kumar Nalini Chandran
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, 446-701, Republic of Korea
| | - Moon-Soo Soh
- Department of Molecular Biology, Sejong University, Seoul, 143-747, Republic of Korea
| | - Jong Tae Song
- School of Applied Biosciences, Kyungpook National University, Daegu, 702-701, Republic of Korea
| | - Gynheung An
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, 446-701, Republic of Korea
| | - Sung Aeong Oh
- School of Applied Biosciences, Kyungpook National University, Daegu, 702-701, Republic of Korea
| | - Soon Ki Park
- School of Applied Biosciences, Kyungpook National University, Daegu, 702-701, Republic of Korea.
| | - Ki-Hong Jung
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, 446-701, Republic of Korea.
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26
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Zhang D. Translational plant biology. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2015; 57:874-875. [PMID: 26555768 DOI: 10.1111/jipb.12431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Affiliation(s)
- Dabing Zhang
- Joint International Research Laboratory of Metabolic & Developmental Sciences, SJTU-University of Adelaide Joint Centre for Agriculture and Health
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