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He J, Zeng C, Li M. Plant Functional Genomics Based on High-Throughput CRISPR Library Knockout Screening: A Perspective. ADVANCED GENETICS (HOBOKEN, N.J.) 2024; 5:2300203. [PMID: 38465224 PMCID: PMC10919289 DOI: 10.1002/ggn2.202300203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 10/19/2023] [Indexed: 03/12/2024]
Abstract
Plant biology studies in the post-genome era have been focused on annotating genome sequences' functions. The established plant mutant collections have greatly accelerated functional genomics research in the past few decades. However, most plant genome sequences' roles and the underlying regulatory networks remain substantially unknown. Clustered, regularly interspaced short palindromic repeat (CRISPR)-associated systems are robust, versatile tools for manipulating plant genomes with various targeted DNA perturbations, providing an excellent opportunity for high-throughput interrogation of DNA elements' roles. This study compares methods frequently used for plant functional genomics and then discusses different DNA multi-targeted strategies to overcome gene redundancy using the CRISPR-Cas9 system. Next, this work summarizes recent reports using CRISPR libraries for high-throughput gene knockout and function discoveries in plants. Finally, this work envisions the future perspective of optimizing and leveraging CRISPR library screening in plant genomes' other uncharacterized DNA sequences.
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Affiliation(s)
- Jianjie He
- Department of BiotechnologyCollege of Life Science and TechnologyHuazhong University of Science and TechnologyWuhan430074China
- Key Laboratory of Molecular Biophysics of the Ministry of EducationWuhan430074China
| | - Can Zeng
- Department of BiotechnologyCollege of Life Science and TechnologyHuazhong University of Science and TechnologyWuhan430074China
- Key Laboratory of Molecular Biophysics of the Ministry of EducationWuhan430074China
| | - Maoteng Li
- Department of BiotechnologyCollege of Life Science and TechnologyHuazhong University of Science and TechnologyWuhan430074China
- Key Laboratory of Molecular Biophysics of the Ministry of EducationWuhan430074China
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Chawla R, Poonia A, Samantara K, Mohapatra SR, Naik SB, Ashwath MN, Djalovic IG, Prasad PVV. Green revolution to genome revolution: driving better resilient crops against environmental instability. Front Genet 2023; 14:1204585. [PMID: 37719711 PMCID: PMC10500607 DOI: 10.3389/fgene.2023.1204585] [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: 04/12/2023] [Accepted: 08/11/2023] [Indexed: 09/19/2023] Open
Abstract
Crop improvement programmes began with traditional breeding practices since the inception of agriculture. Farmers and plant breeders continue to use these strategies for crop improvement due to their broad application in modifying crop genetic compositions. Nonetheless, conventional breeding has significant downsides in regard to effort and time. Crop productivity seems to be hitting a plateau as a consequence of environmental issues and the scarcity of agricultural land. Therefore, continuous pursuit of advancement in crop improvement is essential. Recent technical innovations have resulted in a revolutionary shift in the pattern of breeding methods, leaning further towards molecular approaches. Among the promising approaches, marker-assisted selection, QTL mapping, omics-assisted breeding, genome-wide association studies and genome editing have lately gained prominence. Several governments have progressively relaxed their restrictions relating to genome editing. The present review highlights the evolutionary and revolutionary approaches that have been utilized for crop improvement in a bid to produce climate-resilient crops observing the consequence of climate change. Additionally, it will contribute to the comprehension of plant breeding succession so far. Investing in advanced sequencing technologies and bioinformatics will deepen our understanding of genetic variations and their functional implications, contributing to breakthroughs in crop improvement and biodiversity conservation.
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Affiliation(s)
- Rukoo Chawla
- Department of Genetics and Plant Breeding, Maharana Pratap University of Agriculture and Technology, Udaipur, Rajasthan, India
| | - Atman Poonia
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh Haryana Agricultural University, Bawal, Haryana, India
| | - Kajal Samantara
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Sourav Ranjan Mohapatra
- Department of Forest Biology and Tree Improvement, Odisha University of Agriculture and Technology, Bhubaneswar, Odisha, India
| | - S. Balaji Naik
- Institute of Integrative Biology and Systems, University of Laval, Quebec City, QC, Canada
| | - M. N. Ashwath
- Department of Forest Biology and Tree Improvement, Kerala Agricultural University, Thrissur, Kerala, India
| | - Ivica G. Djalovic
- Institute of Field and Vegetable Crops, National Institute of the Republic of Serbia, Novi Sad, Serbia
| | - P. V. Vara Prasad
- Department of Agronomy, Kansas State University, Manhattan, KS, United States
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Um TY, Hong SY, Han JS, Jung KH, Moon S, Choi BS, Basnet P, Chung YS, Lee SW, Yang WT, Kim DH. Gibberellic acid sensitive dwarf encodes an ARPC2 subunit that mediates gibberellic acid biosynthesis, effects to grain yield in rice. FRONTIERS IN PLANT SCIENCE 2022; 13:1027688. [PMID: 36618614 PMCID: PMC9813395 DOI: 10.3389/fpls.2022.1027688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 12/05/2022] [Indexed: 06/17/2023]
Abstract
The plant hormone gibberellic acid (GA) is important for plant growth and productivity. Actin-related proteins (ARPs) also play central roles in plant growth, including cell elongation and development. However, the relationships between ARPs and GA signaling and biosynthesis are not fully understood. Here, we isolated OsGASD, encoding an ARP subunit from rice (Oryza sativa), using the Ac/Ds knockout system. The osgasd knockout (Ko) mutation reduced GA3 content in shoots as well as plant growth and height. However, GA application restored the plant height of the osgasd Ko mutant to a height similar to that of the wild type (WT). Rice plants overexpressing OsGASD (Ox) showed increased plant height and grain yield compared to the WT. Transcriptome analysis of flag leaves of OsGASD Ox and osgasd Ko plants revealed that OsGASD regulates cell development and the expression of elongation-related genes. These observations suggest that OsGASD is involved in maintaining GA homeostasis to regulate plant development, thereby affecting rice growth and productivity.
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Affiliation(s)
- Tae Young Um
- Department of Agriculture and Life Industry, Kangwon National University, Chuncheon, Republic of Korea
| | - So Yeon Hong
- College of Life Science and Natural Resources, Dong-A University, Busan, Republic of Korea
| | - Ji Sung Han
- College of Life Science and Natural Resources, Dong-A University, Busan, Republic of Korea
| | - Ki Hong Jung
- Graduate School of Green-Bio Science, Kyung Hee University, Yongin, Republic of Korea
| | - Sunok Moon
- Graduate School of Green-Bio Science, Kyung Hee University, Yongin, Republic of Korea
| | - Beom-Soon Choi
- Research Institute, NBIT Co., Ltd., Chuncheon, Republic of Korea
| | - Prakash Basnet
- Department of Agriculture and Life Industry, Kangwon National University, Chuncheon, Republic of Korea
| | - Young Soo Chung
- College of Life Science and Natural Resources, Dong-A University, Busan, Republic of Korea
| | - Seon Woo Lee
- College of Life Science and Natural Resources, Dong-A University, Busan, Republic of Korea
| | - Won Tae Yang
- College of Life Science and Natural Resources, Dong-A University, Busan, Republic of Korea
| | - Doh Hoon Kim
- College of Life Science and Natural Resources, Dong-A University, Busan, Republic of Korea
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Cloning of Maize TED Transposon into Escherichia coli Reveals the Polychromatic Sequence Landscape of Refractorily Propagated Plasmids. Int J Mol Sci 2022; 23:ijms231911993. [PMID: 36233292 PMCID: PMC9569675 DOI: 10.3390/ijms231911993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/27/2022] [Accepted: 10/06/2022] [Indexed: 11/05/2022] Open
Abstract
MuDR, the founder member of the Mutator superfamily and its MURA transcripts, has been identified as toxic sequences to Escherichia coli (E. coli), which heavily hindered the elucidation of the biochemical features of MURA transposase and confined the broader application of the Mutator system in other organisms. To harness less constrained systems as alternatives, we attempted to clone TED and Jittery, two recently isolated autonomous Mutator-like elements (MULEs) from maize, respectively. Their full-length transcripts and genomic copies are successfully cloned when the incubation time for bacteria to recover from heat shock is extended appropriately prior to plating. However, during their proliferation in E. coli, TED transformed plasmids are unstable, as evidenced by derivatives from which frameshift, deletion mutations, or IS transposon insertions are readily detected. Our results suggest that neither leaky expression of the transposase nor the presence of terminal inverse repeats (TIRs) are responsible for the cloning barriers, which were once ascribed to the presence of the Shine–Dalgarno-like sequence. Instead, the internal sequence of TED (from 1250 to 2845 bp), especially the exons in this region, was the most likely causer. The findings provide novel insights into the property and function of the Mutator superfamily and shed light on the dissection of toxic effects on cloning from MULEs.
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Toward the development of Ac/Ds transposon-mediated gene tagging system for functional genomics in oat (Avena sativa L.). Funct Integr Genomics 2022; 22:669-681. [PMID: 35467221 DOI: 10.1007/s10142-022-00861-9] [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: 01/13/2022] [Revised: 04/07/2022] [Accepted: 04/08/2022] [Indexed: 11/04/2022]
Abstract
Cultivated oat (Avena sativa L.) is an important cereal grown worldwide due to its multifunctional uses for animal feed and human food. Oat has lagged behind other cereals in the genetic and genomic studies attributed to its large and complex genomes. Transposon-based genome characterization has been utilized successfully for identifying and determining gene function in large genome cereals. To develop gene tagging and gene-editing resources for oat, maize Activator (Ac) and Dissociation (Ds) transposons were introduced into the oat genome using the biolistic delivery system. A total of 2035 oat calli were bombarded and twenty-four independent, stable transgenic events were obtained. Transformation frequencies were up to 19.0%, and 1.9% for bialaphos and hygromycin selection, respectively. Re-mobilization of the non-autonomous Ds element, by introducing Ac transposase source, led to a transposition frequency up to 16.8%. The properties of ten unique flanking sequences have been characterized to reveal the Ds-tagged sites in the oat genome. Genes at Ds insertion sites showed homology to gibberellin 20-oxidase 3, (1,3;1,4)-beta-D-glucan synthase, and aspartate kinase. This Ac/Ds transposon-based gene tagging system could facilitate and expedite functional genomic studies in oat.
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Wang C, Han B. Twenty years of rice genomics research: From sequencing and functional genomics to quantitative genomics. MOLECULAR PLANT 2022; 15:593-619. [PMID: 35331914 DOI: 10.1016/j.molp.2022.03.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/04/2022] [Accepted: 03/18/2022] [Indexed: 06/14/2023]
Abstract
Since the completion of the rice genome sequencing project in 2005, we have entered the era of rice genomics, which is still in its ascendancy. Rice genomics studies can be classified into three stages: structural genomics, functional genomics, and quantitative genomics. Structural genomics refers primarily to genome sequencing for the construction of a complete map of rice genome sequence. This is fundamental for rice genetics and molecular biology research. Functional genomics aims to decode the functions of rice genes. Quantitative genomics is large-scale sequence- and statistics-based research to define the quantitative traits and genetic features of rice populations. Rice genomics has been a transformative influence on rice biological research and contributes significantly to rice breeding, making rice a good model plant for studying crop sciences.
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Affiliation(s)
- Changsheng Wang
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200233, China.
| | - Bin Han
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200233, China.
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Liu Y, Chen X, Xue S, Quan T, Cui D, Han L, Cong W, Li M, Yun D, Liu B, Xu Z. SET DOMAIN GROUP 721 protein functions in saline-alkaline stress tolerance in the model rice variety Kitaake. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:2576-2588. [PMID: 34416090 PMCID: PMC8633509 DOI: 10.1111/pbi.13683] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 08/07/2021] [Accepted: 08/10/2021] [Indexed: 06/12/2023]
Abstract
To isolate the genetic locus responsible for saline-alkaline stress tolerance, we developed a high-throughput activation tagging-based T-DNA insertion mutagenesis method using the model rice (Oryza sativa L.) variety Kitaake. One of the activation-tagged insertion lines, activation tagging 7 (AC7), showed increased tolerance to saline-alkaline stress. This phenotype resulted from the overexpression of a gene that encodes a SET DOMAIN GROUP 721 protein with H3K4 methyltransferase activity. Transgenic plants overexpressing OsSDG721 showed saline-alkaline stress-tolerant phenotypes, along with increased leaf angle, advanced heading and ripening dates. By contrast, ossdg721 loss-of-function mutants showed increased sensitivity to saline-alkaline stress characterized by decreased survival rates and reduction in plant height, grain size, grain weight and leaf angle. RNA sequencing (RNA-seq) analysis of wild-type Kitaake and ossdg721 mutants indicated that OsSDG721 positively regulates the expression level of HIGH-AFFINITY POTASSIUM (K+ ) TRANSPORTER1;5 (OsHKT1;5), which encodes a Na+ -selective transporter that maintains K+ /Na+ homeostasis under salt stress. Furthermore, we showed that OsSDG721 binds to and deposits the H3K4me3 mark in the promoter and coding region of OsHKT1;5, thereby upregulating OsHKT1;5 expression under saline-alkaline stress. Overall, by generating Kitaake activation-tagging pools, we established that the H3K4 methyltransferase OsSDG721 enhances saline-alkaline stress tolerance in rice.
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Affiliation(s)
- Yutong Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE)Northeast Normal UniversityChangchunP. R. China
| | - Xi Chen
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE)Northeast Normal UniversityChangchunP. R. China
| | - Shangyong Xue
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE)Northeast Normal UniversityChangchunP. R. China
| | - Taiyong Quan
- School of Life ScienceShandong UniversityQingdaoP. R. China
| | - Di Cui
- Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingP. R. China
| | - Longzhi Han
- Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingP. R. China
| | - Weixuan Cong
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE)Northeast Normal UniversityChangchunP. R. China
| | - Mengting Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE)Northeast Normal UniversityChangchunP. R. China
| | - Dae‐Jin Yun
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE)Northeast Normal UniversityChangchunP. R. China
- Department of Biomedical Science and EngineeringKonkuk UniversitySeoulSouth Korea
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE)Northeast Normal UniversityChangchunP. R. China
| | - Zheng‐Yi Xu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE)Northeast Normal UniversityChangchunP. R. China
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Lyu M, Liu H, Waititu JK, Sun Y, Wang H, Fu J, Chen Y, Liu J, Ku L, Cheng X. TEAseq-based identification of 35,696 Dissociation insertional mutations facilitates functional genomic studies in maize. J Genet Genomics 2021; 48:961-971. [PMID: 34654681 DOI: 10.1016/j.jgg.2021.07.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 07/11/2021] [Accepted: 07/17/2021] [Indexed: 11/26/2022]
Abstract
In plants, transposable element (TE)-triggered mutants are important resources for functional genomic studies. However, conventional approaches for genome-wide identification of TE insertion sites are costly and laborious. This study developed a novel, rapid, and high-throughput TE insertion site identification workflow based on next-generation sequencing and named it Transposable Element Amplicon Sequencing (TEAseq). Using TEAseq, we systemically profiled the Dissociation (Ds) insertion sites in 1606 independent Ds insertional mutants in advanced backcross generation using K17 as background. The Ac-containing individuals were excluded for getting rid of the potential somatic insertions. We characterized 35,696 germinal Ds insertions tagging 10,323 genes, representing approximately 23.3% of the total genes in the maize genome. The insertion sites were presented in chromosomal hotspots around the ancestral Ds loci, and insertions occurred preferentially in gene body regions. Furthermore, we mapped a loss-of-function AGL2 gene using bulked segregant RNA-sequencing assay and proved that AGL2 is essential for seed development. We additionally established an open-access database named MEILAM for easy access to Ds insertional mutations. Overall, our results have provided an efficient workflow for TE insertion identification and rich sequence-indexed mutant resources for maize functional genomic studies.
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Affiliation(s)
- Mingjie Lyu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Huafeng Liu
- College of Agronomy, Collaborative Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, Henan 450002, China
| | - Joram Kiriga Waititu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Ying Sun
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Huan Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Junjie Fu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yanhui Chen
- College of Agronomy, Collaborative Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, Henan 450002, China
| | - Jun Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Lixia Ku
- College of Agronomy, Collaborative Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, Henan 450002, China.
| | - Xiliu Cheng
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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Raja KV, Sekhar KM, Reddy VD, Reddy AR, Rao KV. Activation of CDC48 and acetyltransferase encoding genes contributes to enhanced abiotic stress tolerance and improved productivity traits in rice. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 168:329-339. [PMID: 34688194 DOI: 10.1016/j.plaphy.2021.10.021] [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: 06/20/2021] [Revised: 10/13/2021] [Accepted: 10/15/2021] [Indexed: 06/13/2023]
Abstract
World-wide crop productivity is highly impacted by various extreme environmental conditions. In the present investigation, activation tagged (AT) line A10-Ds-RFP6 of rice endowed with improved agronomic attributes was tested for its tolerance ability against drought and salinity stress conditions as well as identification of genes associated with these traits. Under both drought and salinity stress conditions, A10-Ds-RFP6 line exhibited increased seed germination rates and improved plant growth characteristics at seedling, vegetative and reproductive stages as compared to wild-type (WT) plants. Moreover, A10-Ds-RFP6 revealed effective antioxidant systems resulting in decreased accumulation of reactive oxygen species and delayed stress symptoms compared to WT plants. Reduced accumulation of malondialdehyde with concomitant increase in proline and soluble sugars in A10-Ds-RFP6 line further endorse its improved stress tolerance levels. Furthermore, A10-Ds-RFP6 disclosed enhanced plant water content, photosynthetic efficiency, stomatal conductance, water use efficiency and maximum quantum yield compared to WT plants. TAIL and qRT-PCR analyses of AT rice line revealed the integration site of Ds element in the genome and increased expression levels of CDC48 and acetyltransferase genes involved in various aspects of plant development and stress tolerance. As such, the promising AT line plausibly serve as a rare genetic resource for fortifying stress tolerance and productivity traits of elite rice cultivars.
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Affiliation(s)
- Kota Vamsee Raja
- Centre for Plant Molecular Biology, Osmania University, Hyderabad, 500 007, India
| | - Kalva Madhana Sekhar
- Centre for Plant Molecular Biology, Osmania University, Hyderabad, 500 007, India
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Zhou X, Shafique K, Sajid M, Ali Q, Khalili E, Javed MA, Haider MS, Zhou G, Zhu G. Era-like GTP protein gene expression in rice. BRAZ J BIOL 2021; 82:e250700. [PMID: 34259718 DOI: 10.1590/1519-6984.250700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 06/19/2021] [Indexed: 11/22/2022] Open
Abstract
The mutations are genetic changes in the genome sequences and have a significant role in biotechnology, genetics, and molecular biology even to find out the genome sequences of a cell DNA along with the viral RNA sequencing. The mutations are the alterations in DNA that may be natural or spontaneous and induced due to biochemical reactions or radiations which damage cell DNA. There is another cause of mutations which is known as transposons or jumping genes which can change their position in the genome during meiosis or DNA replication. The transposable elements can induce by self in the genome due to cellular and molecular mechanisms including hypermutation which caused the localization of transposable elements to move within the genome. The use of induced mutations for studying the mutagenesis in crop plants is very common as well as a promising method for screening crop plants with new and enhanced traits for the improvement of yield and production. The utilization of insertional mutations through transposons or jumping genes usually generates stable mutant alleles which are mostly tagged for the presence or absence of jumping genes or transposable elements. The transposable elements may be used for the identification of mutated genes in crop plants and even for the stable insertion of transposable elements in mutated crop plants. The guanine nucleotide-binding (GTP) proteins have an important role in inducing tolerance in rice plants to combat abiotic stress conditions.
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Affiliation(s)
- X Zhou
- Linyi University, College of Life Science, Linyi, Shandong, China
| | - K Shafique
- Government Sadiq College Women University, Department of Botany, Bahawalpur, Pakistan
| | - M Sajid
- University of Okara, Faculty of Life Sciences, Department of Biotechnology, Okara, Pakistan
| | - Q Ali
- University of Lahore, Institute of Molecular Biology and Biotechnology, Lahore, Pakistan
| | - E Khalili
- Tarbiat Modarres University, Faculty of Science, Department of Plant Science, Tehran, Iran
| | - M A Javed
- University of the Punjab Lahore, Department of Plant Breeding and Genetics, Lahore, Pakistan
| | - M S Haider
- University of the Punjab Lahore, Department of Plant Pathology, Lahore, Pakistan
| | - G Zhou
- Yangzhou University, The Ministry of Education of China, Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou, Jiangsu, China
| | - G Zhu
- Yangzhou University, The Ministry of Education of China, Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou, Jiangsu, China
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Sato Y, Tsuda K, Yamagata Y, Matsusaka H, Kajiya-Kanegae H, Yoshida Y, Agata A, Ta KN, Shimizu-Sato S, Suzuki T, Nosaka-Takahashi M, Kubo T, Kawamoto S, Nonomura KI, Yasui H, Kumamaru T. Collection, preservation and distribution of Oryza genetic resources by the National Bioresource Project RICE (NBRP-RICE). BREEDING SCIENCE 2021; 71:291-298. [PMID: 34776736 PMCID: PMC8573556 DOI: 10.1270/jsbbs.21005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 03/15/2021] [Indexed: 05/26/2023]
Abstract
Biological resources are the basic infrastructure of bioscience research. Rice (Oryza sativa L.) is a good experimental model for research in cereal crops and monocots and includes important genetic materials used in breeding. The availability of genetic materials, including mutants, is important for rice research. In addition, Oryza species are attractive to researchers for both finding useful genes for breeding and for understanding the mechanism of genome evolution that enables wild plants to adapt to their own habitats. NBRP-RICE contributes to rice research by promoting the usage of genetic materials, especially wild Oryza accessions and mutant lines. Our activity includes collection, preservation and distribution of those materials and the provision of basic information on them, such as morphological and physiological traits and genomic information. In this review paper, we introduce the activities of NBRP-RICE and our database, Oryzabase, which facilitates the access to NBRP-RICE resources and their genomic sequences as well as the current situation of wild Oryza genome sequencing efforts by NBRP-RICE and other institutes.
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Affiliation(s)
- Yutaka Sato
- National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
- Department of Genetics, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), 1111 Yata, Mishima, Shizuoka 411-8540, Japan
| | - Katsutoshi Tsuda
- National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
- Department of Genetics, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), 1111 Yata, Mishima, Shizuoka 411-8540, Japan
| | - Yoshiyuki Yamagata
- Faculty of Agriculture, Kyushu University, 744 Motooka, Nishi-ku Fukuoka 819-0395, Japan
| | - Hiroaki Matsusaka
- Faculty of Agriculture, Kyushu University, 744 Motooka, Nishi-ku Fukuoka 819-0395, Japan
| | - Hiromi Kajiya-Kanegae
- Research Center for Agricultural Information Technology, National Agriculture and Food Research Organization, Chiyoda-ku, Tokyo 100-0013, Japan
| | - Yuri Yoshida
- National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
| | - Ayumi Agata
- National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
| | - Kim Nhung Ta
- National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
| | - Sae Shimizu-Sato
- National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
| | - Toshiya Suzuki
- National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
- Department of Genetics, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), 1111 Yata, Mishima, Shizuoka 411-8540, Japan
| | - Misuzu Nosaka-Takahashi
- National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
- Department of Genetics, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), 1111 Yata, Mishima, Shizuoka 411-8540, Japan
| | - Takahiko Kubo
- Faculty of Agriculture, Kyushu University, 744 Motooka, Nishi-ku Fukuoka 819-0395, Japan
| | - Shoko Kawamoto
- National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
- Department of Genetics, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), 1111 Yata, Mishima, Shizuoka 411-8540, Japan
| | - Ken-Ichi Nonomura
- National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
- Department of Genetics, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), 1111 Yata, Mishima, Shizuoka 411-8540, Japan
| | - Hideshi Yasui
- Faculty of Agriculture, Kyushu University, 744 Motooka, Nishi-ku Fukuoka 819-0395, Japan
| | - Toshihiro Kumamaru
- Faculty of Agriculture, Kyushu University, 744 Motooka, Nishi-ku Fukuoka 819-0395, Japan
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Gaillochet C, Develtere W, Jacobs TB. CRISPR screens in plants: approaches, guidelines, and future prospects. THE PLANT CELL 2021; 33:794-813. [PMID: 33823021 PMCID: PMC8226290 DOI: 10.1093/plcell/koab099] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 04/02/2021] [Indexed: 05/20/2023]
Abstract
Clustered regularly interspaced short palindromic repeat (CRISPR)-associated systems have revolutionized genome engineering by facilitating a wide range of targeted DNA perturbations. These systems have resulted in the development of powerful new screens to test gene functions at the genomic scale. While there is tremendous potential to map and interrogate gene regulatory networks at unprecedented speed and scale using CRISPR screens, their implementation in plants remains in its infancy. Here we discuss the general concepts, tools, and workflows for establishing CRISPR screens in plants and analyze the handful of recent reports describing the use of this strategy to generate mutant knockout collections or to diversify DNA sequences. In addition, we provide insight into how to design CRISPR knockout screens in plants given the current challenges and limitations and examine multiple design options. Finally, we discuss the unique multiplexing capabilities of CRISPR screens to investigate redundant gene functions in highly duplicated plant genomes. Combinatorial mutant screens have the potential to routinely generate higher-order mutant collections and facilitate the characterization of gene networks. By integrating this approach with the numerous genomic profiles that have been generated over the past two decades, the implementation of CRISPR screens offers new opportunities to analyze plant genomes at deeper resolution and will lead to great advances in functional and synthetic biology.
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Affiliation(s)
- Christophe Gaillochet
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
- VIB Center for Plant Systems Biology, Ghent 9052, Belgium
| | - Ward Develtere
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
- VIB Center for Plant Systems Biology, Ghent 9052, Belgium
| | - Thomas B Jacobs
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
- VIB Center for Plant Systems Biology, Ghent 9052, Belgium
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Lin QJ, Kumar V, Chu J, Li ZM, Wu XX, Dong H, Sun Q, Xuan YH. CBL-interacting protein kinase 31 regulates rice resistance to blast disease by modulating cellular potassium levels. Biochem Biophys Res Commun 2021; 563:23-30. [PMID: 34058471 DOI: 10.1016/j.bbrc.2021.05.065] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 05/18/2021] [Indexed: 10/21/2022]
Abstract
Rice blast disease caused by infection with Magnaporthe oryzae, a hemibiotrophic fungal pathogen, significantly reduces the yield production. However, the rice defense mechanism against blast disease remains elusive. To identify the genes involved in the regulation of rice defense to blast disease, dissociation (Ds) transposon tagging mutant lines were analyzed in terms of their response to M. oryzae isolate Guy11. Among them, CBL-interactingprotein kinase31 (CIPK31) mutants were more susceptible than wild-type plants to blast. The CIPK31 transcript was found to be insensitive to Guy11 infection, and the CIPK31-GFP was localized to the cytosol and nucleus. Overexpression of CIPK31 promoted rice defense to blast. Further analysis indicated that CIPK31 interacts with Calcineurin B-like 2 (CBL2) and CBL6 at the plasma membrane, and cbl2 mutants are more susceptible to blast compared with wild-type plants, suggesting that calcium signaling might partially through the CBL2-CIPK31 signaling regulate rice defense. Yeast two-hybrid results showed that AKT1-like (AKT1L), a potential potassium (K+) channel protein, interacted with CIPK31, and the K+ level was significantly lower in the cipk31 mutants than in the wild-type control. In addition, exogenous potassium application increased rice resistance to blast, suggesting that CIPK31 might interact with AKT1L to increase K+ uptake, thereby promoting resistance to blast. Taken together, the results presented here demonstrate that CBL2-CIPK31-AKT1L is a new signaling pathway that regulates rice defense to blast disease.
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Affiliation(s)
- Qiu Jun Lin
- College of Plant Protection, Shenyang Agricultural University, Shenyang, 110866, China
| | - Vikranth Kumar
- Division of Applied Life Science (BK21 Plus Program), Plant Molecular Biology & Biotechnology Research Center (PMBBRC), Gyeongsang National University, Jinju, 52828, Republic of Korea
| | - Jin Chu
- Institute of Plant Protection, Liaoning Academy of Agricultural Sciences, Shenyang, 110161, China
| | - Zhi Min Li
- College of Plant Protection, Shenyang Agricultural University, Shenyang, 110866, China
| | - Xian Xin Wu
- College of Plant Protection, Shenyang Agricultural University, Shenyang, 110866, China
| | - Hai Dong
- Institute of Plant Protection, Liaoning Academy of Agricultural Sciences, Shenyang, 110161, China
| | - Qian Sun
- College of Plant Protection, Shenyang Agricultural University, Shenyang, 110866, China.
| | - Yuan Hu Xuan
- College of Plant Protection, Shenyang Agricultural University, Shenyang, 110866, China.
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Bae KD, Um TY, Yang WT, Park TH, Hong SY, Kim KM, Chung YS, Yun DJ, Kim DH. Characterization of dwarf and narrow leaf ( dnl-4) mutant in rice. PLANT SIGNALING & BEHAVIOR 2021; 16:1849490. [PMID: 33300429 PMCID: PMC7849693 DOI: 10.1080/15592324.2020.1849490] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Height and leaf morphology are important agronomic traits of the major crop plant rice (Oryza sativa). In previous studies, the dwarf and narrow leaf genes (dnl1, dnl2 and dnl3) have identified in rice. Using the Ac/Ds knockout system, we found a new dwarf and narrow leaf (dnl) mutant and identified mutated gene. The dnl-4 mutant showed reduced plant height and leaf blade width compared to the wild type, and increased leaf inclination. The morphological defects of the mutant were caused by the suppressed expression of the DNL-4 gene, which encodes a pfkB carbohydrate kinase protein. These results suggest that DNL-4 expression is involved in modulating plant height and leaf growth. Furthermore, DNL-4 expression also affects productivity in rice: the dnl-4 mutant exhibited reduced panicle length and grain width compared with the wild type. To understand DNL-4 function in rice, we analyzed the expression levels of leaf growth-related genes, such as NAL1, NAL7, and CSLD4, in the dnl-4 mutant. Expression of NAL1 and NAL7 was downregulated in the dnl-4 mutant compared to the wild type. The observation that DNL-4 expression corresponded with that of NAL1 and NAL7 is consistent with the narrow leaf phenotype of the dnl-4 mutant. These results suggest that DNL-4 regulates plant height and leaf structure in rice.
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Affiliation(s)
- Ki-Deuk Bae
- College of Life Science and Natural Resources, Dong-A University, Busan, Korea
| | - Tae-Young Um
- Department of Agriculture and Life Industry, Kangwon National University, Chuncheon, South Korea
| | - Won-Tae Yang
- College of Life Science and Natural Resources, Dong-A University, Busan, Korea
| | - Tae-Hyeon Park
- Graduate School of International Agricultural Technology and Crop Biotechnology Institute/GreenBio Science and Technology, Seoul National University, Pyeongchang, Korea
| | - So-Yeon Hong
- College of Life Science and Natural Resources, Dong-A University, Busan, Korea
| | - Kyung-Min Kim
- College of Agriculture and Life Science, Kyungpook National University, Daegu, Korea
| | - Young-Soo Chung
- College of Life Science and Natural Resources, Dong-A University, Busan, Korea
| | - Dae-Jin Yun
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, Korea
| | - Doh-Hoon Kim
- College of Life Science and Natural Resources, Dong-A University, Busan, Korea
- CONTACT Doh-Hoon KimCollege of Life Science and Natural Resources, Dong-A University, Busan49315, Korea
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Li X, Pan L, Bi D, Tian X, Li L, Xu Z, Wang L, Zou X, Gao X, Yang H, Qu H, Zhao X, Yuan Z, He H, Qu S. Generation of Marker-Free Transgenic Rice Resistant to Rice Blast Disease Using Ac/Ds Transposon-Mediated Transgene Reintegration System. FRONTIERS IN PLANT SCIENCE 2021; 12:644437. [PMID: 33959140 PMCID: PMC8095379 DOI: 10.3389/fpls.2021.644437] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 02/23/2021] [Indexed: 05/14/2023]
Abstract
Rice blast is one of the most serious diseases of rice and a major threat to rice production. Breeding disease-resistant rice is one of the most economical, safe, and effective measures for the control of rice blast. As a complement to traditional crop breeding, the transgenic method can avoid the time-consuming process of crosses and multi-generation selection. In this study, maize (Zea mays) Activator (Ac)/Dissociation (Ds) transposon vectors carrying green fluorescent protein (GFP) and red fluorescent protein (mCherry) genetic markers were used for generating marker-free transgenic rice. Double fluorescent protein-aided counterselection against the presence of T-DNA was performed together with polymerase chain reaction (PCR)-based positive selection for the gene of interest (GOI) to screen marker-free progeny. We cloned an RNAi expression cassette of the rice Pi21 gene that negatively regulates resistance to rice blast as a GOI into the Ds element in the Ac/Ds vector and obtained marker-free T1 rice plants from 13 independent transgenic lines. Marker-free and Ds/GOI-homozygous rice lines were verified by PCR and Southern hybridization analysis to be completely free of transgenic markers and T-DNA sequences. qRT-PCR analysis and rice blast disease inoculation confirmed that the marker-free transgenic rice lines exhibited decreased Pi21 expression levels and increased resistance to rice blast. TAIL-PCR results showed that the Ds (Pi21-RNAi) transgenes in two rice lines were reintegrated in intergenic regions in the rice genome. The Ac/Ds vector with dual fluorescent protein markers offers more reliable screening of marker-free transgenic progeny and can be utilized in the transgenic breeding of rice disease resistance and other agronomic traits.
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Affiliation(s)
- Xin Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Longyu Pan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, China
| | - Dongling Bi
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Xudan Tian
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, China
| | - Lihua Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- College of Plant Protection, Hunan Agricultural University, Changsha, China
| | - Zhaomeng Xu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, China
| | - Lanlan Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Xiaowei Zou
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Xiaoqing Gao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Haihe Yang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Haiyan Qu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Xiangqian Zhao
- Institute of Crop Science and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Zhengjie Yuan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Haiyan He
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Shaohong Qu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- *Correspondence: Shaohong Qu, ; orcid.org/0000-0003-2072-122X
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Rolling Circle Amplification (RCA)-Mediated Genome-Wide ihpRNAi Mutant Library Construction in Brassica napus. Int J Mol Sci 2020; 21:ijms21197243. [PMID: 33008068 PMCID: PMC7582411 DOI: 10.3390/ijms21197243] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 09/25/2020] [Accepted: 09/28/2020] [Indexed: 12/15/2022] Open
Abstract
With the successful completion of genomic sequencing for Brassica napus, identification of novel genes, determination of functions performed by genes, and exploring the molecular mechanisms underlying important agronomic traits were challenged. Mutagenesis-based functional genomics techniques including chemical, physical, and insertional mutagenesis have been used successfully in the functional characterization of genes. However, these techniques had their disadvantages and inherent limitations for allopolyploid Brassica napus, which contained a large number of homologous and redundant genes. Long intron-spliced hairpin RNA (ihpRNA) constructs which contained inverted repeats of the target gene separated by an intron, had been shown to be very effective in triggering RNAi in plants. In the present study, the genome-wide long ihpRNA library of B. napus was constructed with the rolling circle amplification (RCA)-mediated technology. Using the phytoene desaturase (PDS) gene as a target control, it was shown that the RCA-mediated long ihpRNA construct was significantly effective in triggering gene silence in B. napus. Subsequently, the resultant long ihpRNA library was transformed into B. napus to produce corresponding RNAi mutants. Among the obtained transgenic ihpRNA population of B. napus, five ihpRNA lines with observable mutant phenotypes were acquired including alterations in the floral model and the stamen development. The target genes could be quickly identified using specific primers. These results showed that the RCA-mediated ihpRNA construction method was effective for the genome-wide long ihpRNA library of B. napus, therefore providing a platform for study of functional genomics in allopolyploid B. napus.
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Viana VE, Pegoraro C, Busanello C, Costa de Oliveira A. Mutagenesis in Rice: The Basis for Breeding a New Super Plant. FRONTIERS IN PLANT SCIENCE 2019; 10:1326. [PMID: 31781133 PMCID: PMC6857675 DOI: 10.3389/fpls.2019.01326] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 09/24/2019] [Indexed: 05/28/2023]
Abstract
The high selection pressure applied in rice breeding since its domestication thousands of years ago has caused a narrowing in its genetic variability. Obtaining new rice cultivars therefore becomes a major challenge for breeders and developing strategies to increase the genetic variability has demanded the attention of several research groups. Understanding mutations and their applications have paved the way for advances in the elucidation of a genetic, physiological, and biochemical basis of rice traits. Creating variability through mutations has therefore grown to be among the most important tools to improve rice. The small genome size of rice has enabled a faster release of higher quality sequence drafts as compared to other crops. The move from structural to functional genomics is possible due to an array of mutant databases, highlighting mutagenesis as an important player in this progress. Furthermore, due to the synteny among the Poaceae, other grasses can also benefit from these findings. Successful gene modifications have been obtained by random and targeted mutations. Furthermore, following mutation induction pathways, techniques have been applied to identify mutations and the molecular control of DNA damage repair mechanisms in the rice genome. This review highlights findings in generating rice genome resources showing strategies applied for variability increasing, detection and genetic mechanisms of DNA damage repair.
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Affiliation(s)
| | | | | | - Antonio Costa de Oliveira
- Centro de Genômica e Fitomelhoramento, Faculdade de Agronomia Eliseu Maciel, Departamento de Fitotecnia, Universidade Federal de Pelotas, Campus Capão do Leão, Rio Grande do Sul, Brazil
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18
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Chaudhary J, Deshmukh R, Sonah H. Mutagenesis Approaches and Their Role in Crop Improvement. PLANTS (BASEL, SWITZERLAND) 2019; 8:E467. [PMID: 31683624 PMCID: PMC6918138 DOI: 10.3390/plants8110467] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 10/29/2019] [Indexed: 12/20/2022]
Abstract
Induced mutagenesis is one of the most efficient tools that has been utilized extensively to create genetic variation as well as for identification of key regulatory genes for economically important traits toward the crop improvement. Mutations can be induced by several techniques such as physical, chemical, and insertional mutagen treatments; however, these methods are not preferred because of cost and tedious process. Nonetheless, with the advancements in next-generation sequencing (NGS) techniques, millions of mutations can be detected in a very short period of time and, therefore, considered as convenient and cost efficient. Furthermore, induced mutagenesis coupled with whole-genome sequencing has provided a robust platform for forward and reverse genetic applications. Moreover, the availability of whole-genome sequence information for large number of crops has enabled target-specific genome editing techniques as a preferable method to engineer desired mutations. The available genome editing approaches such as ZFNs (Zinc Finger Nucleases), transcription activator like effector nucleases (TALENS), and clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated9 (Cas9) endonuclease have been utilized to perform site-specific mutations in several plant species. In particular, the CRISPR/Cas9 has transformed the genome editing because of its simplicity and robustness, therefore, have been utilized to enhance biotic and abiotic stress resistance. The Special Issue of Plants highlights the efforts by the scientific community utilizing mutagenesis techniques for the identification of novel genes toward crop improvement.
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Affiliation(s)
- Juhi Chaudhary
- Department of Biology, Oberlin College, Oberlin, OH 44074, USA.
| | - Rupesh Deshmukh
- National Agri-Food Biotechnology Institute (NABI), Sector 80, SAS Nagar, Mohali, Punjab 140306, India.
| | - Humira Sonah
- National Agri-Food Biotechnology Institute (NABI), Sector 80, SAS Nagar, Mohali, Punjab 140306, India.
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Insertional Mutagenesis Approaches and Their Use in Rice for Functional Genomics. PLANTS 2019; 8:plants8090310. [PMID: 31470516 PMCID: PMC6783850 DOI: 10.3390/plants8090310] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 08/07/2019] [Accepted: 08/07/2019] [Indexed: 01/01/2023]
Abstract
Insertional mutagenesis is an indispensable tool for engendering a mutant population using exogenous DNA as the mutagen. The advancement in the next-generation sequencing platform has allowed for faster screening and analysis of generated mutated populations. Rice is a major staple crop for more than half of the world's population; however, the functions of most of the genes in its genome are yet to be analyzed. Various mutant populations represent extremely valuable resources in order to achieve this goal. Here, we have reviewed different insertional mutagenesis approaches that have been used in rice, and have discussed their principles, strengths, and limitations. Comparisons between transfer DNA (T-DNA), transposons, and entrapment tagging approaches have highlighted their utilization in functional genomics studies in rice. We have also summarised different forward and reverse genetics approaches used for screening of insertional mutant populations. Furthermore, we have compiled information from several efforts made using insertional mutagenesis approaches in rice. The information presented here would serve as a database for rice insertional mutagenesis populations. We have also included various examples which illustrate how these populations have been useful for rice functional genomics studies. The information provided here will be very helpful for future functional genomics studies in rice aimed at its genetic improvement.
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Vishal B, Krishnamurthy P, Ramamoorthy R, Kumar PP. OsTPS8 controls yield-related traits and confers salt stress tolerance in rice by enhancing suberin deposition. THE NEW PHYTOLOGIST 2019; 221:1369-1386. [PMID: 30289560 DOI: 10.1111/nph.15464] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 08/26/2018] [Indexed: 05/11/2023]
Abstract
Class I TREHALOSE-PHOSPHATE-SYNTHASE (TPS) genes affect salinity tolerance and plant development. However, the function of class IITPS genes and their underlying mechanisms of action are unknown. We report the identification and functional analysis of a rice class IITPS gene (OsTPS8). The ostps8 mutant was characterised by GC-MS analysis, an abscisic acid (ABA) sensitivity test and by generating transgenic lines. To identify the underlying mechanism, gene expression analyses, genetic complementation and examination of suberin deposition in the roots were conducted. The ostps8 mutant showed salt sensitivity, ABA sensitivity and altered agronomic traits compared to the wild-type (WT), which could be rescued upon complementation. The dsRNAi line phenocopied the mutant, while the overexpression lines exhibited enhanced salt tolerance. The ostps8 mutant showed significantly reduced soluble sugars, Casparian bands and suberin deposition in the roots compared to the WT and overexpression lines. The mutant also showed downregulation of SAPKs (rice SnRK2s) and ABA-responsive genes. Furthermore, ostps8pUBI::SAPK9 rescued the salt-sensitive phenotype of ostps8. Our results suggest that OsTPS8 may regulate suberin deposition in rice through ABA signalling. Additionally, SAPK9-mediated regulation of altered ABA-responsive genes helps to confer salinity tolerance. Overexpression of OsTPS8 was adequate to confer enhanced salinity tolerance without any yield penalty, suggesting its usefulness in rice genetic improvement.
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Affiliation(s)
- Bhushan Vishal
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore City, 117543, Singapore
| | - Pannaga Krishnamurthy
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore City, 117543, Singapore
| | - Rengasamy Ramamoorthy
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore City, 117543, Singapore
| | - Prakash P Kumar
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore City, 117543, Singapore
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21
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Moin M, Bakshi A, Madhav MS, Kirti PB. Cas9/sgRNA-based genome editing and other reverse genetic approaches for functional genomic studies in rice. Brief Funct Genomics 2018; 17:339-351. [PMID: 29579147 DOI: 10.1093/bfgp/ely010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
One of the important and direct ways of investigating the function of a gene is to characterize the phenotypic consequences associated with loss or gain-of-function of the corresponding gene. These mutagenesis strategies have been successfully deployed in Arabidopsis, and subsequently extended to crop species including rice. Researchers have made vast advancements in the area of rice genomics and functional genomics, as it is a diploid plant with a relatively smaller genome size unlike other cereals. The advent of rice genome research and the annotation of high-quality genome sequencing along with the developments in databases and computer searches have enabled the functional characterization of unknown genes in rice. Further, with the improvements in the efficiency of regeneration and transformation protocols, it has now become feasible to produce sizable mutant populations in indica rice varieties also. In this review, various mutagenesis methods, the current status of the mutant resources, limitations and strengths of insertional mutagenesis approaches and also results obtained with suitable screens for stress tolerance in rice are discussed. In addition, targeted genome editing using clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) or Cas9/single-guide RNA system and its potential applications in generating transgene-free rice plants through genome engineering as an efficient alternative to classical transgenic technology are also discussed.
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Affiliation(s)
- Mazahar Moin
- Department of Biotechnology, ICAR-Indian Institute of Rice Research (IIRR), India
- Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Achala Bakshi
- Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - M S Madhav
- Department of Biotechnology, ICAR-Indian Institute of Rice Research (IIRR), India
| | - P B Kirti
- Department of Plant Sciences, University of Hyderabad, Hyderabad, India
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Moin M, Bakshi A, Saha A, Dutta M, Kirti PB. Gain-of-function mutagenesis approaches in rice for functional genomics and improvement of crop productivity. Brief Funct Genomics 2018; 16:238-247. [PMID: 28137760 DOI: 10.1093/bfgp/elw041] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
The epitome of any genome research is to identify all the existing genes in a genome and investigate their roles. Various techniques have been applied to unveil the functions either by silencing or over-expressing the genes by targeted expression or random mutagenesis. Rice is the most appropriate model crop for generating a mutant resource for functional genomic studies because of the availability of high-quality genome sequence and relatively smaller genome size. Rice has syntenic relationships with members of other cereals. Hence, characterization of functionally unknown genes in rice will possibly provide key genetic insights and can lead to comparative genomics involving other cereals. The current review attempts to discuss the available gain-of-function mutagenesis techniques for functional genomics, emphasizing the contemporary approach, activation tagging and alterations to this method for the enhancement of yield and productivity of rice.
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23
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Ramamoorthy R, Vishal B, Ramachandran S, Kumar PP. The OsPS1-F gene regulates growth and development in rice by modulating photosynthetic electron transport rate. PLANT CELL REPORTS 2018; 37:377-385. [PMID: 29149369 DOI: 10.1007/s00299-017-2235-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 11/08/2017] [Indexed: 05/24/2023]
Abstract
Ds insertion in rice OsPS1-F gene results in semi-dwarf plants with reduced tiller number and grain yield, while genetic complementation with OsPS1-F rescued the mutant phenotype. Photosynthetic electron transport is regulated in the chloroplast thylakoid membrane by multi-protein complexes. Studies about photosynthetic machinery and its subunits in crop plants are necessary, because they could be crucial for yield enhancement in the long term. Here, we report the characterization of OsPS1-F (encoding Oryza sativa PHOTOSYSTEM 1-F subunit) using a single copy Ds insertion rice mutant line. The homozygous mutant (osps1-f) showed striking difference in growth and development compared to the wild type (WT), including, reduction in plant height, tiller number, grain yield as well as pale yellow leaf coloration. Chlorophyll concentration and electron transport rate were significantly reduced in the mutant compared to the WT. OsPS1-F gene was highly expressed in rice leaves compared to other tissues at different developmental stages tested. Upon complementation of the mutant with proUBI::OsPS1-F, the observed mutant phenotypes were rescued. Our results illustrate that OsPS1-F plays an important role in regulating proper growth and development of rice plants.
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Affiliation(s)
- Rengasamy Ramamoorthy
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, 117543, Republic of Singapore
| | - Bhushan Vishal
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, 117543, Republic of Singapore
| | - Srinivasan Ramachandran
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Republic of Singapore
| | - Prakash P Kumar
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, 117543, Republic of Singapore.
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Ling J, Li R, Nwafor CC, Cheng J, Li M, Xu Q, Wu J, Gan L, Yang Q, Liu C, Chen M, Zhou Y, Cahoon EB, Zhang C. Development of iFOX-hunting as a functional genomic tool and demonstration of its use to identify early senescence-related genes in the polyploid Brassica napus. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:591-602. [PMID: 28718508 PMCID: PMC5787830 DOI: 10.1111/pbi.12799] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 06/29/2017] [Accepted: 07/12/2017] [Indexed: 05/20/2023]
Abstract
Functional genomic studies of many polyploid crops, including rapeseed (Brassica napus), are constrained by limited tool sets. Here we report development of a gain-of-function platform, termed 'iFOX (inducible Full-length cDNA OvereXpressor gene)-Hunting', for inducible expression of B. napus seed cDNAs in Arabidopsis. A Gateway-compatible plant gene expression vector containing a methoxyfenozide-inducible constitutive promoter for transgene expression was developed. This vector was used for cloning of random cDNAs from developing B. napus seeds and subsequent Agrobacterium-mediated transformation of Arabidopsis. The inducible promoter of this vector enabled identification of genes upon induction that are otherwise lethal when constitutively overexpressed and to control developmental timing of transgene expression. Evaluation of a subset of the resulting ~6000 Arabidopsis transformants revealed a high percentage of lines with full-length B. napus transgene insertions. Upon induction, numerous iFOX lines with visible phenotypes were identified, including one that displayed early leaf senescence. Phenotypic analysis of this line (rsl-1327) after methoxyfenozide induction indicated high degree of leaf chlorosis. The integrated B. napuscDNA was identified as a homolog of an Arabidopsis acyl-CoA binding protein (ACBP) gene designated BnACBP1-like. The early senescence phenotype conferred by BnACBP1-like was confirmed by constitutive expression of this gene in Arabidopsis and B. napus. Use of the inducible promoter in the iFOX line coupled with RNA-Seq analyses allowed mechanistic clues and a working model for the phenotype associated with BnACBP1-like expression. Our results demonstrate the utility of iFOX-Hunting as a tool for gene discovery and functional characterization of Brassica napus genome.
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Affiliation(s)
- Juan Ling
- National Research Centre of Rapeseed Engineering and TechnologyCollege of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Renjie Li
- National Research Centre of Rapeseed Engineering and TechnologyCollege of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Chinedu Charles Nwafor
- National Research Centre of Rapeseed Engineering and TechnologyCollege of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
- Department of Crop ScienceBenson Idahosa UniversityBenin CityNigeria
| | - Junluo Cheng
- National Research Centre of Rapeseed Engineering and TechnologyCollege of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Maoteng Li
- Department of BiotechnologyCollege of Life Science and TechnologyHuazhong University of Science and TechnologyWuhanChina
| | - Qing Xu
- National Research Centre of Rapeseed Engineering and TechnologyCollege of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Jian Wu
- Jiangsu Provincial Key Laboratory of Crop Genetics and PhysiologyYangzhou UniversityYangzhouChina
| | - Lu Gan
- National Research Centre of Rapeseed Engineering and TechnologyCollege of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Qingyong Yang
- National Research Centre of Rapeseed Engineering and TechnologyCollege of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Chao Liu
- National Research Centre of Rapeseed Engineering and TechnologyCollege of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Ming Chen
- Center for Plant Science Innovation and Department of BiochemistryUniversity of Nebraska‐LincolnLincolnNEUSA
| | - Yongming Zhou
- National Research Centre of Rapeseed Engineering and TechnologyCollege of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Edgar B. Cahoon
- National Research Centre of Rapeseed Engineering and TechnologyCollege of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
- Center for Plant Science Innovation and Department of BiochemistryUniversity of Nebraska‐LincolnLincolnNEUSA
| | - Chunyu Zhang
- National Research Centre of Rapeseed Engineering and TechnologyCollege of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
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25
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Sevanthi AMV, Kandwal P, Kale PB, Prakash C, Ramkumar MK, Yadav N, Mahato AK, Sureshkumar V, Behera M, Deshmukh RK, Jeyaparakash P, Kar MK, Manonmani S, Muthurajan R, Gopala KS, Neelamraju S, Sheshshayee MS, Swain P, Singh AK, Singh NK, Mohapatra T, Sharma RP. Whole Genome Characterization of a Few EMS-Induced Mutants of Upland Rice Variety Nagina 22 Reveals a Staggeringly High Frequency of SNPs Which Show High Phenotypic Plasticity Towards the Wild-Type. FRONTIERS IN PLANT SCIENCE 2018; 9:1179. [PMID: 0 PMCID: PMC6132179 DOI: 10.3389/fpls.2018.01179] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 07/24/2018] [Indexed: 05/07/2023]
Abstract
The Indian initiative, in creating mutant resources for the functional genomics in rice, has been instrumental in the development of 87,000 ethylmethanesulfonate (EMS)-induced mutants, of which 7,000 are in advanced generations. The mutants have been created in the background of Nagina 22, a popular drought- and heat-tolerant upland cultivar. As it is a pregreen revolution cultivar, as many as 573 dwarf mutants identified from this resource could be useful as an alternate source of dwarfing. A total of 541 mutants, including the macromutants and the trait-specific ones, obtained after appropriate screening, are being maintained in the mutant garden. Here, we report on the detailed characterizations of the 541 mutants based on the distinctness, uniformity, and stability (DUS) descriptors at two different locations. About 90% of the mutants were found to be similar to the wild type (WT) with high similarity index (>0.6) at both the locations. All 541 mutants were characterized for chlorophyll and epicuticular wax contents, while a subset of 84 mutants were characterized for their ionomes, namely, phosphorous, silicon, and chloride contents. Genotyping of these mutants with 54 genomewide simple sequence repeat (SSR) markers revealed 93% of the mutants to be either completely identical to WT or nearly identical with just one polymorphic locus. Whole genome resequencing (WGS) of four mutants, which have minimal differences in the SSR fingerprint pattern and DUS characters from the WT, revealed a staggeringly high number of single nucleotide polymorphisms (SNPs) on an average (16,453 per mutant) in the genic sequences. Of these, nearly 50% of the SNPs led to non-synonymous codons, while 30% resulted in synonymous codons. The number of insertions and deletions (InDels) varied from 898 to 2,595, with more than 80% of them being 1-2 bp long. Such a high number of SNPs could pose a serious challenge in identifying gene(s) governing the mutant phenotype by next generation sequencing-based mapping approaches such as Mutmap. From the WGS data of the WT and the mutants, we developed a genic resource of the WT with a novel analysis pipeline. The entire information about this resource along with the panicle architecture of the 493 mutants is made available in a mutant database EMSgardeN22 (http://14.139.229.201/EMSgardeN22).
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Affiliation(s)
- Amitha M. V. Sevanthi
- ICAR-National Research Centre on Plant Biotechnology, New Delhi, India
- *Correspondence: Amitha M. V. Sevanthi,
| | - Prashant Kandwal
- ICAR-National Research Centre on Plant Biotechnology, New Delhi, India
| | - Prashant B. Kale
- ICAR-National Research Centre on Plant Biotechnology, New Delhi, India
| | - Chandra Prakash
- ICAR-National Research Centre on Plant Biotechnology, New Delhi, India
| | - M. K. Ramkumar
- ICAR-National Research Centre on Plant Biotechnology, New Delhi, India
| | - Neera Yadav
- ICAR-National Research Centre on Plant Biotechnology, New Delhi, India
| | - Ajay K. Mahato
- ICAR-National Research Centre on Plant Biotechnology, New Delhi, India
| | - V. Sureshkumar
- ICAR-National Research Centre on Plant Biotechnology, New Delhi, India
| | | | | | | | - Meera K. Kar
- ICAR-National Rice Research Institute, Cuttack, India
| | - S. Manonmani
- Tamil Nadu Agricultural University, Coimbatore, India
| | | | - K. S. Gopala
- ICAR-Indian Agricultural Research Institute, New Delhi, India
| | | | | | - P. Swain
- ICAR-National Rice Research Institute, Cuttack, India
| | - Ashok K. Singh
- ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - N. K. Singh
- ICAR-National Research Centre on Plant Biotechnology, New Delhi, India
| | | | - R. P. Sharma
- ICAR-National Research Centre on Plant Biotechnology, New Delhi, India
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26
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Manimaran P, Venkata Reddy S, Moin M, Raghurami Reddy M, Yugandhar P, Mohanraj SS, Balachandran SM, Kirti PB. Activation-tagging in indica rice identifies a novel transcription factor subunit, NF-YC13 associated with salt tolerance. Sci Rep 2017; 7:9341. [PMID: 28839256 PMCID: PMC5570948 DOI: 10.1038/s41598-017-10022-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 08/02/2017] [Indexed: 12/19/2022] Open
Abstract
Nuclear factor Y (NF-Y) is a heterotrimeric transcription factor with three distinct NF-YA, NF-YB and NF-YC subunits. It plays important roles in plant growth, development and stress responses. We have reported earlier on development of gain-of-function mutants in an indica rice cultivar, BPT-5204. Now, we screened 927 seeds from 70 Ac/Ds plants for salinity tolerance and identified one activation-tagged salt tolerant DS plant (DS-16, T3 generation) that showed enhanced expression of a novel 'histone-like transcription factor' belonging to rice NF-Y subfamily C and was named as OsNF-YC13. Localization studies using GFP-fusion showed that the protein is localized to nucleus and cytoplasm. Real time expression analysis confirmed upregulation of transcript levels of OsNF-YC13 during salt treatment in a tissue specific manner. Biochemical and physiological characterization of the DS-16 revealed enhanced K+/Na+ ratio, proline content, chlorophyll content, enzymes with antioxidant activity etc. DS-16 also showed transcriptional up-regulation of genes that are involved in salinity tolerance. In-silico analysis of OsNF-YC13 promoter region evidenced the presence of various key stress-responsive cis-regulatory elements. OsNF-YC13 subunit alone does not appear to have the capacity for direct transcription activation, but appears to interact with the B- subunits in the process of transactivation.
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Affiliation(s)
- P Manimaran
- Department of Plant Sciences, University of Hyderabad, Hyderabad, 5000046, India.
| | - S Venkata Reddy
- Department of Plant Sciences, University of Hyderabad, Hyderabad, 5000046, India
| | - Mazahar Moin
- Department of Plant Sciences, University of Hyderabad, Hyderabad, 5000046, India
| | - M Raghurami Reddy
- Indian Institute of Rice Research, Rajendranagar, Hyderabad, 500030, India
| | - Poli Yugandhar
- Indian Institute of Rice Research, Rajendranagar, Hyderabad, 500030, India
| | - S S Mohanraj
- Department of Plant Sciences, University of Hyderabad, Hyderabad, 5000046, India
| | - S M Balachandran
- Indian Institute of Rice Research, Rajendranagar, Hyderabad, 500030, India
| | - P B Kirti
- Department of Plant Sciences, University of Hyderabad, Hyderabad, 5000046, India.
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27
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Zhou MB, Hu H, Miskey C, Lazarow K, Ivics Z, Kunze R, Yang G, Izsvák Z, Tang DQ. Transposition of the bamboo Mariner-like element Ppmar1 in yeast. Mol Phylogenet Evol 2017; 109:367-374. [PMID: 28189615 DOI: 10.1016/j.ympev.2017.02.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Revised: 01/26/2017] [Accepted: 02/03/2017] [Indexed: 12/30/2022]
Abstract
The moso bamboo genome contains the two structurally intact and thus potentially functional mariner-like elements Ppmar1 and Ppmar2. Both elements contain perfect terminal inverted repeats (TIRs) and a full-length intact transposase gene. Here we investigated whether Ppmar1 is functional in yeast (Saccharomyces cerevisiae). We have designed a two-component system consisting of a transposase expression cassette and a non-autonomous transposon on two separate plasmids. We demonstrate that the Ppmar1 transposase Pptpase1 catalyses excision of the non-autonomous Ppmar1NA element from the plasmid and reintegration at TA dinucleotide sequences in the yeast chromosomes. In addition, we generated 14 hyperactive Ppmar1 transposase variants by systematic single amino acid substitutions. The most active transposase variant, S171A, induces 10-fold more frequent Ppmar1NA excisions in yeast than the wild type transposase. The Ppmar1 transposon is a promising tool for insertion mutagenesis in moso bamboo and may be used in other plants as an alternative to the established transposon tagging systems.
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Affiliation(s)
- Ming-Bing Zhou
- The Nurturing Station for the State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, LinAn, China
| | - Hui Hu
- The Nurturing Station for the State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, LinAn, China
| | - Csaba Miskey
- Paul Ehrlich Institute, Paul Ehrlich Str. 51-59, 63225 Langen, Germany
| | - Katina Lazarow
- Institute of Biology, Dahlem Centre of Plant Sciences, Freie Universität Berlin, 14195 Berlin, Germany
| | - Zoltán Ivics
- Paul Ehrlich Institute, Paul Ehrlich Str. 51-59, 63225 Langen, Germany
| | - Reinhard Kunze
- Institute of Biology, Dahlem Centre of Plant Sciences, Freie Universität Berlin, 14195 Berlin, Germany
| | - Guojun Yang
- Department of Biology, University of Toronto, Mississauga, ON, Canada
| | - Zsuzsanna Izsvák
- Max Delbrück Center for Molecular Medicine in the Helmholtz Society, Berlin, Germany.
| | - Ding-Qin Tang
- The Nurturing Station for the State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, LinAn, China.
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28
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Moin M, Bakshi A, Saha A, Udaya Kumar M, Reddy AR, Rao KV, Siddiq EA, Kirti PB. Activation tagging in indica rice identifies ribosomal proteins as potential targets for manipulation of water-use efficiency and abiotic stress tolerance in plants. PLANT, CELL & ENVIRONMENT 2016; 39:2440-2459. [PMID: 27411514 DOI: 10.1111/pce.12796] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Revised: 07/01/2016] [Accepted: 07/03/2016] [Indexed: 05/23/2023]
Abstract
We have generated 3900 enhancer-based activation-tagged plants, in addition to 1030 stable Dissociator-enhancer plants in a widely cultivated indica rice variety, BPT-5204. Of them, 3000 were screened for water-use efficiency (WUE) by analysing photosynthetic quantum efficiency and yield-related attributes under water-limiting conditions that identified 200 activation-tagged mutants, which were analysed for flanking sequences at the site of enhancer integration in the genome. We have further selected five plants with low Δ13 C, high quantum efficiency and increased plant yield compared with wild type for a detailed investigation. Expression studies of 18 genes in these mutants revealed that in four plants one of the three to four tagged genes became activated, while two genes were concurrently up-regulated in the fifth plant. Two genes coding for proteins involved in 60S ribosomal assembly, RPL6 and RPL23A, were among those that became activated by enhancers. Quantitative expression analysis of these two genes also corroborated the results on activating-tagging. The high up-regulation of RPL6 and RPL23A in various stress treatments and the presence of significant cis-regulatory elements in their promoter regions along with the high up-regulation of several of RPL genes in various stress treatments indicate that they are potential targets for manipulating WUE/abiotic stress tolerance.
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Affiliation(s)
- Mazahar Moin
- Department of Plant Sciences, University of Hyderabad, Hyderabad, 500046, India
| | - Achala Bakshi
- Department of Plant Sciences, University of Hyderabad, Hyderabad, 500046, India
| | - Anusree Saha
- Department of Plant Sciences, University of Hyderabad, Hyderabad, 500046, India
| | - M Udaya Kumar
- Department of Crop Physiology, University of Agricultural Sciences - GKVK, Hebbal, Bangalore, India
| | - Attipalli R Reddy
- Department of Plant Sciences, University of Hyderabad, Hyderabad, 500046, India
| | - K V Rao
- Center for Plant Molecular Biology, Osmania University, Hyderabad, 500007, India
| | - E A Siddiq
- Institute of Agricultural Biotechnology, PJTS Agricultural University, Rajendranagar, Hyderabad, 500030, India
| | - P B Kirti
- Department of Plant Sciences, University of Hyderabad, Hyderabad, 500046, India.
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29
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Abe K, Ichikawa H. Gene Overexpression Resources in Cereals for Functional Genomics and Discovery of Useful Genes. FRONTIERS IN PLANT SCIENCE 2016; 7:1359. [PMID: 27708649 PMCID: PMC5030214 DOI: 10.3389/fpls.2016.01359] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 08/26/2016] [Indexed: 05/12/2023]
Abstract
Identification and elucidation of functions of plant genes is valuable for both basic and applied research. In addition to natural variation in model plants, numerous loss-of-function resources have been produced by mutagenesis with chemicals, irradiation, or insertions of transposable elements or T-DNA. However, we may be unable to observe loss-of-function phenotypes for genes with functionally redundant homologs and for those essential for growth and development. To offset such disadvantages, gain-of-function transgenic resources have been exploited. Activation-tagged lines have been generated using obligatory overexpression of endogenous genes by random insertion of an enhancer. Recent progress in DNA sequencing technology and bioinformatics has enabled the preparation of genomewide collections of full-length cDNAs (fl-cDNAs) in some model species. Using the fl-cDNA clones, a novel gain-of-function strategy, Fl-cDNA OvereXpressor gene (FOX)-hunting system, has been developed. A mutant phenotype in a FOX line can be directly attributed to the overexpressed fl-cDNA. Investigating a large population of FOX lines could reveal important genes conferring favorable phenotypes for crop breeding. Alternatively, a unique loss-of-function approach Chimeric REpressor gene Silencing Technology (CRES-T) has been developed. In CRES-T, overexpression of a chimeric repressor, composed of the coding sequence of a transcription factor (TF) and short peptide designated as the repression domain, could interfere with the action of endogenous TF in plants. Although plant TFs usually consist of gene families, CRES-T is effective, in principle, even for the TFs with functional redundancy. In this review, we focus on the current status of the gene-overexpression strategies and resources for identifying and elucidating novel functions of cereal genes. We discuss the potential of these research tools for identifying useful genes and phenotypes for application in crop breeding.
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Affiliation(s)
| | - Hiroaki Ichikawa
- Institute of Agrobiological Sciences, National Agriculture and Food Research OrganizationTsukuba, Japan
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30
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Xuan YH, Kim CM, Je BI, Liu JM, Li TY, Lee GS, Kim TH, Han CD. Transposon Ds-Mediated Insertional Mutagenesis in Rice (Oryza sativa). CURRENT PROTOCOLS IN PLANT BIOLOGY 2016; 1:466-487. [PMID: 31725960 DOI: 10.1002/cppb.20030] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Rice (Oryza sativa) is the most important consumed staple food for a large and diverse population worldwide. Since databases of genomic sequences became available, functional genomics and genetic manipulations have been widely practiced in rice research communities. Insertional mutants are the most common genetic materials utilized to analyze gene function. To mutagenize rice genomes, we exploited the transpositional activity of an Activator/Dissociation (Ac/Ds) system in rice. To mobilize Ds in rice genomes, a maize Ac cDNA was expressed under the CaMV35S promoter, and a gene trap Ds was utilized to detect expression of host genes via the reporter gene GUS. Conventional transposon-mediated gene-tagging systems rely on genetic crossing and selection markers. Furthermore, the activities of transposases have to be monitored. By taking advantage of the fact that Ds becomes highly active during tissue culture, a plant regeneration system employing tissue culture was employed to generate a large Ds transposant population in rice. This system overcomes the requirement for markers and the monitoring of Ac activity. In the regenerated populations, more than 70% of the plant lines contained independent Ds insertions and 12% expressed GUS at seedling stages. This protocol describes the method for producing a Ds-mediated insertional population via tissue culture regeneration systems. © 2016 by John Wiley & Sons, Inc.
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Affiliation(s)
- Yuan Hu Xuan
- College of Plant Protection, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Chul Min Kim
- Division of Applied Life Science (BK21 program), Plant Molecular Biology & Biotechnology Research Center (PMBBRC), Gyeongsang National University, Jinju, Korea
| | - Byoung Il Je
- Division of Applied Life Science (BK21 program), Plant Molecular Biology & Biotechnology Research Center (PMBBRC), Gyeongsang National University, Jinju, Korea
| | - Jing Miao Liu
- Division of Applied Life Science (BK21 program), Plant Molecular Biology & Biotechnology Research Center (PMBBRC), Gyeongsang National University, Jinju, Korea
| | - Tian Ya Li
- College of Plant Protection, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Gang-Seob Lee
- Biosafty Division, Department of Agricultural Biotechnology, National Institute of Agricultural Science (NIAS), RDA, Jeonju, Korea
| | - Tae-Ho Kim
- Genomics Division, Department of Agricultural Biotechnology, National Institute of Agricultural Science (NIAS), RDA, Jeonju, Korea
| | - Chang-Deok Han
- Division of Applied Life Science (BK21 program), Plant Molecular Biology & Biotechnology Research Center (PMBBRC), Gyeongsang National University, Jinju, Korea
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31
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Campbell BW, Stupar RM. Soybean (Glycine max) Mutant and Germplasm Resources: Current Status and Future Prospects. ACTA ACUST UNITED AC 2016; 1:307-327. [PMID: 30775866 DOI: 10.1002/cppb.20015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Genetic bottlenecks during domestication and modern breeding limited the genetic diversity of soybean (Glycine max (L.) Merr.). Therefore, expanding and diversifying soybean genetic resources is a major priority for the research community. These resources, consisting of natural and induced genetic variants, are valuable tools for improving soybean and furthering soybean biological knowledge. During the twentieth century, researchers gathered a wealth of genetic variation in the forms of landraces, Glycine soja accessions, Glycine tertiary germplasm, and the U.S. Department of Agriculture (USDA) Type and Isoline Collections. During the twenty-first century, soybean researchers have added several new genetic and genomic resources. These include the reference genome sequence, genotype data for the USDA soybean germplasm collection, next-generation mapping populations, new irradiation and transposon-based mutagenesis populations, and designer nuclease platforms for genome engineering. This paper briefly surveys the publicly accessible soybean genetic resources currently available or in development and provides recommendations for developing such genetic resources in the future. © 2016 by John Wiley & Sons, Inc.
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Affiliation(s)
- Benjamin W Campbell
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota
| | - Robert M Stupar
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota
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32
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Mustafiz A, Kumari S, Karan R. Ascribing Functions to Genes: Journey Towards Genetic Improvement of Rice Via Functional Genomics. Curr Genomics 2016; 17:155-76. [PMID: 27252584 PMCID: PMC4869004 DOI: 10.2174/1389202917666160202215135] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Revised: 07/01/2015] [Accepted: 07/06/2015] [Indexed: 11/22/2022] Open
Abstract
Rice, one of the most important cereal crops for mankind, feeds more than half the world population. Rice has been heralded as a model cereal owing to its small genome size, amenability to easy transformation, high synteny to other cereal crops and availability of complete genome sequence. Moreover, sequence wealth in rice is getting more refined and precise due to resequencing efforts. This humungous resource of sequence data has confronted research fraternity with a herculean challenge as well as an excellent opportunity to functionally validate expressed as well as regulatory portions of the genome. This will not only help us in understanding the genetic basis of plant architecture and physiology but would also steer us towards developing improved cultivars. No single technique can achieve such a mammoth task. Functional genomics through its diverse tools viz. loss and gain of function mutants, multifarious omics strategies like transcriptomics, proteomics, metabolomics and phenomics provide us with the necessary handle. A paradigm shift in technological advances in functional genomics strategies has been instrumental in generating considerable amount of information w.r.t functionality of rice genome. We now have several databases and online resources for functionally validated genes but despite that we are far from reaching the desired milestone of functionally characterizing each and every rice gene. There is an urgent need for a common platform, for information already available in rice, and collaborative efforts between researchers in a concerted manner as well as healthy public-private partnership, for genetic improvement of rice crop better able to handle the pressures of climate change and exponentially increasing population.
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Affiliation(s)
- Ananda Mustafiz
- South Asian University, Akbar Bhawan, Chanakyapuri, New Delhi
| | - Sumita Kumari
- Sher-e-Kashmir University of Agriculture Sciences and Technology, Jammu 180009, India
| | - Ratna Karan
- Agronomy Department, Institute of Food and Agricultural Sciences, University of Florida, Gainesville - 32611, Florida, USA
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33
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Liu F, Gong D, Zhang Q, Wang D, Cui M, Zhang Z, Liu G, Wu J, Wang Y. High-throughput generation of an activation-tagged mutant library for functional genomic analyses in tobacco. PLANTA 2015; 241:629-40. [PMID: 25408504 DOI: 10.1007/s00425-014-2186-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Accepted: 09/29/2014] [Indexed: 06/04/2023]
Abstract
Tobacco (Nicotiana tabacum L.) is an ideal model system for molecular biological and genetic studies. In this study, activation tagging was used to generate approximately 100,000 transgenic tobacco plants. Southern blot analysis indicated that there were 1.6 T-DNA inserts per line on average in our transformed population. The phenotypes observed include abnormalities in leaf and flower morphology, plant height, flowering time, branching, and fertility. Among 6,000 plants in the T0 generation, 57 displayed obvious phenotypes. Among 4,105 lines in the T1 generation, 311 displayed abnormal phenotypes. Fusion primer and nested integrated PCR was used to identify 963 independent genomic loci of T-DNA insertion sites in 1,257 T1 lines. The distribution of T-DNA insertions was non-uniform and correlated well with the predicted gene density along each chromosome. The insertions were biased toward genic regions and noncoding regions within 5 kb of a gene. Fifteen plants that showed the same phenotype as their parent with a dominant pattern in the T2 generation were chosen randomly to detect the expression levels of genes adjacent to the T-DNA integration sites by semi-quantitative RT-PCR. Fifteen candidate genes were identified. Activation was observed in 7 out of the 15 adjacent genes, including one that was located 13.1 kb away from the enhancer sequence. The activation-tagged population described in this paper will be a highly valuable resource for tobacco functional genomics research using both forward and reverse genetic approaches.
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Affiliation(s)
- Feng Liu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
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34
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Gao X, Zhou J, Li J, Zou X, Zhao J, Li Q, Xia R, Yang R, Wang D, Zuo Z, Tu J, Tao Y, Chen X, Xie Q, Zhu Z, Qu S. Efficient generation of marker-free transgenic rice plants using an improved transposon-mediated transgene reintegration strategy. PLANT PHYSIOLOGY 2015; 167:11-24. [PMID: 25371551 PMCID: PMC4280998 DOI: 10.1104/pp.114.246173] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Accepted: 11/02/2014] [Indexed: 05/27/2023]
Abstract
Marker-free transgenic plants can be developed through transposon-mediated transgene reintegration, which allows intact transgene insertion with defined boundaries and requires only a few primary transformants. In this study, we improved the selection strategy and validated that the maize (Zea mays) Activator/Dissociation (Ds) transposable element can be routinely used to generate marker-free transgenic plants. A Ds-based gene of interest was linked to green fluorescent protein in transfer DNA (T-DNA), and a green fluorescent protein-aided counterselection against T-DNA was used together with polymerase chain reaction (PCR)-based positive selection for the gene of interest to screen marker-free progeny. To test the efficacy of this strategy, we cloned the Bacillus thuringiensis (Bt) δ-endotoxin gene into the Ds elements and transformed transposon vectors into rice (Oryza sativa) cultivars via Agrobacterium tumefaciens. PCR assays of the transposon empty donor site exhibited transposition in somatic cells in 60.5% to 100% of the rice transformants. Marker-free (T-DNA-free) transgenic rice plants derived from unlinked germinal transposition were obtained from the T1 generation of 26.1% of the primary transformants. Individual marker-free transgenic rice lines were subjected to thermal asymmetric interlaced-PCR to determine Ds(Bt) reintegration positions, reverse transcription-PCR and enzyme-linked immunosorbent assay to detect Bt expression levels, and bioassays to confirm resistance against the striped stem borer Chilo suppressalis. Overall, we efficiently generated marker-free transgenic plants with optimized transgene insertion and expression. The transposon-mediated marker-free platform established in this study can be used in rice and possibly in other important crops.
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Affiliation(s)
- Xiaoqing Gao
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control and Institute of Virology and Biotechnology (X.G., J.Zho., J.L., X.Z., J.Zha., Y.T., S.Q.), Institute of Crop Science and Nuclear Technology Utilization (D.W.), and Institute of Quality Standards for Agricultural Products (X.C.), Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang 310021, China;Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China (Q.L., R.X., Q.X.); andInstitute of Crop Science (R.Y., J.T.) and Institute of Insect Sciences (Z.Zu., Z.Zh.), Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Jie Zhou
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control and Institute of Virology and Biotechnology (X.G., J.Zho., J.L., X.Z., J.Zha., Y.T., S.Q.), Institute of Crop Science and Nuclear Technology Utilization (D.W.), and Institute of Quality Standards for Agricultural Products (X.C.), Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang 310021, China;Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China (Q.L., R.X., Q.X.); andInstitute of Crop Science (R.Y., J.T.) and Institute of Insect Sciences (Z.Zu., Z.Zh.), Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Jun Li
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control and Institute of Virology and Biotechnology (X.G., J.Zho., J.L., X.Z., J.Zha., Y.T., S.Q.), Institute of Crop Science and Nuclear Technology Utilization (D.W.), and Institute of Quality Standards for Agricultural Products (X.C.), Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang 310021, China;Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China (Q.L., R.X., Q.X.); andInstitute of Crop Science (R.Y., J.T.) and Institute of Insect Sciences (Z.Zu., Z.Zh.), Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Xiaowei Zou
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control and Institute of Virology and Biotechnology (X.G., J.Zho., J.L., X.Z., J.Zha., Y.T., S.Q.), Institute of Crop Science and Nuclear Technology Utilization (D.W.), and Institute of Quality Standards for Agricultural Products (X.C.), Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang 310021, China;Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China (Q.L., R.X., Q.X.); andInstitute of Crop Science (R.Y., J.T.) and Institute of Insect Sciences (Z.Zu., Z.Zh.), Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Jianhua Zhao
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control and Institute of Virology and Biotechnology (X.G., J.Zho., J.L., X.Z., J.Zha., Y.T., S.Q.), Institute of Crop Science and Nuclear Technology Utilization (D.W.), and Institute of Quality Standards for Agricultural Products (X.C.), Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang 310021, China;Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China (Q.L., R.X., Q.X.); andInstitute of Crop Science (R.Y., J.T.) and Institute of Insect Sciences (Z.Zu., Z.Zh.), Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Qingliang Li
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control and Institute of Virology and Biotechnology (X.G., J.Zho., J.L., X.Z., J.Zha., Y.T., S.Q.), Institute of Crop Science and Nuclear Technology Utilization (D.W.), and Institute of Quality Standards for Agricultural Products (X.C.), Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang 310021, China;Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China (Q.L., R.X., Q.X.); andInstitute of Crop Science (R.Y., J.T.) and Institute of Insect Sciences (Z.Zu., Z.Zh.), Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Ran Xia
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control and Institute of Virology and Biotechnology (X.G., J.Zho., J.L., X.Z., J.Zha., Y.T., S.Q.), Institute of Crop Science and Nuclear Technology Utilization (D.W.), and Institute of Quality Standards for Agricultural Products (X.C.), Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang 310021, China;Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China (Q.L., R.X., Q.X.); andInstitute of Crop Science (R.Y., J.T.) and Institute of Insect Sciences (Z.Zu., Z.Zh.), Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Ruifang Yang
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control and Institute of Virology and Biotechnology (X.G., J.Zho., J.L., X.Z., J.Zha., Y.T., S.Q.), Institute of Crop Science and Nuclear Technology Utilization (D.W.), and Institute of Quality Standards for Agricultural Products (X.C.), Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang 310021, China;Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China (Q.L., R.X., Q.X.); andInstitute of Crop Science (R.Y., J.T.) and Institute of Insect Sciences (Z.Zu., Z.Zh.), Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Dekai Wang
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control and Institute of Virology and Biotechnology (X.G., J.Zho., J.L., X.Z., J.Zha., Y.T., S.Q.), Institute of Crop Science and Nuclear Technology Utilization (D.W.), and Institute of Quality Standards for Agricultural Products (X.C.), Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang 310021, China;Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China (Q.L., R.X., Q.X.); andInstitute of Crop Science (R.Y., J.T.) and Institute of Insect Sciences (Z.Zu., Z.Zh.), Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Zhaoxue Zuo
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control and Institute of Virology and Biotechnology (X.G., J.Zho., J.L., X.Z., J.Zha., Y.T., S.Q.), Institute of Crop Science and Nuclear Technology Utilization (D.W.), and Institute of Quality Standards for Agricultural Products (X.C.), Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang 310021, China;Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China (Q.L., R.X., Q.X.); andInstitute of Crop Science (R.Y., J.T.) and Institute of Insect Sciences (Z.Zu., Z.Zh.), Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Jumin Tu
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control and Institute of Virology and Biotechnology (X.G., J.Zho., J.L., X.Z., J.Zha., Y.T., S.Q.), Institute of Crop Science and Nuclear Technology Utilization (D.W.), and Institute of Quality Standards for Agricultural Products (X.C.), Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang 310021, China;Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China (Q.L., R.X., Q.X.); andInstitute of Crop Science (R.Y., J.T.) and Institute of Insect Sciences (Z.Zu., Z.Zh.), Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Yuezhi Tao
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control and Institute of Virology and Biotechnology (X.G., J.Zho., J.L., X.Z., J.Zha., Y.T., S.Q.), Institute of Crop Science and Nuclear Technology Utilization (D.W.), and Institute of Quality Standards for Agricultural Products (X.C.), Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang 310021, China;Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China (Q.L., R.X., Q.X.); andInstitute of Crop Science (R.Y., J.T.) and Institute of Insect Sciences (Z.Zu., Z.Zh.), Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Xiaoyun Chen
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control and Institute of Virology and Biotechnology (X.G., J.Zho., J.L., X.Z., J.Zha., Y.T., S.Q.), Institute of Crop Science and Nuclear Technology Utilization (D.W.), and Institute of Quality Standards for Agricultural Products (X.C.), Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang 310021, China;Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China (Q.L., R.X., Q.X.); andInstitute of Crop Science (R.Y., J.T.) and Institute of Insect Sciences (Z.Zu., Z.Zh.), Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Qi Xie
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control and Institute of Virology and Biotechnology (X.G., J.Zho., J.L., X.Z., J.Zha., Y.T., S.Q.), Institute of Crop Science and Nuclear Technology Utilization (D.W.), and Institute of Quality Standards for Agricultural Products (X.C.), Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang 310021, China;Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China (Q.L., R.X., Q.X.); andInstitute of Crop Science (R.Y., J.T.) and Institute of Insect Sciences (Z.Zu., Z.Zh.), Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Zengrong Zhu
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control and Institute of Virology and Biotechnology (X.G., J.Zho., J.L., X.Z., J.Zha., Y.T., S.Q.), Institute of Crop Science and Nuclear Technology Utilization (D.W.), and Institute of Quality Standards for Agricultural Products (X.C.), Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang 310021, China;Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China (Q.L., R.X., Q.X.); andInstitute of Crop Science (R.Y., J.T.) and Institute of Insect Sciences (Z.Zu., Z.Zh.), Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Shaohong Qu
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control and Institute of Virology and Biotechnology (X.G., J.Zho., J.L., X.Z., J.Zha., Y.T., S.Q.), Institute of Crop Science and Nuclear Technology Utilization (D.W.), and Institute of Quality Standards for Agricultural Products (X.C.), Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang 310021, China;Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China (Q.L., R.X., Q.X.); andInstitute of Crop Science (R.Y., J.T.) and Institute of Insect Sciences (Z.Zu., Z.Zh.), Zhejiang University, Hangzhou, Zhejiang 310058, China
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Li Y, Takano T, Liu S. Discovery and characterization of two novel salt-tolerance genes in Puccinellia tenuiflora. Int J Mol Sci 2014; 15:16469-83. [PMID: 25238412 PMCID: PMC4200785 DOI: 10.3390/ijms150916469] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Revised: 08/25/2014] [Accepted: 09/05/2014] [Indexed: 01/25/2023] Open
Abstract
Puccinellia tenuiflora is a monocotyledonous halophyte that is able to survive in extreme saline soil environments at an alkaline pH range of 9-10. In this study, we transformed full-length cDNAs of P. tenuiflora into Saccharomyces cerevisiae by using the full-length cDNA over-expressing gene-hunting system to identify novel salt-tolerance genes. In all, 32 yeast clones overexpressing P. tenuiflora cDNA were obtained by screening under NaCl stress conditions; of these, 31 clones showed stronger tolerance to NaCl and were amplified using polymerase chain reaction (PCR) and sequenced. Four novel genes encoding proteins with unknown function were identified; these genes had no homology with genes from higher plants. Of the four isolated genes, two that encoded proteins with two transmembrane domains showed the strongest resistance to 1.3 M NaCl. RT-PCR and northern blot analysis of P. tenuiflora cultured cells confirmed the endogenous NaCl-induced expression of the two proteins. Both of the proteins conferred better tolerance in yeasts to high salt, alkaline and osmotic conditions, some heavy metals and H2O2 stress. Thus, we inferred that the two novel proteins might alleviate oxidative and other stresses in P. tenuiflora.
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Affiliation(s)
- Ying Li
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration in Oil Field (SAVER), Ministry of Education, Alkali Soil Natural Environmental Science Center (ASNESC), Northeast Forestry University, Harbin Hexing Road, Harbin 150040, China.
| | - Tetsuo Takano
- Asian Natural Environmental Science Center, University of Tokyo, Nishitokyo-shi, Tokyo 188-0002, Japan.
| | - Shenkui Liu
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration in Oil Field (SAVER), Ministry of Education, Alkali Soil Natural Environmental Science Center (ASNESC), Northeast Forestry University, Harbin Hexing Road, Harbin 150040, China.
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Chen L, Hao L, Parry MAJ, Phillips AL, Hu YG. Progress in TILLING as a tool for functional genomics and improvement of crops. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2014; 56:425-43. [PMID: 24618006 DOI: 10.1111/jipb.12192] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Accepted: 03/11/2014] [Indexed: 05/18/2023]
Abstract
Food security is a global concern and substantial yield increases in crops are required to feed the growing world population. Mutagenesis is an important tool in crop improvement and is free of the regulatory restrictions imposed on genetically modified organisms. Targeting Induced Local Lesions in Genomes (TILLING), which combines traditional chemical mutagenesis with high-throughput genome-wide screening for point mutations in desired genes, offers a powerful way to create novel mutant alleles for both functional genomics and improvement of crops. TILLING is generally applicable to genomes whether small or large, diploid or even allohexaploid, and shows great potential to address the major challenge of linking sequence information to the function of genes and to modulate key traits for plant breeding. TILLING has been successfully applied in many crop species and recent progress in TILLING is summarized below, especially on the developments in mutation detection technology, application of TILLING in gene functional studies and crop breeding. The potential of TILLING/EcoTILLING for functional genetics and crop improvement is also discussed. Furthermore, a small-scale forward strategy including backcross and selfing was conducted to release the potential mutant phenotypes masked in M2 (or M3) plants.
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Affiliation(s)
- Liang Chen
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China
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Lu G, Wang X, Liu J, Yu K, Gao Y, Liu H, Wang C, Wang W, Wang G, Liu M, Mao G, Li B, Qin J, Xia M, Zhou J, Liu J, Jiang S, Mo H, Cui J, Nagasawa N, Sivasankar S, Albertsen MC, Sakai H, Mazur BJ, Lassner MW, Broglie RM. Application of T-DNA activation tagging to identify glutamate receptor-like genes that enhance drought tolerance in plants. PLANT CELL REPORTS 2014; 33:617-31. [PMID: 24682459 DOI: 10.1007/s00299-014-1586-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2013] [Revised: 02/05/2014] [Accepted: 02/06/2014] [Indexed: 05/26/2023]
Abstract
A high-quality rice activation tagging population has been developed and screened for drought-tolerant lines using various water stress assays. One drought-tolerant line activated two rice glutamate receptor-like genes. Transgenic overexpression of the rice glutamate receptor-like genes conferred drought tolerance to rice and Arabidopsis. Rice (Oryza sativa) is a multi-billion dollar crop grown in more than one hundred countries, as well as a useful functional genetic tool for trait discovery. We have developed a population of more than 200,000 activation-tagged rice lines for use in forward genetic screens to identify genes that improve drought tolerance and other traits that improve yield and agronomic productivity. The population has an expected coverage of more than 90 % of rice genes. About 80 % of the lines have a single T-DNA insertion locus and this molecular feature simplifies gene identification. One of the lines identified in our screens, AH01486, exhibits improved drought tolerance. The AH01486 T-DNA locus is located in a region with two glutamate receptor-like genes. Constitutive overexpression of either glutamate receptor-like gene significantly enhances the drought tolerance of rice and Arabidopsis, thus revealing a novel function of this important gene family in plant biology.
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Affiliation(s)
- Guihua Lu
- Beijing Kaituo DNA Biotech Research Center, Co., Ltd., Beijing, 102206, China,
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Zhang J, Liu X, Li S, Cheng Z, Li C. The rice semi-dwarf mutant sd37, caused by a mutation in CYP96B4, plays an important role in the fine-tuning of plant growth. PLoS One 2014; 9:e88068. [PMID: 24498428 PMCID: PMC3912173 DOI: 10.1371/journal.pone.0088068] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2013] [Accepted: 01/06/2014] [Indexed: 12/02/2022] Open
Abstract
Plant cytochrome P450 has diverse roles in developmental processes and in the response to environmental cues. Here, we characterized the rice (Oryza sativa L ssp. indica cultivar 3037) semi-dwarf mutant sd37, in which the gene CYP96B4 (Cytochrome P450 96B subfamily) was identified and confirmed as the target by map-based cloning and a complementation test. A point mutation in the SRS2 domain of CYP96B4 resulted in a threonine to lysine substitution in the sd37 mutant. Examination of the subcellular localization of the protein revealed that SD37 was ER-localized protein. And SD37 was predominantly expressed in the shoot apical meristem and developing leaf and root maturation zone but not in the root apical meristem. The sd37 leaves, panicles, and seeds were smaller than those of the wild type. Histological analysis further revealed that a decrease in cell number in the mutant, specifically in the shoots, was the main cause of the dwarf phenotype. Microarray analysis demonstrated that the expression of several cell division-related genes was disturbed in the sd37 mutant. In addition, mutation or strongly overexpression of SD37 results in dwarf plants but moderate overexpression increases plant height. These data suggest that CYP96B4 may be an important regulator of plant growth that affects plant height in rice.
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Affiliation(s)
- Jie Zhang
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- National Engineering Research Center for Vegetables, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing, China
| | - Xiaoqiang Liu
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Shuyu Li
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Zhukuan Cheng
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Chuanyou Li
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- * E-mail:
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Induced Genetic Variation, TILLING and NGS-Based Cloning. BIOTECHNOLOGICAL APPROACHES TO BARLEY IMPROVEMENT 2014. [DOI: 10.1007/978-3-662-44406-1_15] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Wang L, Zheng J, Luo Y, Xu T, Zhang Q, Zhang L, Xu M, Wan J, Wang MB, Zhang C, Fan Y. Construction of a genomewide RNAi mutant library in rice. PLANT BIOTECHNOLOGY JOURNAL 2013; 11:997-1005. [PMID: 23910936 DOI: 10.1111/pbi.12093] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2013] [Revised: 05/18/2013] [Accepted: 05/24/2013] [Indexed: 05/04/2023]
Abstract
Long hairpin RNA (hpRNA) transgenes are a powerful tool for gene function studies in plants, but a genomewide RNAi mutant library using hpRNA transgenes has not been reported for plants. Here, we report the construction of a hpRNA library for the genomewide identification of gene function in rice using an improved rolling circle amplification-mediated hpRNA (RMHR) method. Transformation of rice with the library resulted in thousands of transgenic lines containing hpRNAs targeting genes of various function. The target mRNA was down-regulated in the hpRNA lines, and this was correlated with the accumulation of siRNAs corresponding to the double-stranded arms of the hpRNA. Multiple members of a gene family were simultaneously silenced by hpRNAs derived from a single member, but the degree of such cross-silencing depended on the level of sequence homology between the members as well as the abundance of matching siRNAs. The silencing of key genes tended to cause a severe phenotype, but these transgenic lines usually survived in the field long enough for phenotypic and molecular analyses to be conducted. Deep sequencing analysis of small RNAs showed that the hpRNA-derived siRNAs were characteristic of Argonaute-binding small RNAs. Our results indicate that RNAi mutant library is a high-efficient approach for genomewide gene identification in plants.
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Affiliation(s)
- Lei Wang
- Biotechnology Research Institute, The National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China
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Yang Y, Li Y, Wu C. Genomic resources for functional analyses of the rice genome. CURRENT OPINION IN PLANT BIOLOGY 2013; 16:157-63. [PMID: 23571012 DOI: 10.1016/j.pbi.2013.03.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2012] [Revised: 03/15/2013] [Accepted: 03/15/2013] [Indexed: 05/07/2023]
Abstract
With the availability of the rice genome sequence, rice research communities are entering a new era of plant functional genomics. The last decade has seen rapid worldwide progress on establishing platforms for rice functional genomic research. These platforms offer practical toolkits and genomic resources for high-throughput identification of genes and pathways. In this review, we summarize available genomic resources for functional analyses of the rice genome. These genomic resources include high-quality bacterial artificial chromosome libraries, large-scale expression sequence tags, full-length cDNA collections, large amounts of data on global expression profiles, various mutant libraries and integrated bioinformatics databases. We not only present the current status of genomic resources but also discuss their usage in elucidating gene functions of the rice genome.
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Affiliation(s)
- Ying Yang
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China
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Wang N, Long T, Yao W, Xiong L, Zhang Q, Wu C. Mutant resources for the functional analysis of the rice genome. MOLECULAR PLANT 2013; 6:596-604. [PMID: 23204502 DOI: 10.1093/mp/sss142] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Rice is one of the most important crops worldwide, both as a staple food and as a model system for genomic research. In order to systematically assign functions to all predicted genes in the rice genome, a large number of rice mutant lines, including those created by T-DNA insertion, Ds/dSpm tagging, Tos17 tagging, and chemical/irradiation mutagenesis, have been generated by groups around the world. In this study, we have reviewed the current status of mutant resources for functional analysis of the rice genome. A total of 246 566 flanking sequence tags from rice mutant libraries with T-DNA, Ds/dSpm, or Tos17 insertion have been collected and analyzed. The results show that, among 211 470 unique hits, inserts located in the genic region account for 68.16%, and 60.49% of nuclear genes contain at least one insertion. Currently, 57% of non-transposable-element-related genes in rice have insertional tags. In addition, chemical/irradiation-induced rice mutant libraries have contributed a lot to both gene identification and new technology for the identification of mutant sites. In this review, we summarize how these tools have been used to generate a large collection of mutants. In addition, we discuss the merits of classic mutation strategies. In order to achieve saturation of mutagenesis in rice, DNA targeting, and new resources like RiceFox for gene functional identification are reviewed from a perspective of the future generation of rice mutant resources.
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Affiliation(s)
- Nili Wang
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China
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Pantazis CJ, Fisk S, Mills K, Flinn BS, Shulaev V, Veilleux RE, Dan Y. Development of an efficient transformation method by Agrobacterium tumefaciens and high throughput spray assay to identify transgenic plants for woodland strawberry (Fragaria vesca) using NPTII selection. PLANT CELL REPORTS 2013; 32:329-337. [PMID: 23160638 DOI: 10.1007/s00299-012-1366-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2012] [Revised: 10/19/2012] [Accepted: 10/29/2012] [Indexed: 06/01/2023]
Abstract
KEY MESSAGE : We developed an efficient Agrobacterium -mediated transformation method using an Ac/Ds transposon tagging construct for F. vesca and high throughput paromomycin spray assay to identify its transformants for strawberry functional genomics. Genomic resources for Rosaceae species are now readily available, including the Fragaria vesca genome, EST sequences, markers, linkage maps, and physical maps. The Rosaceae Genomic Executive Committee has promoted strawberry as a translational genomics model due to its unique biological features and transformability for fruit trait improvement. Our overall research goal is to use functional genomic and metabolic approaches to pursue high throughput gene discovery in the diploid woodland strawberry. F. vesca offers several advantages of a fleshy fruit typical of most fruit crops, short life cycle (seed to seed in 12-16 weeks), small genome size (206 Mbb/C), small plant size, self-compatibility, and many seeds per plant. We have developed an efficient Agrobacterium tumefaciens-mediated strawberry transformation method using kanamycin selection, and high throughput paromomycin spray assay to efficiently identify transgenic strawberry plants. Using our kanamycin transformation method, we were able to produce up to 98 independent kanamycin resistant insertional mutant lines using a T-DNA construct carrying an Ac/Ds transposon Launchpad system from a single transformation experiment involving inoculation of 22 leaf explants of F. vesca accession 551572 within approx. 11 weeks (from inoculation to soil). Transgenic plants with 1-2 copies of a transgene were confirmed by Southern blot analysis. Using our paromomycin spray assay, transgenic F. vesca plants were rapidly identified within 10 days after spraying.
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Affiliation(s)
- Christopher J Pantazis
- Institute for Advanced Learning and Research, 150 Slayton Avenue Danville, Danville, VA 24540, USA
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Chen YL, Liang HL, Ma XL, Lou SL, Xie YY, Liu ZL, Chen LT, Liu YG. An efficient rice mutagenesis system based on suspension-cultured cells. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2013; 55:122-30. [PMID: 23126685 DOI: 10.1111/jipb.12000] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Plant mutants are important bio-resources for crop breeding and gene functional studies. Conventional methods for generating mutant libraries by mutagenesis of seeds with physical or chemical agents are of low efficiency. Here, we developed a highly-efficient ethyl methanesulfonate (EMS) mutagenesis system based on suspension-cultured cells, with rice (Oryza sativa L.) as an example. We show that treatment of suspension-cultured tiny cell clusters with 0.4% EMS for 18-22 h followed by differentiation and regeneration produced as high as 29.4% independent mutant lines with visible phenotypic variations, including a number of important agronomic traits such as grain size, panicle size, grain or panicle shape, tiller number and angle, heading date, male sterility, and disease sensitivity. No mosaic mutant was observed in the mutant lines tested. In this mutant library, we obtained a mutant with an abnormally elongated uppermost internode. Sequencing and functional analysis revealed that this is a new allelic mutant of eui (elongated uppermost internode) caused by two point mutations in the first exon of the EUI gene, representing a successful example of this mutagenesis system.
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Affiliation(s)
- Yuan-Ling Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
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Sharma R, Cao P, Jung KH, Sharma MK, Ronald PC. Construction of a rice glycoside hydrolase phylogenomic database and identification of targets for biofuel research. FRONTIERS IN PLANT SCIENCE 2013; 4:330. [PMID: 23986771 PMCID: PMC3752443 DOI: 10.3389/fpls.2013.00330] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Accepted: 08/05/2013] [Indexed: 05/19/2023]
Abstract
Glycoside hydrolases (GH) catalyze the hydrolysis of glycosidic bonds in cell wall polymers and can have major effects on cell wall architecture. Taking advantage of the massive datasets available in public databases, we have constructed a rice phylogenomic database of GHs (http://ricephylogenomics.ucdavis.edu/cellwalls/gh/). This database integrates multiple data types including the structural features, orthologous relationships, mutant availability, and gene expression patterns for each GH family in a phylogenomic context. The rice genome encodes 437 GH genes classified into 34 families. Based on pairwise comparison with eight dicot and four monocot genomes, we identified 138 GH genes that are highly diverged between monocots and dicots, 57 of which have diverged further in rice as compared with four monocot genomes scanned in this study. Chromosomal localization and expression analysis suggest a role for both whole-genome and localized gene duplications in expansion and diversification of GH families in rice. We examined the meta-profiles of expression patterns of GH genes in twenty different anatomical tissues of rice. Transcripts of 51 genes exhibit tissue or developmental stage-preferential expression, whereas, seventeen other genes preferentially accumulate in actively growing tissues. When queried in RiceNet, a probabilistic functional gene network that facilitates functional gene predictions, nine out of seventeen genes form a regulatory network with the well-characterized genes involved in biosynthesis of cell wall polymers including cellulose synthase and cellulose synthase-like genes of rice. Two-thirds of the GH genes in rice are up regulated in response to biotic and abiotic stress treatments indicating a role in stress adaptation. Our analyses identify potential GH targets for cell wall modification.
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Affiliation(s)
- Rita Sharma
- Department of Plant Pathology and The Genome Center, University of California, DavisDavis, CA, USA
- Feedstocks Divison, Joint BioEnergy InstituteEmeryville, CA, USA
| | - Peijian Cao
- Department of Plant Pathology and The Genome Center, University of California, DavisDavis, CA, USA
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research InstituteZhengzhou, China
| | - Ki-Hong Jung
- Department of Plant Pathology and The Genome Center, University of California, DavisDavis, CA, USA
- Department of Plant Molecular Systems Biotechnology and Crop Biotech Institute, Kyung Hee UniversityYongin, South Korea
| | - Manoj K. Sharma
- Department of Plant Pathology and The Genome Center, University of California, DavisDavis, CA, USA
- Feedstocks Divison, Joint BioEnergy InstituteEmeryville, CA, USA
| | - Pamela C. Ronald
- Department of Plant Pathology and The Genome Center, University of California, DavisDavis, CA, USA
- Feedstocks Divison, Joint BioEnergy InstituteEmeryville, CA, USA
- Department of Plant Molecular Systems Biotechnology and Crop Biotech Institute, Kyung Hee UniversityYongin, South Korea
- *Correspondence: Pamela C. Ronald, Department of Plant Pathology and the Genome Center, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA e-mail:
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Abstract
Maize Activator (Ac) is one of the prototype transposable elements of the hAT transposon superfamily, members of which were identified in plants, fungi, and animals. The autonomous Ac and nonautonomous Dissociation (Ds) elements are mobilized by the single transposase protein encoded by Ac. To date Ac/Ds transposons were shown to be functional in approximately 20 plant species and have become the most widely used transposable elements for gene tagging and functional genomics approaches in plants. In this chapter we review the biology, regulation, and transposition mechanism of Ac/Ds elements in maize and heterologous plants. We discuss the parameters that are known to influence the functionality and transposition efficiency of Ac/Ds transposons and need to be considered when designing Ac transposase expression constructs and Ds elements for application in heterologous plant species.
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Affiliation(s)
- Katina Lazarow
- Leibniz-Institute for Molecular Pharmacology (FMP), Berlin, Germany
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Yasuda K, Ito M, Sugita T, Tsukiyama T, Saito H, Naito K, Teraishi M, Tanisaka T, Okumoto Y. Utilization of transposable element mPing as a novel genetic tool for modification of the stress response in rice. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2013; 32:505-516. [PMID: 24078785 PMCID: PMC3782648 DOI: 10.1007/s11032-013-9885-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2012] [Accepted: 05/06/2013] [Indexed: 05/02/2023]
Abstract
Transposable elements (TEs) are DNA fragments that have the ability to move from one chromosomal location to another. The insertion of TEs into gene-rich regions often affects changes in the expression of neighboring genes. Miniature Ping (mPing) is an active miniature inverted-repeat TE discovered in the rice genome. It has been found to show exceptionally active transposition in a few japonica rice varieties, including Gimbozu, where mPing insertion rendered adjacent genes stress-inducible. In the Gimbozu population, it is highly possible that several genes with modified expression profiles are segregating due to the de novo mPing insertions. In our study, we utilized a screening system for detecting de novo mPing insertions in the upstream region of target genes and evaluated the effect of mPing on the stress response of the target genes. Screening for 17 targeted genes revealed five genes with the mPing insertion in their promoters. In most cases, the alteration of gene expression was observed under stress conditions, and there was no change in the expression levels of those five genes under normal conditions. These results indicate that the mPing insertion can be used as a genetic tool to modify an expression pattern of a target gene under stress conditions without changing the expression profiles of those under natural conditions.
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Affiliation(s)
- Kanako Yasuda
- Graduate School of Agriculture, Kyoto University, Kitashirakawa, Sakyo-ku, Kyoto, 606-8502 Japan
| | - Makoto Ito
- Graduate School of Agriculture, Kyoto University, Kitashirakawa, Sakyo-ku, Kyoto, 606-8502 Japan
| | - Tomohiko Sugita
- Graduate School of Agriculture, Kyoto University, Kitashirakawa, Sakyo-ku, Kyoto, 606-8502 Japan
| | - Takuji Tsukiyama
- Graduate School of Agriculture, Kyoto University, Kitashirakawa, Sakyo-ku, Kyoto, 606-8502 Japan
| | - Hiroki Saito
- Graduate School of Agriculture, Kyoto University, Kitashirakawa, Sakyo-ku, Kyoto, 606-8502 Japan
| | - Ken Naito
- Genebank, National Institute of Agrobiological Sciences, Kannondai 2-1-2, Tsukuba, Ibaraki 305-8602 Japan
| | - Masayoshi Teraishi
- Graduate School of Agriculture, Kyoto University, Kitashirakawa, Sakyo-ku, Kyoto, 606-8502 Japan
| | - Takatoshi Tanisaka
- Graduate School of Agriculture, Kyoto University, Kitashirakawa, Sakyo-ku, Kyoto, 606-8502 Japan
| | - Yutaka Okumoto
- Graduate School of Agriculture, Kyoto University, Kitashirakawa, Sakyo-ku, Kyoto, 606-8502 Japan
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Yu C, Han F, Zhang J, Birchler J, Peterson T. A transgenic system for generation of transposon Ac/Ds-induced chromosome rearrangements in rice. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 125:1449-62. [PMID: 22798058 PMCID: PMC3470690 DOI: 10.1007/s00122-012-1925-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2012] [Accepted: 06/16/2012] [Indexed: 05/04/2023]
Abstract
The maize Activator (Ac)/Dissociation (Ds) transposable element system has been used in a variety of plants for insertional mutagenesis. Ac/Ds elements can also generate genome rearrangements via alternative transposition reactions which involve the termini of closely linked transposons. Here, we introduced a transgene containing reverse-oriented Ac/Ds termini together with an Ac transposase gene into rice (Oryza sativa ssp. japonica cv. Nipponbare). Among the transgenic progeny, we identified and characterized 25 independent genome rearrangements at three different chromosomal loci. The rearrangements include chromosomal deletions and inversions and one translocation. Most of the deletions occurred within the T-DNA region, but two cases showed the loss of 72 kilobase pairs (kb) and 79 kb of rice genomic DNA flanking the transgene. In addition to deletions, we obtained chromosomal inversions ranging in size from less than 10 kb (within the transgene DNA) to over 1 million base pairs (Mb). For 11 inversions, we cloned and sequenced both inversion breakpoints; in all 11 cases, the inversion junctions contained the typical 8 base pairs (bp) Ac/Ds target site duplications, confirming their origin as transposition products. Together, our results indicate that alternative Ac/Ds transposition can be an efficient tool for functional genomics and chromosomal manipulation in rice.
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Affiliation(s)
- Chuanhe Yu
- Department of Genetics, Development and Cell Biology, Department of Agronomy, Iowa State University, Ames, IA 50011 USA
| | - Fangpu Han
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211 USA
- State Key Lab of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101 Beijing, China
| | - Jianbo Zhang
- Department of Genetics, Development and Cell Biology, Department of Agronomy, Iowa State University, Ames, IA 50011 USA
| | - James Birchler
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211 USA
| | - Thomas Peterson
- Department of Genetics, Development and Cell Biology, Department of Agronomy, Iowa State University, Ames, IA 50011 USA
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The screening and preliminary construction of quality mutant population for cultivar “Nipponbare” in japonica rice (Oryza sativa). Biologia (Bratisl) 2012. [DOI: 10.2478/s11756-012-0106-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Ramamoorthy R, Kumar PP. A simplified protocol for genetic transformation of switchgrass (Panicum virgatum L.). PLANT CELL REPORTS 2012; 31:1923-31. [PMID: 22733209 DOI: 10.1007/s00299-012-1305-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2012] [Accepted: 06/12/2012] [Indexed: 05/02/2023]
Abstract
UNLABELLED The increasing interest in renewable energy has attracted more research attention on biofuels. In order to generate sustainable amount of biomass feedstock from dedicated biofuel crops such as switchgrass they need to be genetically improved. Genetic transformation is one of the techniques to achieve this goal. The aim of our study was to devise a simplified protocol for switchgrass genetic transformation. We have used NB(0) as the basal medium and mature seeds of the cultivar Alamo as the starting material. The nutrient medium used and scutellum-derived callus are fashioned after rice genetic transformation protocols. We obtained friable calluses, which were similar to the type II calluses in other monocotyledonous species. Calluses were amenable for Agrobacterium-mediated genetic transformation with at least 6 % transformation efficiency. The concentration of hygromycin was optimized for successful selection of transgenic calluses. The Green Fluorescent Protein gene was used to monitor and demonstrate successful genetic transformation. Compared to the previously published methods for genetic transformation of switchgrass, our protocol is simpler and equally efficient. KEY MESSAGE An efficient, simplified switchgrass genetic transformation method with NB(0) basal medium and mature seeds as inoculum was developed. The appropriate concentrations of hormones and selection agent are described.
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Affiliation(s)
- Rengasamy Ramamoorthy
- Department of Biological Sciences, Faculty of Science, National University of Singapore, 10 Science Drive 4, Singapore, 117543, Singapore
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