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Wu A, Lian B, Hao P, Fu X, Zhang M, Lu J, Ma L, Yu S, Wei H, Wang H. GhMYB30-GhMUR3 affects fiber elongation and secondary wall thickening in cotton. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:694-712. [PMID: 37988560 DOI: 10.1111/tpj.16523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Revised: 10/17/2023] [Accepted: 10/23/2023] [Indexed: 11/23/2023]
Abstract
Xyloglucan, an important hemicellulose, plays a crucial role in maintaining cell wall structure and cell elongation. However, the effects of xyloglucan on cotton fiber development are not well understood. GhMUR3 encodes a xyloglucan galactosyltransferase that is essential for xyloglucan synthesis and is highly expressed during fiber elongation. In this study, we report that GhMUR3 participates in cotton fiber development under the regulation of GhMYB30. Overexpression GhMUR3 affects the fiber elongation and cell wall thickening. Transcriptome showed that the expression of genes involved in secondary cell wall synthesis was prematurely activated in OE-MUR3 lines. In addition, GhMYB30 was identified as a key regulator of GhMUR3 by Y1H, Dual-Luc, and electrophoretic mobility shift assay (EMSA) assays. GhMYB30 directly bound the GhMUR3 promoter and activated GhMUR3 expression. Furthermore, DAP-seq of GhMYB30 was performed to identify its target genes in the whole genome. The results showed that many target genes were associated with fiber development, including cell wall synthesis-related genes, BR-related genes, reactive oxygen species pathway genes, and VLCFA synthesis genes. It was demonstrated that GhMYB30 may regulate fiber development through multiple pathways. Additionally, GhMYB46 was confirmed to be a target gene of GhMYB30 by EMSA, and GhMYB46 was significantly increased in GhMYB30-silenced lines, indicating that GhMYB30 inhibited GhMYB46 expression. Overall, these results revealed that GhMUR3 under the regulation of GhMYB30 and plays an essential role in cotton fiber elongation and secondary wall thickening. Additionally, GhMYB30 plays an important role in the regulation of fiber development and regulates fiber secondary wall synthesis by inhibiting the expression of GhMYB46.
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Affiliation(s)
- Aimin Wu
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430000, Hubei, China
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Boying Lian
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Pengbo Hao
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Xiaokang Fu
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Meng Zhang
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Jianhua Lu
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Liang Ma
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Shuxun Yu
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430000, Hubei, China
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Hengling Wei
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Hantao Wang
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji, 831100, Xinjiang, China
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Magembe EM, Li H, Taheri A, Zhou S, Ghislain M. Identification of T-DNA structure and insertion site in transgenic crops using targeted capture sequencing. FRONTIERS IN PLANT SCIENCE 2023; 14:1156665. [PMID: 37502707 PMCID: PMC10369180 DOI: 10.3389/fpls.2023.1156665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 06/15/2023] [Indexed: 07/29/2023]
Abstract
The commercialization of GE crops requires a rigorous safety assessment, which includes a precise DNA level characterization of inserted T-DNA. In the past, several strategies have been developed for identifying T-DNA insertion sites including, Southern blot and different PCR-based methods. However, these methods are often challenging to scale up for screening of dozens of transgenic events and for crops with complex genomes, like potato. Here, we report using target capture sequencing (TCS) to characterize the T-DNA structure and insertion sites of 34 transgenic events in potato. This T-DNA is an 18 kb fragment between left and right borders and carries three resistance (R) genes (RB, Rpi-blb2 and Rpi-vnt1.1 genes) that result in complete resistance to late blight disease. Using TCS, we obtained a high sequence read coverage within the T-DNA and junction regions. We identified the T-DNA breakpoints on either ends for 85% of the transgenic events. About 74% of the transgenic events had their T-DNA with 3R gene sequences intact. The flanking sequences of the T-DNA were from the potato genome for half of the transgenic events, and about a third (11) of the transgenic events have a single T-DNA insertion mapped into the potato genome, of which five events do not interrupt an existing potato gene. The TCS results were confirmed using PCR and Sanger sequencing for 6 of the best transgenic events representing 20% of the transgenic events suitable for regulatory approval. These results demonstrate the wide applicability of TCS for the precise T-DNA insertion characterization in transgenic crops.
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Affiliation(s)
- Eric Maina Magembe
- Potato Agri-food Systems Program, International Potato Center, Nairobi, Kenya
- Department of Agricultural and Environmental Sciences, College of Agriculture, Tennessee State University, Nashville, TN, United States
| | - Hui Li
- Department of Agricultural and Environmental Sciences, College of Agriculture, Tennessee State University, Nashville, TN, United States
| | - Ali Taheri
- Department of Agricultural and Environmental Sciences, College of Agriculture, Tennessee State University, Nashville, TN, United States
| | - Suping Zhou
- Department of Agricultural and Environmental Sciences, College of Agriculture, Tennessee State University, Nashville, TN, United States
| | - Marc Ghislain
- Potato Agri-food Systems Program, International Potato Center, Nairobi, Kenya
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Peng C, Mei Y, Ding L, Wang X, Chen X, Wang J, Xu J. Using Combined Methods of Genetic Mapping and Nanopore-Based Sequencing Technology to Analyze the Insertion Positions of G10evo-EPSPS and Cry1Ab/Cry2Aj Transgenes in Maize. FRONTIERS IN PLANT SCIENCE 2021; 12:690951. [PMID: 34394143 PMCID: PMC8358107 DOI: 10.3389/fpls.2021.690951] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 06/29/2021] [Indexed: 06/13/2023]
Abstract
The insertion position of the exogenous fragment sequence in a genetically modified organism (GMO) is important for the safety assessment and labeling of GMOs. SK12-5 is a newly developed transgenic maize line transformed with two trait genes [i.e., G10evo-5-enolpyrul-shikimate-3-phosphate synthase (EPSPS) and Cry1Ab/Cry2Aj] that was recently approved for commercial use in China. In this study, we tried to determine the insertion position of the exogenous fragment for SK12-5. The transgene-host left border and right border integration junctions were obtained from SK12-5 genomic DNA by using the thermal asymmetric interlaced polymerase chain reaction (TAIL-PCR) and next-generation Illumina sequencing technology. However, a Basic Local Alignment Search Tool (BLAST) analysis revealed that the flanking sequences in the maize genome are unspecific and that the insertion position is located in a repetitive sequence area in the maize genome. To locate the fine-scale insertion position in SK12-5, we combined the methods of genetic mapping and nanopore-based sequencing technology. From a classical bulked-segregant analysis (BSA), the insertion position in SK12-5 was mapped onto Bin9.03 of chromosome 9 between the simple sequence repeat (SSR) markers umc2337 and umc1743 (26,822,048-100,724,531 bp). The nanopore sequencing results uncovered 10 reads for which one end was mapped onto the vector and the other end was mapped onto the maize genome. These observations indicated that the exogenous T-DNA fragments were putatively integrated at the position from 82,329,568 to 82,379,296 bp of chromosome 9 in the transgenic maize SK12-5. This study is helpful for the safety assessment of the novel transgenic maize SK12-5 and shows that the combined method of genetic mapping and the nanopore-based sequencing technology will be a useful approach for identifying the insertion positions of transgenic sequences in other GM plants with relatively large and complex genomes.
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Affiliation(s)
- Cheng Peng
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Yingting Mei
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lin Ding
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Xiaofu Wang
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Xiaoyun Chen
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Junmin Wang
- Institute of Crops and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Junfeng Xu
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
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Cai YM, Dudley QM, Patron NJ. Measurement of Transgene Copy Number in Plants Using Droplet Digital PCR. Bio Protoc 2021; 11:e4075. [PMID: 34327272 PMCID: PMC8292117 DOI: 10.21769/bioprotoc.4075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 03/25/2021] [Accepted: 03/30/2021] [Indexed: 11/02/2022] Open
Abstract
Transgenic plants are produced both to investigate gene function and to confer desirable traits into crops. Transgene copy number is known to influence expression levels, and consequently, phenotypes. Similarly, knowledge of transgene zygosity is desirable for making quantitative assessments of phenotype and tracking the inheritance of transgenes in progeny generations. Since the first transgenic plants were produced, several methods for determining copy number have been applied, including Southern blotting, quantitative real-time PCR, and more recently, sequencing methods; however, each method has specific disadvantages, compromising throughput, accuracy, or expense. Digital PCR (dPCR) divides reactions into partitions, converting the exponential, analogue nature of PCR into a linear, digital signal that allows the frequency of occurrence of specific sequences to be accurately estimated. Confidence increases with the number of partitions; therefore, the availability of emulsion technologies that enable reactions to be divided into tens of thousands of nanodroplets allows accurate determination of copy number in what has become known as digital droplet PCR (ddPCR). ddPCR offers similar benefits of low costs and scalability as other PCR techniques but with superior accuracy and reliability. Graphic abstract: Digital PCR (dPCR) divides reactions into partitions, converting the exponential, analogue nature of PCR into a linear, digital signal that allows the frequency of transgene copy number to be accurately assessed.
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Affiliation(s)
- Yao-Min Cai
- Earlham Institute, Norwich Research Park, Colney lane, Norwich, UK
| | | | - Nicola J. Patron
- Earlham Institute, Norwich Research Park, Colney lane, Norwich, UK
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Slane D, Lee CH, Kolb M, Dent C, Miao Y, Franz-Wachtel M, Lau S, Maček B, Balasubramanian S, Bayer M, Jürgens G. The integral spliceosomal component CWC15 is required for development in Arabidopsis. Sci Rep 2020; 10:13336. [PMID: 32770129 PMCID: PMC7415139 DOI: 10.1038/s41598-020-70324-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Accepted: 07/27/2020] [Indexed: 01/01/2023] Open
Abstract
Efficient mRNA splicing is a prerequisite for protein biosynthesis and the eukaryotic splicing machinery is evolutionarily conserved among species of various phyla. At its catalytic core resides the activated splicing complex Bact consisting of the three small nuclear ribonucleoprotein complexes (snRNPs) U2, U5 and U6 and the so-called NineTeen complex (NTC) which is important for spliceosomal activation. CWC15 is an integral part of the NTC in humans and it is associated with the NTC in other species. Here we show the ubiquitous expression and developmental importance of the Arabidopsis ortholog of yeast CWC15. CWC15 associates with core components of the Arabidopsis NTC and its loss leads to inefficient splicing. Consistent with the central role of CWC15 in RNA splicing, cwc15 mutants are embryo lethal and additionally display strong defects in the female haploid phase. Interestingly, the haploid male gametophyte or pollen in Arabidopsis, on the other hand, can cope without functional CWC15, suggesting that developing pollen might be more tolerant to CWC15-mediated defects in splicing than either embryo or female gametophyte.
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Affiliation(s)
- Daniel Slane
- Max Planck Institute for Developmental Biology, Cell Biology, 72076, Tübingen, Germany
| | - Cameron H Lee
- Howard Hughes Medical Institute, Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Martina Kolb
- Max Planck Institute for Developmental Biology, Cell Biology, 72076, Tübingen, Germany
| | - Craig Dent
- School of Biological Sciences, Monash University, Clayton Campus, Clayton, VIC, 3800, Australia
| | - Yingjing Miao
- Max Planck Institute for Developmental Biology, Cell Biology, 72076, Tübingen, Germany
| | - Mirita Franz-Wachtel
- Proteome Center Tübingen, University of Tübingen, Auf der Morgenstelle 15, 72076, Tübingen, Germany
| | - Steffen Lau
- Max Planck Institute for Developmental Biology, Cell Biology, 72076, Tübingen, Germany
| | - Boris Maček
- Proteome Center Tübingen, University of Tübingen, Auf der Morgenstelle 15, 72076, Tübingen, Germany
| | | | - Martin Bayer
- Max Planck Institute for Developmental Biology, Cell Biology, 72076, Tübingen, Germany
| | - Gerd Jürgens
- Max Planck Institute for Developmental Biology, Cell Biology, 72076, Tübingen, Germany.
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Li S, Jia S, Hou L, Nguyen H, Sato S, Holding D, Cahoon E, Zhang C, Clemente T, Yu B. Mapping of transgenic alleles in soybean using a nanopore-based sequencing strategy. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:3825-3833. [PMID: 31037287 PMCID: PMC6685662 DOI: 10.1093/jxb/erz202] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 04/15/2019] [Indexed: 05/23/2023]
Abstract
Transgenic technology was developed to introduce transgenes into various organisms to validate gene function and add genetic variations >40 years ago. However, the identification of the transgene insertion position is still challenging in organisms with complex genomes. Here, we report a nanopore-based method to map the insertion position of a Ds transposable element originating in maize in the soybean genome. In this method, an oligo probe is used to capture the DNA fragments containing the Ds element from pooled DNA samples of transgenic soybean plants. The Ds element-enriched DNAs are then sequenced using the MinION-based platform of Nanopore. This method allowed us to rapidly map the Ds insertion positions in 51 transgenic soybean lines through a single sequencing run. This strategy is high throughput, convenient, reliable, and cost-efficient. The transgenic allele mapping protocol can be easily translated to other eukaryotes with complex genomes.
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Affiliation(s)
- Shengjun Li
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, USA
- Qingdao Engineering Research Center of Biomass Resources and Environment, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Shangang Jia
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, USA
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Lili Hou
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, USA
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Hanh Nguyen
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, USA
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Shirley Sato
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, USA
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - David Holding
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, USA
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Edgar Cahoon
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, USA
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Chi Zhang
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Tom Clemente
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, USA
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Bin Yu
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, USA
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Characterization of Plant Genetic Modifications Using Next-Generation Sequencing. Synth Biol (Oxf) 2018. [DOI: 10.1007/978-981-10-8693-9_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
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Salisu IB, Shahid AA, Yaqoob A, Ali Q, Bajwa KS, Rao AQ, Husnain T. Molecular Approaches for High Throughput Detection and Quantification of Genetically Modified Crops: A Review. FRONTIERS IN PLANT SCIENCE 2017; 8:1670. [PMID: 29085378 PMCID: PMC5650622 DOI: 10.3389/fpls.2017.01670] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 09/11/2017] [Indexed: 06/01/2023]
Abstract
As long as the genetically modified crops are gaining attention globally, their proper approval and commercialization need accurate and reliable diagnostic methods for the transgenic content. These diagnostic techniques are mainly divided into two major groups, i.e., identification of transgenic (1) DNA and (2) proteins from GMOs and their products. Conventional methods such as PCR (polymerase chain reaction) and enzyme-linked immunosorbent assay (ELISA) were routinely employed for DNA and protein based quantification respectively. Although, these Techniques (PCR and ELISA) are considered as significantly convenient and productive, but there is need for more advance technologies that allow for high throughput detection and the quantification of GM event as the production of more complex GMO is increasing day by day. Therefore, recent approaches like microarray, capillary gel electrophoresis, digital PCR and next generation sequencing are more promising due to their accuracy and precise detection of transgenic contents. The present article is a brief comparative study of all such detection techniques on the basis of their advent, feasibility, accuracy, and cost effectiveness. However, these emerging technologies have a lot to do with detection of a specific event, contamination of different events and determination of fusion as well as stacked gene protein are the critical issues to be addressed in future.
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Affiliation(s)
- Ibrahim B. Salisu
- Department of Animal Science, Faculty of Agriculture, Federal University Dutse, Jigawa, Nigeria
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Ahmad A. Shahid
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Amina Yaqoob
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Qurban Ali
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
- Institute of Molecular Biology and Biotechnology, University of Lahore, Lahore, Pakistan
| | - Kamran S. Bajwa
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Abdul Q. Rao
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Tayyab Husnain
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
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Veerappan V, Jani M, Kadel K, Troiani T, Gale R, Mayes T, Shulaev E, Wen J, Mysore KS, Azad RK, Dickstein R. Rapid identification of causative insertions underlying Medicago truncatula Tnt1 mutants defective in symbiotic nitrogen fixation from a forward genetic screen by whole genome sequencing. BMC Genomics 2016; 17:141. [PMID: 26920390 PMCID: PMC4769575 DOI: 10.1186/s12864-016-2452-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 02/09/2016] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND In the model legume Medicago truncatula, the near saturation genome-wide Tnt1 insertion mutant population in ecotype R108 is a valuable tool in functional genomics studies. Forward genetic screens have identified many Tnt1 mutants defective in nodule development and symbiotic nitrogen fixation (SNF). However, progress toward identifying the causative mutations of these symbiotic mutants has been slow because of the high copy number of Tnt1 insertions in some mutant plants and inefficient recovery of flanking sequence tags (FSTs) by thermal asymmetric interlaced PCR (TAIL-PCR) and other techniques. RESULTS Two Tnt1 symbiotic mutants, NF11217 and NF10547, with defects in nodulation and SNF were isolated during a forward genetic screen. Both TAIL-PCR and whole genome sequencing (WGS) approaches were used in attempts to find the relevant mutant genes in NF11217 and NF10547. Illumina paired-end WGS generated ~16 Gb of sequence data from a 500 bp insert library for each mutant, yielding ~40X genome coverage. Bioinformatics analysis of the sequence data identified 97 and 65 high confidence independent Tnt1 insertion loci in NF11217 and NF10547, respectively. In comparison to TAIL-PCR, WGS recovered more Tnt1 insertions. From the WGS data, we found Tnt1 insertions in the exons of the previously described PHOSPHOLIPASE C (PLC)-like and NODULE INCEPTION (NIN) genes in NF11217 and NF10547 mutants, respectively. Co-segregation analyses confirmed that the symbiotic phenotypes of NF11217 and NF10547 are tightly linked to the Tnt1 insertions in PLC-like and NIN genes, respectively. CONCLUSIONS In this work, we demonstrate that WGS is an efficient approach for identification of causative genes underlying SNF defective phenotypes in M. truncatula Tnt1 insertion mutants obtained via forward genetic screens.
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Affiliation(s)
- Vijaykumar Veerappan
- Department of Biological Sciences, University of North Texas, 1155 Union Circle #305220, Denton, TX, 76203, USA.
| | - Mehul Jani
- Department of Biological Sciences, University of North Texas, 1155 Union Circle #305220, Denton, TX, 76203, USA.
| | - Khem Kadel
- Department of Biological Sciences, University of North Texas, 1155 Union Circle #305220, Denton, TX, 76203, USA.
| | - Taylor Troiani
- Department of Biological Sciences, University of North Texas, 1155 Union Circle #305220, Denton, TX, 76203, USA.
| | - Ronny Gale
- Department of Biological Sciences, University of North Texas, 1155 Union Circle #305220, Denton, TX, 76203, USA.
| | - Tyler Mayes
- Department of Biological Sciences, University of North Texas, 1155 Union Circle #305220, Denton, TX, 76203, USA.
| | - Elena Shulaev
- Department of Biological Sciences, University of North Texas, 1155 Union Circle #305220, Denton, TX, 76203, USA.
| | - Jiangqi Wen
- Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, OK, 73401, USA.
| | - Kirankumar S Mysore
- Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, OK, 73401, USA.
| | - Rajeev K Azad
- Department of Biological Sciences, University of North Texas, 1155 Union Circle #305220, Denton, TX, 76203, USA. .,Department of Mathematics, University of North Texas, Denton, TX, 76203, USA.
| | - Rebecca Dickstein
- Department of Biological Sciences, University of North Texas, 1155 Union Circle #305220, Denton, TX, 76203, USA.
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Veerappan V, Jani M, Kadel K, Troiani T, Gale R, Mayes T, Shulaev E, Wen J, Mysore KS, Azad RK, Dickstein R. Rapid identification of causative insertions underlying Medicago truncatula Tnt1 mutants defective in symbiotic nitrogen fixation from a forward genetic screen by whole genome sequencing. BMC Genomics 2016. [PMID: 26920390 DOI: 10.1186/s12864-12016-12452-12865] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/05/2023] Open
Abstract
BACKGROUND In the model legume Medicago truncatula, the near saturation genome-wide Tnt1 insertion mutant population in ecotype R108 is a valuable tool in functional genomics studies. Forward genetic screens have identified many Tnt1 mutants defective in nodule development and symbiotic nitrogen fixation (SNF). However, progress toward identifying the causative mutations of these symbiotic mutants has been slow because of the high copy number of Tnt1 insertions in some mutant plants and inefficient recovery of flanking sequence tags (FSTs) by thermal asymmetric interlaced PCR (TAIL-PCR) and other techniques. RESULTS Two Tnt1 symbiotic mutants, NF11217 and NF10547, with defects in nodulation and SNF were isolated during a forward genetic screen. Both TAIL-PCR and whole genome sequencing (WGS) approaches were used in attempts to find the relevant mutant genes in NF11217 and NF10547. Illumina paired-end WGS generated ~16 Gb of sequence data from a 500 bp insert library for each mutant, yielding ~40X genome coverage. Bioinformatics analysis of the sequence data identified 97 and 65 high confidence independent Tnt1 insertion loci in NF11217 and NF10547, respectively. In comparison to TAIL-PCR, WGS recovered more Tnt1 insertions. From the WGS data, we found Tnt1 insertions in the exons of the previously described PHOSPHOLIPASE C (PLC)-like and NODULE INCEPTION (NIN) genes in NF11217 and NF10547 mutants, respectively. Co-segregation analyses confirmed that the symbiotic phenotypes of NF11217 and NF10547 are tightly linked to the Tnt1 insertions in PLC-like and NIN genes, respectively. CONCLUSIONS In this work, we demonstrate that WGS is an efficient approach for identification of causative genes underlying SNF defective phenotypes in M. truncatula Tnt1 insertion mutants obtained via forward genetic screens.
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Affiliation(s)
- Vijaykumar Veerappan
- Department of Biological Sciences, University of North Texas, 1155 Union Circle #305220, Denton, TX, 76203, USA.
| | - Mehul Jani
- Department of Biological Sciences, University of North Texas, 1155 Union Circle #305220, Denton, TX, 76203, USA.
| | - Khem Kadel
- Department of Biological Sciences, University of North Texas, 1155 Union Circle #305220, Denton, TX, 76203, USA.
| | - Taylor Troiani
- Department of Biological Sciences, University of North Texas, 1155 Union Circle #305220, Denton, TX, 76203, USA.
| | - Ronny Gale
- Department of Biological Sciences, University of North Texas, 1155 Union Circle #305220, Denton, TX, 76203, USA.
| | - Tyler Mayes
- Department of Biological Sciences, University of North Texas, 1155 Union Circle #305220, Denton, TX, 76203, USA.
| | - Elena Shulaev
- Department of Biological Sciences, University of North Texas, 1155 Union Circle #305220, Denton, TX, 76203, USA.
| | - Jiangqi Wen
- Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, OK, 73401, USA.
| | - Kirankumar S Mysore
- Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, OK, 73401, USA.
| | - Rajeev K Azad
- Department of Biological Sciences, University of North Texas, 1155 Union Circle #305220, Denton, TX, 76203, USA. .,Department of Mathematics, University of North Texas, Denton, TX, 76203, USA.
| | - Rebecca Dickstein
- Department of Biological Sciences, University of North Texas, 1155 Union Circle #305220, Denton, TX, 76203, USA.
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11
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Polko JK, van Rooij JA, Vanneste S, Pierik R, Ammerlaan AMH, Vergeer-van Eijk MH, McLoughlin F, Gühl K, Van Isterdael G, Voesenek LACJ, Millenaar FF, Beeckman T, Peeters AJM, Marée AFM, van Zanten M. Ethylene-Mediated Regulation of A2-Type CYCLINs Modulates Hyponastic Growth in Arabidopsis. PLANT PHYSIOLOGY 2015; 169:194-208. [PMID: 26041787 PMCID: PMC4577382 DOI: 10.1104/pp.15.00343] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 06/02/2015] [Indexed: 05/06/2023]
Abstract
Upward leaf movement (hyponastic growth) is frequently observed in response to changing environmental conditions and can be induced by the phytohormone ethylene. Hyponasty results from differential growth (i.e. enhanced cell elongation at the proximal abaxial side of the petiole relative to the adaxial side). Here, we characterize Enhanced Hyponasty-d, an activation-tagged Arabidopsis (Arabidopsis thaliana) line with exaggerated hyponasty. This phenotype is associated with overexpression of the mitotic cyclin CYCLINA2;1 (CYCA2;1), which hints at a role for cell divisions in regulating hyponasty. Indeed, mathematical analysis suggested that the observed changes in abaxial cell elongation rates during ethylene treatment should result in a larger hyponastic amplitude than observed, unless a decrease in cell proliferation rate at the proximal abaxial side of the petiole relative to the adaxial side was implemented. Our model predicts that when this differential proliferation mechanism is disrupted by either ectopic overexpression or mutation of CYCA2;1, the hyponastic growth response becomes exaggerated. This is in accordance with experimental observations on CYCA2;1 overexpression lines and cyca2;1 knockouts. We therefore propose a bipartite mechanism controlling leaf movement: ethylene induces longitudinal cell expansion in the abaxial petiole epidermis to induce hyponasty and simultaneously affects its amplitude by controlling cell proliferation through CYCA2;1. Further corroborating the model, we found that ethylene treatment results in transcriptional down-regulation of A2-type CYCLINs and propose that this, and possibly other regulatory mechanisms affecting CYCA2;1, may contribute to this attenuation of hyponastic growth.
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Affiliation(s)
- Joanna K Polko
- Plant Ecophysiology, Institute of Environmental Biology (J.K.P., R.P., A.M.H.A., M.H.V.-v.E., F.M., K.G., L.A.C.J.V., F.F.M., A.J.M.P., M.v.Z.), and Theoretical Biology and Bioinformatics (J.A.v.R.), Utrecht University, 3584 CH Utrecht, The Netherlands;Computational and Systems Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom (J.A.v.R., A.F.M.M.);Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium (S.V., G.V.I., T.B.); andDepartment of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (S.V., G.V.I., T.B.)
| | - Jop A van Rooij
- Plant Ecophysiology, Institute of Environmental Biology (J.K.P., R.P., A.M.H.A., M.H.V.-v.E., F.M., K.G., L.A.C.J.V., F.F.M., A.J.M.P., M.v.Z.), and Theoretical Biology and Bioinformatics (J.A.v.R.), Utrecht University, 3584 CH Utrecht, The Netherlands;Computational and Systems Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom (J.A.v.R., A.F.M.M.);Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium (S.V., G.V.I., T.B.); andDepartment of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (S.V., G.V.I., T.B.)
| | - Steffen Vanneste
- Plant Ecophysiology, Institute of Environmental Biology (J.K.P., R.P., A.M.H.A., M.H.V.-v.E., F.M., K.G., L.A.C.J.V., F.F.M., A.J.M.P., M.v.Z.), and Theoretical Biology and Bioinformatics (J.A.v.R.), Utrecht University, 3584 CH Utrecht, The Netherlands;Computational and Systems Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom (J.A.v.R., A.F.M.M.);Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium (S.V., G.V.I., T.B.); andDepartment of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (S.V., G.V.I., T.B.)
| | - Ronald Pierik
- Plant Ecophysiology, Institute of Environmental Biology (J.K.P., R.P., A.M.H.A., M.H.V.-v.E., F.M., K.G., L.A.C.J.V., F.F.M., A.J.M.P., M.v.Z.), and Theoretical Biology and Bioinformatics (J.A.v.R.), Utrecht University, 3584 CH Utrecht, The Netherlands;Computational and Systems Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom (J.A.v.R., A.F.M.M.);Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium (S.V., G.V.I., T.B.); andDepartment of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (S.V., G.V.I., T.B.)
| | - Ankie M H Ammerlaan
- Plant Ecophysiology, Institute of Environmental Biology (J.K.P., R.P., A.M.H.A., M.H.V.-v.E., F.M., K.G., L.A.C.J.V., F.F.M., A.J.M.P., M.v.Z.), and Theoretical Biology and Bioinformatics (J.A.v.R.), Utrecht University, 3584 CH Utrecht, The Netherlands;Computational and Systems Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom (J.A.v.R., A.F.M.M.);Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium (S.V., G.V.I., T.B.); andDepartment of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (S.V., G.V.I., T.B.)
| | - Marleen H Vergeer-van Eijk
- Plant Ecophysiology, Institute of Environmental Biology (J.K.P., R.P., A.M.H.A., M.H.V.-v.E., F.M., K.G., L.A.C.J.V., F.F.M., A.J.M.P., M.v.Z.), and Theoretical Biology and Bioinformatics (J.A.v.R.), Utrecht University, 3584 CH Utrecht, The Netherlands;Computational and Systems Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom (J.A.v.R., A.F.M.M.);Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium (S.V., G.V.I., T.B.); andDepartment of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (S.V., G.V.I., T.B.)
| | - Fionn McLoughlin
- Plant Ecophysiology, Institute of Environmental Biology (J.K.P., R.P., A.M.H.A., M.H.V.-v.E., F.M., K.G., L.A.C.J.V., F.F.M., A.J.M.P., M.v.Z.), and Theoretical Biology and Bioinformatics (J.A.v.R.), Utrecht University, 3584 CH Utrecht, The Netherlands;Computational and Systems Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom (J.A.v.R., A.F.M.M.);Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium (S.V., G.V.I., T.B.); andDepartment of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (S.V., G.V.I., T.B.)
| | - Kerstin Gühl
- Plant Ecophysiology, Institute of Environmental Biology (J.K.P., R.P., A.M.H.A., M.H.V.-v.E., F.M., K.G., L.A.C.J.V., F.F.M., A.J.M.P., M.v.Z.), and Theoretical Biology and Bioinformatics (J.A.v.R.), Utrecht University, 3584 CH Utrecht, The Netherlands;Computational and Systems Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom (J.A.v.R., A.F.M.M.);Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium (S.V., G.V.I., T.B.); andDepartment of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (S.V., G.V.I., T.B.)
| | - Gert Van Isterdael
- Plant Ecophysiology, Institute of Environmental Biology (J.K.P., R.P., A.M.H.A., M.H.V.-v.E., F.M., K.G., L.A.C.J.V., F.F.M., A.J.M.P., M.v.Z.), and Theoretical Biology and Bioinformatics (J.A.v.R.), Utrecht University, 3584 CH Utrecht, The Netherlands;Computational and Systems Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom (J.A.v.R., A.F.M.M.);Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium (S.V., G.V.I., T.B.); andDepartment of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (S.V., G.V.I., T.B.)
| | - Laurentius A C J Voesenek
- Plant Ecophysiology, Institute of Environmental Biology (J.K.P., R.P., A.M.H.A., M.H.V.-v.E., F.M., K.G., L.A.C.J.V., F.F.M., A.J.M.P., M.v.Z.), and Theoretical Biology and Bioinformatics (J.A.v.R.), Utrecht University, 3584 CH Utrecht, The Netherlands;Computational and Systems Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom (J.A.v.R., A.F.M.M.);Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium (S.V., G.V.I., T.B.); andDepartment of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (S.V., G.V.I., T.B.)
| | - Frank F Millenaar
- Plant Ecophysiology, Institute of Environmental Biology (J.K.P., R.P., A.M.H.A., M.H.V.-v.E., F.M., K.G., L.A.C.J.V., F.F.M., A.J.M.P., M.v.Z.), and Theoretical Biology and Bioinformatics (J.A.v.R.), Utrecht University, 3584 CH Utrecht, The Netherlands;Computational and Systems Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom (J.A.v.R., A.F.M.M.);Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium (S.V., G.V.I., T.B.); andDepartment of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (S.V., G.V.I., T.B.)
| | - Tom Beeckman
- Plant Ecophysiology, Institute of Environmental Biology (J.K.P., R.P., A.M.H.A., M.H.V.-v.E., F.M., K.G., L.A.C.J.V., F.F.M., A.J.M.P., M.v.Z.), and Theoretical Biology and Bioinformatics (J.A.v.R.), Utrecht University, 3584 CH Utrecht, The Netherlands;Computational and Systems Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom (J.A.v.R., A.F.M.M.);Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium (S.V., G.V.I., T.B.); andDepartment of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (S.V., G.V.I., T.B.)
| | - Anton J M Peeters
- Plant Ecophysiology, Institute of Environmental Biology (J.K.P., R.P., A.M.H.A., M.H.V.-v.E., F.M., K.G., L.A.C.J.V., F.F.M., A.J.M.P., M.v.Z.), and Theoretical Biology and Bioinformatics (J.A.v.R.), Utrecht University, 3584 CH Utrecht, The Netherlands;Computational and Systems Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom (J.A.v.R., A.F.M.M.);Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium (S.V., G.V.I., T.B.); andDepartment of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (S.V., G.V.I., T.B.)
| | - Athanasius F M Marée
- Plant Ecophysiology, Institute of Environmental Biology (J.K.P., R.P., A.M.H.A., M.H.V.-v.E., F.M., K.G., L.A.C.J.V., F.F.M., A.J.M.P., M.v.Z.), and Theoretical Biology and Bioinformatics (J.A.v.R.), Utrecht University, 3584 CH Utrecht, The Netherlands;Computational and Systems Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom (J.A.v.R., A.F.M.M.);Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium (S.V., G.V.I., T.B.); andDepartment of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (S.V., G.V.I., T.B.)
| | - Martijn van Zanten
- Plant Ecophysiology, Institute of Environmental Biology (J.K.P., R.P., A.M.H.A., M.H.V.-v.E., F.M., K.G., L.A.C.J.V., F.F.M., A.J.M.P., M.v.Z.), and Theoretical Biology and Bioinformatics (J.A.v.R.), Utrecht University, 3584 CH Utrecht, The Netherlands;Computational and Systems Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom (J.A.v.R., A.F.M.M.);Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium (S.V., G.V.I., T.B.); andDepartment of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (S.V., G.V.I., T.B.)
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12
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Fitzgerald TL, Powell JJ, Schneebeli K, Hsia MM, Gardiner DM, Bragg JN, McIntyre CL, Manners JM, Ayliffe M, Watt M, Vogel JP, Henry RJ, Kazan K. Brachypodium as an emerging model for cereal-pathogen interactions. ANNALS OF BOTANY 2015; 115:717-31. [PMID: 25808446 PMCID: PMC4373291 DOI: 10.1093/aob/mcv010] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Revised: 11/03/2014] [Accepted: 12/22/2014] [Indexed: 05/22/2023]
Abstract
BACKGROUND Cereal diseases cause tens of billions of dollars of losses annually and have devastating humanitarian consequences in the developing world. Increased understanding of the molecular basis of cereal host-pathogen interactions should facilitate development of novel resistance strategies. However, achieving this in most cereals can be challenging due to large and complex genomes, long generation times and large plant size, as well as quarantine and intellectual property issues that may constrain the development and use of community resources. Brachypodium distachyon (brachypodium) with its small, diploid and sequenced genome, short generation time, high transformability and rapidly expanding community resources is emerging as a tractable cereal model. SCOPE Recent research reviewed here has demonstrated that brachypodium is either susceptible or partially susceptible to many of the major cereal pathogens. Thus, the study of brachypodium-pathogen interactions appears to hold great potential to improve understanding of cereal disease resistance, and to guide approaches to enhance this resistance. This paper reviews brachypodium experimental pathosystems for the study of fungal, bacterial and viral cereal pathogens; the current status of the use of brachypodium for functional analysis of cereal disease resistance; and comparative genomic approaches undertaken using brachypodium to assist characterization of cereal resistance genes. Additionally, it explores future prospects for brachypodium as a model to study cereal-pathogen interactions. CONCLUSIONS The study of brachypodium-pathogen interactions appears to be a productive strategy for understanding mechanisms of disease resistance in cereal species. Knowledge obtained from this model interaction has strong potential to be exploited for crop improvement.
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Affiliation(s)
- Timothy L Fitzgerald
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture Flagship, Brisbane, QLD 4067, Australia, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072, Australia, Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture Flagship, Canberra, ACT 2601, Australia, United States Department of Agriculture Agricultural Research Service (USDA-ARS), Western Regional Research Center (WRRC), Albany, CA 94710, USA, Department of Plant and Microbial Biology, University of California, Berkeley, CA 94710, USA and Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Jonathan J Powell
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture Flagship, Brisbane, QLD 4067, Australia, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072, Australia, Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture Flagship, Canberra, ACT 2601, Australia, United States Department of Agriculture Agricultural Research Service (USDA-ARS), Western Regional Research Center (WRRC), Albany, CA 94710, USA, Department of Plant and Microbial Biology, University of California, Berkeley, CA 94710, USA and Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture Flagship, Brisbane, QLD 4067, Australia, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072, Australia, Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture Flagship, Canberra, ACT 2601, Australia, United States Department of Agriculture Agricultural Research Service (USDA-ARS), Western Regional Research Center (WRRC), Albany, CA 94710, USA, Department of Plant and Microbial Biology, University of California, Berkeley, CA 94710, USA and Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Katharina Schneebeli
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture Flagship, Brisbane, QLD 4067, Australia, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072, Australia, Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture Flagship, Canberra, ACT 2601, Australia, United States Department of Agriculture Agricultural Research Service (USDA-ARS), Western Regional Research Center (WRRC), Albany, CA 94710, USA, Department of Plant and Microbial Biology, University of California, Berkeley, CA 94710, USA and Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - M Mandy Hsia
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture Flagship, Brisbane, QLD 4067, Australia, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072, Australia, Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture Flagship, Canberra, ACT 2601, Australia, United States Department of Agriculture Agricultural Research Service (USDA-ARS), Western Regional Research Center (WRRC), Albany, CA 94710, USA, Department of Plant and Microbial Biology, University of California, Berkeley, CA 94710, USA and Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Donald M Gardiner
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture Flagship, Brisbane, QLD 4067, Australia, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072, Australia, Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture Flagship, Canberra, ACT 2601, Australia, United States Department of Agriculture Agricultural Research Service (USDA-ARS), Western Regional Research Center (WRRC), Albany, CA 94710, USA, Department of Plant and Microbial Biology, University of California, Berkeley, CA 94710, USA and Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Jennifer N Bragg
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture Flagship, Brisbane, QLD 4067, Australia, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072, Australia, Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture Flagship, Canberra, ACT 2601, Australia, United States Department of Agriculture Agricultural Research Service (USDA-ARS), Western Regional Research Center (WRRC), Albany, CA 94710, USA, Department of Plant and Microbial Biology, University of California, Berkeley, CA 94710, USA and Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture Flagship, Brisbane, QLD 4067, Australia, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072, Australia, Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture Flagship, Canberra, ACT 2601, Australia, United States Department of Agriculture Agricultural Research Service (USDA-ARS), Western Regional Research Center (WRRC), Albany, CA 94710, USA, Department of Plant and Microbial Biology, University of California, Berkeley, CA 94710, USA and Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - C Lynne McIntyre
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture Flagship, Brisbane, QLD 4067, Australia, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072, Australia, Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture Flagship, Canberra, ACT 2601, Australia, United States Department of Agriculture Agricultural Research Service (USDA-ARS), Western Regional Research Center (WRRC), Albany, CA 94710, USA, Department of Plant and Microbial Biology, University of California, Berkeley, CA 94710, USA and Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - John M Manners
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture Flagship, Brisbane, QLD 4067, Australia, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072, Australia, Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture Flagship, Canberra, ACT 2601, Australia, United States Department of Agriculture Agricultural Research Service (USDA-ARS), Western Regional Research Center (WRRC), Albany, CA 94710, USA, Department of Plant and Microbial Biology, University of California, Berkeley, CA 94710, USA and Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Mick Ayliffe
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture Flagship, Brisbane, QLD 4067, Australia, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072, Australia, Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture Flagship, Canberra, ACT 2601, Australia, United States Department of Agriculture Agricultural Research Service (USDA-ARS), Western Regional Research Center (WRRC), Albany, CA 94710, USA, Department of Plant and Microbial Biology, University of California, Berkeley, CA 94710, USA and Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Michelle Watt
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture Flagship, Brisbane, QLD 4067, Australia, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072, Australia, Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture Flagship, Canberra, ACT 2601, Australia, United States Department of Agriculture Agricultural Research Service (USDA-ARS), Western Regional Research Center (WRRC), Albany, CA 94710, USA, Department of Plant and Microbial Biology, University of California, Berkeley, CA 94710, USA and Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - John P Vogel
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture Flagship, Brisbane, QLD 4067, Australia, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072, Australia, Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture Flagship, Canberra, ACT 2601, Australia, United States Department of Agriculture Agricultural Research Service (USDA-ARS), Western Regional Research Center (WRRC), Albany, CA 94710, USA, Department of Plant and Microbial Biology, University of California, Berkeley, CA 94710, USA and Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Robert J Henry
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture Flagship, Brisbane, QLD 4067, Australia, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072, Australia, Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture Flagship, Canberra, ACT 2601, Australia, United States Department of Agriculture Agricultural Research Service (USDA-ARS), Western Regional Research Center (WRRC), Albany, CA 94710, USA, Department of Plant and Microbial Biology, University of California, Berkeley, CA 94710, USA and Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Kemal Kazan
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture Flagship, Brisbane, QLD 4067, Australia, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072, Australia, Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture Flagship, Canberra, ACT 2601, Australia, United States Department of Agriculture Agricultural Research Service (USDA-ARS), Western Regional Research Center (WRRC), Albany, CA 94710, USA, Department of Plant and Microbial Biology, University of California, Berkeley, CA 94710, USA and Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture Flagship, Brisbane, QLD 4067, Australia, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072, Australia, Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture Flagship, Canberra, ACT 2601, Australia, United States Department of Agriculture Agricultural Research Service (USDA-ARS), Western Regional Research Center (WRRC), Albany, CA 94710, USA, Department of Plant and Microbial Biology, University of California, Berkeley, CA 94710, USA and Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
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13
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Wilson-Sánchez D, Rubio-Díaz S, Muñoz-Viana R, Pérez-Pérez JM, Jover-Gil S, Ponce MR, Micol JL. Leaf phenomics: a systematic reverse genetic screen for Arabidopsis leaf mutants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 79:878-91. [PMID: 24946828 DOI: 10.1111/tpj.12595] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Revised: 06/07/2014] [Accepted: 06/09/2014] [Indexed: 05/10/2023]
Abstract
The study and eventual manipulation of leaf development in plants requires a thorough understanding of the genetic basis of leaf organogenesis. Forward genetic screens have identified hundreds of Arabidopsis mutants with altered leaf development, but the genome has not yet been saturated. To identify genes required for leaf development we are screening the Arabidopsis Salk Unimutant collection. We have identified 608 lines that exhibit a leaf phenotype with full penetrance and almost constant expressivity and 98 additional lines with segregating mutant phenotypes. To allow indexing and integration with other mutants, the mutant phenotypes were described using a custom leaf phenotype ontology. We found that the indexed mutation is present in the annotated locus for 78% of the 553 mutants genotyped, and that in half of these the annotated T-DNA is responsible for the phenotype. To quickly map non-annotated T-DNA insertions, we developed a reliable, cost-effective and easy method based on whole-genome sequencing. To enable comprehensive access to our data, we implemented a public web application named PhenoLeaf (http://genetics.umh.es/phenoleaf) that allows researchers to query the results of our screen, including text and visual phenotype information. We demonstrated how this new resource can facilitate gene function discovery by identifying and characterizing At1g77600, which we found to be required for proximal-distal cell cycle-driven leaf growth, and At3g62870, which encodes a ribosomal protein needed for cell proliferation and chloroplast function. This collection provides a valuable tool for the study of leaf development, characterization of biomass feedstocks and examination of other traits in this fundamental photosynthetic organ.
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Affiliation(s)
- David Wilson-Sánchez
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202, Elche, Spain
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14
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Milavec M, Dobnik D, Yang L, Zhang D, Gruden K, Zel J. GMO quantification: valuable experience and insights for the future. Anal Bioanal Chem 2014; 406:6485-97. [PMID: 25182968 DOI: 10.1007/s00216-014-8077-0] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Revised: 07/23/2014] [Accepted: 07/28/2014] [Indexed: 11/30/2022]
Abstract
Cultivation and marketing of genetically modified organisms (GMOs) have been unevenly adopted worldwide. To facilitate international trade and to provide information to consumers, labelling requirements have been set up in many countries. Quantitative real-time polymerase chain reaction (qPCR) is currently the method of choice for detection, identification and quantification of GMOs. This has been critically assessed and the requirements for the method performance have been set. Nevertheless, there are challenges that should still be highlighted, such as measuring the quantity and quality of DNA, and determining the qPCR efficiency, possible sequence mismatches, characteristics of taxon-specific genes and appropriate units of measurement, as these remain potential sources of measurement uncertainty. To overcome these problems and to cope with the continuous increase in the number and variety of GMOs, new approaches are needed. Statistical strategies of quantification have already been proposed and expanded with the development of digital PCR. The first attempts have been made to use new generation sequencing also for quantitative purposes, although accurate quantification of the contents of GMOs using this technology is still a challenge for the future, and especially for mixed samples. New approaches are needed also for the quantification of stacks, and for potential quantification of organisms produced by new plant breeding techniques.
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Affiliation(s)
- Mojca Milavec
- Department of Biotechnology and Systems Biology, National Institute of Biology (NIB), Večna pot 111, 1000, Ljubljana, Slovenia,
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15
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Arai-Kichise Y, Shiwa Y, Ebana K, Shibata-Hatta M, Yoshikawa H, Yano M, Wakasa K. Genome-wide DNA polymorphisms in seven rice cultivars of temperate and tropical japonica groups. PLoS One 2014; 9:e86312. [PMID: 24466017 PMCID: PMC3897683 DOI: 10.1371/journal.pone.0086312] [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: 07/05/2013] [Accepted: 12/09/2013] [Indexed: 01/04/2023] Open
Abstract
Elucidation of the rice genome is expected to broaden our understanding of genes related to the agronomic characteristics and the genetic relationship among cultivars. In this study, we conducted whole-genome sequencings of 6 cultivars, including 5 temperate japonica cultivars and 1 tropical japonica cultivar (Moroberekan), by using next-generation sequencing (NGS) with Nipponbare genome as a reference. The temperate japonica cultivars contained 2 sake brewing (Yamadanishiki and Gohyakumangoku), 1 landrace (Kameji), and 2 modern cultivars (Koshihikari and Norin 8). Almost >83% of the whole genome sequences of the Nipponbare genome could be covered by sequenced short-reads of each cultivar, including Omachi, which has previously been reported to be a temperate japonica cultivar. Numerous single nucleotide polymorphisms (SNPs), insertions, and deletions were detected among the various cultivars and the Nipponbare genomes. Comparison of SNPs detected in each cultivar suggested that Moroberekan had 5-fold more SNPs than the temperate japonica cultivars. Success of the 2 approaches to improve the efficacy of sequence data by using NGS revealed that sequencing depth was directly related to sequencing coverage of coding DNA sequences: in excess of 30× genome sequencing was required to cover approximately 80% of the genes in the rice genome. Further, the contigs prepared using the assembly of unmapped reads could increase the value of NGS short-reads and, consequently, cover previously unavailable sequences. These approaches facilitated the identification of new genes in coding DNA sequences and the increase of mapping efficiency in different regions. The DNA polymorphism information between the 7 cultivars and Nipponbare are available at NGRC_Rices_Build1.0 (http://www.nodai-genome.org/oryza_sativa_en.html).
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Affiliation(s)
- Yuko Arai-Kichise
- Genome Research Center, NODAI Research Institute, Tokyo University of Agriculture, Setagaya, Tokyo, Japan
- * E-mail:
| | - Yuh Shiwa
- Genome Research Center, NODAI Research Institute, Tokyo University of Agriculture, Setagaya, Tokyo, Japan
| | - Kaworu Ebana
- Genetic Resources Center, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan
| | - Mari Shibata-Hatta
- Genome Research Center, NODAI Research Institute, Tokyo University of Agriculture, Setagaya, Tokyo, Japan
| | - Hirofumi Yoshikawa
- Genome Research Center, NODAI Research Institute, Tokyo University of Agriculture, Setagaya, Tokyo, Japan
- Department of Bioscience, Tokyo University of Agriculture, Tokyo, Japan
| | - Masahiro Yano
- Agrogenomics Research Center, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan
| | - Kyo Wakasa
- Genome Research Center, NODAI Research Institute, Tokyo University of Agriculture, Setagaya, Tokyo, Japan
- Department of Bioscience, Tokyo University of Agriculture, Tokyo, Japan
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16
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Time- and cost-efficient identification of T-DNA insertion sites through targeted genomic sequencing. PLoS One 2013; 8:e70912. [PMID: 23951038 PMCID: PMC3741346 DOI: 10.1371/journal.pone.0070912] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Accepted: 06/24/2013] [Indexed: 12/13/2022] Open
Abstract
Forward genetic screens enable the unbiased identification of genes involved in biological processes. In Arabidopsis, several mutant collections are publicly available, which greatly facilitates such practice. Most of these collections were generated by agrotransformation of a T-DNA at random sites in the plant genome. However, precise mapping of T-DNA insertion sites in mutants isolated from such screens is a laborious and time-consuming task. Here we report a simple, low-cost and time efficient approach to precisely map T-DNA insertions simultaneously in many different mutants. By combining sequence capture, next-generation sequencing and 2D-PCR pooling, we developed a new method that allowed the rapid localization of T-DNA insertion sites in 55 out of 64 mutant plants isolated in a screen for gyrase inhibition hypersensitivity.
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17
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Polko JK, Pierik R, van Zanten M, Tarkowská D, Strnad M, Voesenek LACJ, Peeters AJM. Ethylene promotes hyponastic growth through interaction with ROTUNDIFOLIA3/CYP90C1 in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2013; 64:613-24. [PMID: 23264517 PMCID: PMC3542051 DOI: 10.1093/jxb/ers356] [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] [Indexed: 05/20/2023]
Abstract
Upward leaf movement, called hyponastic growth, is employed by plants to cope with adverse environmental conditions. Ethylene is a key regulator of this process and, in Arabidopsis thaliana, hyponasty is induced by this phytohormone via promotion of epidermal cell expansion in a proximal zone of the abaxial side of the petiole. ROTUNDIFOLIA3/CYP90C1 encodes an enzyme which was shown to catalyse C-23 hydroxylation of several brassinosteroids (BRs) - phytohormones involved in, for example, organ growth, cell expansion, cell division, and responses to abiotic and biotic stresses. This study tested the interaction between ethylene and BRs in regulating hyponastic growth. A mutant isolated in a forward genetic screen, with reduced hyponastic response to ethylene treatment, was allelic to rot3. The cause of the reduced hyponastic growth in this mutant was examined by studying ethylene-BR interaction during local cell expansion, pharmacological inhibition of BR synthesis and ethylene effects on transcription of BR-related genes. This work demonstrates that rot3 mutants are impaired in local cell expansion driving hyponasty. Moreover, the inhibition of BR biosynthesis reduces ethylene-induced hyponastic growth and ethylene increases sensitivity to BR in promoting cell elongation in Arabidopsis hypocotyls. Together, the results show that ROT3 modulates ethylene-induced petiole movement and that this function is likely BR related.
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Affiliation(s)
- Joanna K. Polko
- Plant Ecophysiology, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Ronald Pierik
- Plant Ecophysiology, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Martijn van Zanten
- Plant Ecophysiology, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
- Molecular Plant Physiology, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Danuše Tarkowská
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany AS CR, v.v.i., Šlechtitelů 11, CZ-783 71 Olomouc, Czech Republic
| | - Miroslav Strnad
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany AS CR, v.v.i., Šlechtitelů 11, CZ-783 71 Olomouc, Czech Republic
- Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 21, CZ-783 71 Olomouc, Czech Republic
| | - Laurentius A. C. J. Voesenek
- Plant Ecophysiology, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Anton J. M. Peeters
- Plant Ecophysiology, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
- Institute of Education, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
- * To whom correspondence should be addressed. E-mail:
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18
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Chang Y, Long T, Wu C. Effort and contribution of T-DNA Insertion mutant library for rice functional genomics research in China: review and perspective. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2012; 54:953-966. [PMID: 23020748 DOI: 10.1111/j.1744-7909.2012.01171.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
With the completion of the rice (Oryza sativa L.) genome-sequencing project, the rice research community proposed to characterize the function of every predicted gene in rice by 2020. One of the most effective and high-throughput strategies for studying gene function is to employ genetic mutations induced by insertion elements such as T-DNA or transposons. Since 1999, with support from the Ministry of Science and Technology of China for Rice Functional Genomics Programs, large-scale T-DNA insertion mutant populations have been generated in Huazhong Agricultural University, the Chinese Academy of Sciences and the Chinese Academy of Agricultural Sciences. Currently, a total of 372,346 mutant lines have been generated, and 58,226 T-DNA or Tos17 flanking sequence tags have been isolated. Using these mutant resources, more than 40 genes with potential applications in rice breeding have already been identified. These include genes involved in biotic or abiotic stress responses, nutrient metabolism, pollen development, and plant architecture. The functional analysis of these genes will not only deepen our understanding of the fundamental biological questions in rice, but will also offer valuable gene resources for developing Green Super Rice that is high-yielding with few inputs even under the poor growth conditions of many regions of Africa and Asia.
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Affiliation(s)
- Yuxiao Chang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research-Wuhan, Huazhong Agricultural University, Wuhan 430070, China
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