1
|
M. T. APL, Ramchander S, K. K. K, Muthamilarasan M, Pillai MA. Assessment of efficacy of mutagenesis of gamma-irradiation in plant height and days to maturity through expression analysis in rice. PLoS One 2021; 16:e0245603. [PMID: 33449977 PMCID: PMC7810314 DOI: 10.1371/journal.pone.0245603] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 01/04/2021] [Indexed: 12/19/2022] Open
Abstract
Introduction of semi-dwarfism and early maturity in rice cultivars is important to achieve improved plant architecture, lodging resistance and high yield. Gamma rays induced mutations are routinely used to achieve these traits. We report the development of a semi-dwarf, early maturing and high-yielding mutant of rice cultivar ‘Improved White Ponni’, a popular cosmopolitan variety in south India preferred for its superior grain quality traits. Through gamma rays induced mutagenesis, several mutants were developed and subjected to selection up to six generations (M6) until the superior mutants were stabilized. In the M6 generation, significant reduction in days to flowering (up to 11.81% reduction) and plant height (up to 40% reduction) combined with an increase in single plant yield (up to 45.73% increase) was observed in the mutant population. The cooking quality traits viz., linear elongation ratio, breadthwise expansion ratio, gel consistency and gelatinization temperature of the mutants were similar to the parent variety Improved White Ponni. The genetic characterization with SSR markers showed variability between the semi-dwarf-early mutants and the Improved White Ponni. Gibberellin responsiveness study and quantitative real-time PCR showed a faulty gibberellin pathway and epistatic control between the genes such as OsKOL4 and OsBRD2 causing semi-dwarfism in a mutant. These mutants have potential as new rice varieties and can be used as new sources of semi-dwarfism and earliness for improving high grain quality rice varieties.
Collapse
Affiliation(s)
- Andrew-Peter-Leon M. T.
- Department of Plant Breeding and Genetics, Agricultural College and Research Institute, Tamil Nadu Agricultural University, Killikulam, Tuticorin, Tamil Nadu, India
| | - S. Ramchander
- Visiting Scientist (SERB–National Post-Doctoral Fellow), IRRI-South Asia Hub, ICRISAT, Patancheru, Hyderabad, India
| | - Kumar K. K.
- Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | | | - M. Arumugam Pillai
- Department of Plant Breeding and Genetics, Agricultural College and Research Institute, Tamil Nadu Agricultural University, Killikulam, Tuticorin, Tamil Nadu, India
- * E-mail:
| |
Collapse
|
2
|
Rutter MT, Murren CJ, Callahan HS, Bisner AM, Leebens-Mack J, Wolyniak MJ, Strand AE. Distributed phenomics with the unPAK project reveals the effects of mutations. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 100:199-211. [PMID: 31155775 DOI: 10.1111/tpj.14427] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 05/01/2019] [Accepted: 05/10/2019] [Indexed: 06/09/2023]
Abstract
Determining how genes are associated with traits in plants and other organisms is a major challenge in modern biology. The unPAK project - undergraduates phenotyping Arabidopsis knockouts - has generated phenotype data for thousands of non-lethal insertion mutation lines within a single Arabidopsis thaliana genomic background. The focal phenotypes examined by unPAK are complex macroscopic fitness-related traits, which have ecological, evolutionary and agricultural importance. These phenotypes are placed in the context of the wild-type and also natural accessions (phytometers), and standardized for environmental differences between assays. Data from the unPAK project are used to describe broad patterns in the phenotypic consequences of insertion mutation, and to identify individual mutant lines with distinct phenotypes as candidates for further study. Inclusion of undergraduate researchers is at the core of unPAK activities, and an important broader impact of the project is providing students an opportunity to obtain research experience.
Collapse
Affiliation(s)
- Matthew T Rutter
- Department of Biology, College of Charleston, 66 George Street, Charleston, SC, 29424, USA
| | - Courtney J Murren
- Department of Biology, College of Charleston, 66 George Street, Charleston, SC, 29424, USA
| | - Hilary S Callahan
- Department of Biology, Barnard College, 3009 Broadway, New York, NY, 10027, USA
| | - April M Bisner
- Department of Biology, College of Charleston, 66 George Street, Charleston, SC, 29424, USA
| | - Jim Leebens-Mack
- Department of Plant Biology, University of Georgia, 120 Carlton St, Athens, GA, 30602, USA
| | | | - Allan E Strand
- Department of Biology, College of Charleston, 66 George Street, Charleston, SC, 29424, USA
| |
Collapse
|
3
|
An effective strategy to establish a male sterility mutant mini-library by CRISPR/Cas9-mediated knockout of anther-specific genes in rice. J Genet Genomics 2019; 46:273-275. [DOI: 10.1016/j.jgg.2019.03.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 03/17/2019] [Indexed: 02/02/2023]
|
4
|
Anupama A, Bhugra S, Lall B, Chaudhury S, Chugh A. Assessing the correlation of genotypic and phenotypic responses of indica rice varieties under drought stress. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2018; 127:343-354. [PMID: 29655154 DOI: 10.1016/j.plaphy.2018.04.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 04/03/2018] [Indexed: 06/08/2023]
Abstract
Drought is one of the severe abiotic stress that affects the productivity of rice, an important staple crop that is consumed all over the world. The traits responsible for enhancing or adapting drought resistance in rice plants can be selected and studied to improve their growth under stress conditions. Experiments have been conducted on indica rice varieties comprising Sahabhagidhan as drought tolerant variety and IR64, MTU1010 categorized as drought sensitive varieties. Various root related biochemical and morphological traits such as root length, relative water content (RWC), xylem number, xylem area, proline content, and malondialdehyde content have been investigated for a comparative study of the plant response to drought stress in different rice varieties. The results of differential root transcriptome analysis have revealed that there is a notable difference in gene expression of OsPIP2;5 and OsNIP2;1 in various indica varieties of rice at different time periods of stress. The present work aims at assessing the correlation between genotypic and phenotypic traits that can contribute towards the emerging field of rice phenomics.
Collapse
Affiliation(s)
- Anupama Anupama
- Kusuma School of Biological Sciences, Indian Institute of Technology, Delhi, New Delhi 110016, India.
| | - Swati Bhugra
- Department of Electrical Engineering, Indian Institute of Technology, Delhi, New Delhi 110016, India.
| | - Brejesh Lall
- Department of Electrical Engineering, Indian Institute of Technology, Delhi, New Delhi 110016, India.
| | - Santanu Chaudhury
- Department of Electrical Engineering, Indian Institute of Technology, Delhi, New Delhi 110016, India.
| | - Archana Chugh
- Kusuma School of Biological Sciences, Indian Institute of Technology, Delhi, New Delhi 110016, India.
| |
Collapse
|
5
|
Wu HP, Wei FJ, Wu CC, Lo SF, Chen LJ, Fan MJ, Chen S, Wen IC, Yu SM, Ho THD, Lai MH, Hsing YIC. Large-scale phenomics analysis of a T-DNA tagged mutant population. Gigascience 2018; 6:1-7. [PMID: 28854617 PMCID: PMC5570018 DOI: 10.1093/gigascience/gix055] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 07/04/2017] [Indexed: 01/26/2023] Open
Abstract
Rice, Oryza sativa L., is one of the most important crops in the world. With the rising world population, feeding people in a more sustainable and environmentally friendly way becomes increasingly important. Therefore, the rice research community needs to share resources to better understand the functions of rice genes that are the foundation for future agricultural biotechnology development, and one way to achieve this goal is via the extensive study of insertional mutants. We have constructed a large rice insertional mutant population in a japonica rice variety, Tainung 67. The collection contains about 93 000 mutant lines, among them 85% with phenomics data and 65% with flanking sequence data. We screened the phenotypes of 12 individual plants for each line grown under field conditions according to 68 subcategories and 3 quantitative traits. Both phenotypes and integration sites are searchable in the Taiwan Rice Insertional Mutants Database. Detailed analyses of phenomics data, T-DNA flanking sequences, and whole-genome sequencing data for rice insertional mutants can lead to the discovery of novel genes. In addition, studies of mutant phenotypes can reveal relationships among varieties, cultivation locations, and cropping seasons.
Collapse
Affiliation(s)
- Hshin-Ping Wu
- Institute of Plant and Microbial Biology, Academia Sinica, 128, Section 2, Yien-chu-yuan Road, Nankang, Taipei 115, Taiwan
| | - Fu-Jin Wei
- Institute of Plant and Microbial Biology, Academia Sinica, 128, Section 2, Yien-chu-yuan Road, Nankang, Taipei 115, Taiwan
| | - Cheng-Chieh Wu
- Institute of Plant and Microbial Biology, Academia Sinica, 128, Section 2, Yien-chu-yuan Road, Nankang, Taipei 115, Taiwan.,Institute of Plant Biology, National Taiwan University, 1, Section 4, Roosevelt Road, Taipei 106, Taiwan
| | - Shuen-Fang Lo
- Institute of Molecular Biology, Academia Sinica, 128, Section 2, Yien-chu-yuan Road, Nankang, Taipei 115, Taiwan.,Agricultural Biotechnology Center, National Chung Hsing University, 145, Xingda Road, Taichung 402, Taiwan
| | - Liang-Jwu Chen
- Institute of Molecular Biology, National Chung Hsing University, 145, Xingda Road, Taichung 402, Taiwan
| | - Ming-Jen Fan
- Department of Biotechnology, Asia University, 500, Lioufeng Road, Taichung 413, Taiwan
| | - Shu Chen
- Plant Germplasm Division, Taiwan Agricultural Research Institute, 189, Zhongzheng Road, Taichung 413, Taiwan
| | - Ien-Chie Wen
- Plant Germplasm Division, Taiwan Agricultural Research Institute, 189, Zhongzheng Road, Taichung 413, Taiwan
| | - Su-May Yu
- Institute of Molecular Biology, Academia Sinica, 128, Section 2, Yien-chu-yuan Road, Nankang, Taipei 115, Taiwan.,Agricultural Biotechnology Center, National Chung Hsing University, 145, Xingda Road, Taichung 402, Taiwan.,Department of Life Sciences, National Chung Hsing University, 145, Xingda Road, Taichung 402, Taiwan
| | - Tuan-Hua David Ho
- Institute of Plant and Microbial Biology, Academia Sinica, 128, Section 2, Yien-chu-yuan Road, Nankang, Taipei 115, Taiwan.,Agricultural Biotechnology Center, National Chung Hsing University, 145, Xingda Road, Taichung 402, Taiwan.,Department of Life Sciences, National Chung Hsing University, 145, Xingda Road, Taichung 402, Taiwan
| | - Ming-Hsin Lai
- Crop Science Division, Taiwan Agricultural Research Institute, 189, Zhongzheng Road, Taichung 413, Taiwan
| | - Yue-Ie C Hsing
- Institute of Plant and Microbial Biology, Academia Sinica, 128, Section 2, Yien-chu-yuan Road, Nankang, Taipei 115, Taiwan.,Department of Agronomy, National Taiwan University, 1, Section 4, Roosevelt Road, Taipei 106, Taiwan
| |
Collapse
|
6
|
Hinrichs M, Fleck AT, Biedermann E, Ngo NS, Schreiber L, Schenk MK. An ABC Transporter Is Involved in the Silicon-Induced Formation of Casparian Bands in the Exodermis of Rice. FRONTIERS IN PLANT SCIENCE 2017; 8:671. [PMID: 28503184 PMCID: PMC5408559 DOI: 10.3389/fpls.2017.00671] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 04/12/2017] [Indexed: 05/18/2023]
Abstract
Silicon (Si) promotes the formation of Casparian bands (CB) in rice and reduces radial oxygen loss (ROL). Further transcriptomic approaches revealed several candidate genes involved in the Si-induced formation of CB such as ATP binding cassette (ABC) transporter, Class III peroxidases, ligases and transferases. Investigation of these genes by means of overexpression (OE) and knockout (KO) mutants revealed the contribution of the ABC transporter (OsABCG25) to CB formation in the exodermis, which was also reflected in the expression of other OsABCG25 in the Si-promoted formation of CB genes related to the phenylpropanoid pathway, such as phenylalanine-ammonia-lyase, diacylglycerol O-acyltransferase and 4-coumarate-CoA ligase. Differential CB development in mutants and Si supply also affected the barrier function of the exodermis. OE of the ABC transporter and Si supply reduced the ROL from roots and Fe uptake. No effect on ROL and Fe uptake could be observed for the KO mutant. The presented research confirms the impact of the OsABCG25 in the Si-promoted formation of CB and its barrier functions.
Collapse
Affiliation(s)
- Martin Hinrichs
- Institute of Plant Nutrition, Faculty of Natural Science, Leibniz Universität HannoverHannover, Germany
- *Correspondence: Martin Hinrichs,
| | - Alexander T. Fleck
- Institute of Plant Nutrition, Faculty of Natural Science, Leibniz Universität HannoverHannover, Germany
| | - Eline Biedermann
- Institute of Plant Nutrition, Faculty of Natural Science, Leibniz Universität HannoverHannover, Germany
| | - Ngoc S. Ngo
- Institute of Plant Nutrition, Faculty of Natural Science, Leibniz Universität HannoverHannover, Germany
| | - Lukas Schreiber
- Institute of Cellular and Molecular Botany, Department of Ecophysiology, University of BonnBonn, Germany
| | - Manfred K. Schenk
- Institute of Plant Nutrition, Faculty of Natural Science, Leibniz Universität HannoverHannover, Germany
| |
Collapse
|
7
|
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.
Collapse
Affiliation(s)
| | - Hiroaki Ichikawa
- Institute of Agrobiological Sciences, National Agriculture and Food Research OrganizationTsukuba, Japan
| |
Collapse
|
8
|
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.
Collapse
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
| |
Collapse
|
9
|
Wei FJ, Tsai YC, Hsu YM, Chen YA, Huang CT, Wu HP, Huang LT, Lai MH, Kuang LY, Lo SF, Yu SM, Lin YR, Hsing YIC. Lack of Genotype and Phenotype Correlation in a Rice T-DNA Tagged Line Is Likely Caused by Introgression in the Seed Source. PLoS One 2016; 11:e0155768. [PMID: 27186981 PMCID: PMC4871347 DOI: 10.1371/journal.pone.0155768] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 05/03/2016] [Indexed: 01/12/2023] Open
Abstract
Rice (Oryza sativa) is one of the most important crops in the world. Several rice insertional mutant libraries are publicly available for systematic analysis of gene functions. However, the tagging efficiency of these mutant resources-the relationship between genotype and phenotype-is very low. We used whole-genome sequencing to analyze a T-DNA-tagged transformant from the Taiwan Rice Insertional Mutants (TRIM) resource. The phenomics records for M0028590, one of the TRIM lines, revealed three phenotypes-wild type, large grains, and tillering dwarf-in the 12 T1 plants. Using the sequencing data for 7 plants from three generations of this specific line, we demonstrate that introgression from an indica rice variety might occur in one generation before the seed was used for callus generation and transformation of this line. In addition, the large-grain trait came from the GS3 gene of the introgressed region and the tillering dwarf phenotype came from a single nucleotide change in the D17 gene that occurred during the callus induction to regeneration of the transformant. As well, another regenerant showed completely heterozygous single-nucleotide polymorphisms across the whole genome. In addition to the known sequence changes such as T-DNA integration, single nucleotide polymorphism, insertion, deletion, chromosome rearrangement and doubling, spontaneous outcrossing occurred in the rice field may also explain some mutated traits in a tagged mutant population. Thus, the co-segregation of an integration event and the phenotype should be checked when using these mutant populations.
Collapse
Affiliation(s)
- Fu-Jin Wei
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
- Department of Agronomy, National Taiwan University, Taipei, Taiwan
| | - Yuan-Ching Tsai
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Yu-Ming Hsu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Yu-An Chen
- Department of Agronomy, National Taiwan University, Taipei, Taiwan
| | - Ching-Ting Huang
- Department of Agronomy, National Taiwan University, Taipei, Taiwan
| | - Hshin-Ping Wu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Lin-Tzu Huang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Ming-Hsin Lai
- Crop Science Division, Taiwan Agriculture Research Institute, Taichung, Taiwan
| | - Lin-Yun Kuang
- Transgenic Plant Core Facility, Academia Sinica, Taipei, Taiwan
| | - Shuen-Fang Lo
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Su-May Yu
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Yann-Rong Lin
- Department of Agronomy, National Taiwan University, Taipei, Taiwan
| | - Yue-Ie Caroline Hsing
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
- Department of Agronomy, National Taiwan University, Taipei, Taiwan
- * E-mail:
| |
Collapse
|
10
|
Lo SF, Fan MJ, Hsing YI, Chen LJ, Chen S, Wen IC, Liu YL, Chen KT, Jiang MJ, Lin MK, Rao MY, Yu LC, Ho THD, Yu SM. Genetic resources offer efficient tools for rice functional genomics research. PLANT, CELL & ENVIRONMENT 2016; 39:998-1013. [PMID: 26301381 DOI: 10.1111/pce.12632] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Revised: 08/13/2015] [Accepted: 08/16/2015] [Indexed: 05/07/2023]
Abstract
Rice is an important crop and major model plant for monocot functional genomics studies. With the establishment of various genetic resources for rice genomics, the next challenge is to systematically assign functions to predicted genes in the rice genome. Compared with the robustness of genome sequencing and bioinformatics techniques, progress in understanding the function of rice genes has lagged, hampering the utilization of rice genes for cereal crop improvement. The use of transfer DNA (T-DNA) insertional mutagenesis offers the advantage of uniform distribution throughout the rice genome, but preferentially in gene-rich regions, resulting in direct gene knockout or activation of genes within 20-30 kb up- and downstream of the T-DNA insertion site and high gene tagging efficiency. Here, we summarize the recent progress in functional genomics using the T-DNA-tagged rice mutant population. We also discuss important features of T-DNA activation- and knockout-tagging and promoter-trapping of the rice genome in relation to mutant and candidate gene characterizations and how to more efficiently utilize rice mutant populations and datasets for high-throughput functional genomics and phenomics studies by forward and reverse genetics approaches. These studies may facilitate the translation of rice functional genomics research to improvements of rice and other cereal crops.
Collapse
Affiliation(s)
- Shuen-Fang Lo
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, 115, Taiwan, ROC
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung, 402, Taiwan, ROC
| | - Ming-Jen Fan
- Department of Biotechnology, Asia University, Lioufeng Road, Wufeng, Taichung, 413, Taiwan, ROC
| | - Yue-Ie Hsing
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 115, Taiwan, ROC
| | - Liang-Jwu Chen
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung, 402, Taiwan, ROC
- Institute of Molecular Biology, National Chung Hsing University, Taichung, 402, Taiwan, ROC
| | - Shu Chen
- Plant Germplasm Division, Taiwan Agricultural Research Institute, Wufeng, Taichung, 413, Taiwan, ROC
| | - Ien-Chie Wen
- Plant Germplasm Division, Taiwan Agricultural Research Institute, Wufeng, Taichung, 413, Taiwan, ROC
| | - Yi-Lun Liu
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, 115, Taiwan, ROC
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung, 402, Taiwan, ROC
| | - Ku-Ting Chen
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, 115, Taiwan, ROC
| | - Mirng-Jier Jiang
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, 115, Taiwan, ROC
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung, 402, Taiwan, ROC
| | - Ming-Kuang Lin
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, 115, Taiwan, ROC
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung, 402, Taiwan, ROC
| | - Meng-Yen Rao
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, 115, Taiwan, ROC
| | - Lin-Chih Yu
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, 115, Taiwan, ROC
| | - Tuan-Hua David Ho
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung, 402, Taiwan, ROC
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 115, Taiwan, ROC
- Department of Life Sciences, National Chung Hsing University, Taichung, 402, Taiwan, ROC
| | - Su-May Yu
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, 115, Taiwan, ROC
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung, 402, Taiwan, ROC
- Department of Life Sciences, National Chung Hsing University, Taichung, 402, Taiwan, ROC
| |
Collapse
|
11
|
Wei FJ, Kuang LY, Oung HM, Cheng SY, Wu HP, Huang LT, Tseng YT, Chiou WY, Hsieh-Feng V, Chung CH, Yu SM, Lee LY, Gelvin SB, Hsing YIC. Somaclonal variation does not preclude the use of rice transformants for genetic screening. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 85:648-59. [PMID: 26833589 DOI: 10.1111/tpj.13132] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 12/21/2015] [Accepted: 01/20/2016] [Indexed: 05/07/2023]
Abstract
Rice (Oryza sativa) is one of the world's most important crops. Rice researchers make extensive use of insertional mutants for the study of gene function. Approximately half a million flanking sequence tags from rice insertional mutant libraries are publicly available. However, the relationship between genotype and phenotype is very weak. Transgenic plant assays have been used frequently for complementation, overexpression or antisense analysis, but sequence changes caused by callus growth, Agrobacterium incubation medium, virulence genes, transformation and selection conditions are unknown. We used high-throughput sequencing of DNA from rice lines derived from Tainung 67 to analyze non-transformed and transgenic rice plants for mutations caused by these parameters. For comparison, we also analyzed sequence changes for two additional rice varieties and four T-DNA tagged transformants from the Taiwan Rice Insertional Mutant resource. We identified single-nucleotide polymorphisms, small indels, large deletions, chromosome doubling and chromosome translocations in these lines. Using standard rice regeneration/transformation procedures, the mutation rates of regenerants and transformants were relatively low, with no significant differences among eight tested treatments in the Tainung 67 background and in the cultivars Taikeng 9 and IR64. Thus, we could not conclusively detect sequence changes resulting from Agrobacterium-mediated transformation in addition to those caused by tissue culture-induced somaclonal variation. However, the mutation frequencies within the two publically available tagged mutant populations, including TRIM transformants or Tos17 lines, were about 10-fold higher than the frequency of standard transformants, probably because mass production of embryogenic calli and longer callus growth periods were required to generate these large libraries.
Collapse
Affiliation(s)
- Fu-Jin Wei
- Institute of Plant and Microbial Biology, Academia Sinica, No. 128, Section 2, Yien-Chu-Yuan Road, Taipei, 11529, Taiwan
- Department of Agronomy, National Taiwan University, No. 1, Section 4, Roosevelt Rd, Taipei, 10617, Taiwan
| | - Lin-Yun Kuang
- Transgenic Plant Core Facility, Academia Sinica, No. 128, Section 2, Yien-Chu-Yuan Road, Taipei, 11529, Taiwan
| | - Hui-Min Oung
- Institute of Plant and Microbial Biology, Academia Sinica, No. 128, Section 2, Yien-Chu-Yuan Road, Taipei, 11529, Taiwan
| | - Sin-Yuan Cheng
- Institute of Plant and Microbial Biology, Academia Sinica, No. 128, Section 2, Yien-Chu-Yuan Road, Taipei, 11529, Taiwan
| | - Hshin-Ping Wu
- Institute of Plant and Microbial Biology, Academia Sinica, No. 128, Section 2, Yien-Chu-Yuan Road, Taipei, 11529, Taiwan
| | - Lin-Tzu Huang
- Institute of Plant and Microbial Biology, Academia Sinica, No. 128, Section 2, Yien-Chu-Yuan Road, Taipei, 11529, Taiwan
| | - Yi-Tzu Tseng
- Institute of Plant and Microbial Biology, Academia Sinica, No. 128, Section 2, Yien-Chu-Yuan Road, Taipei, 11529, Taiwan
- Institute of Plant Biology, National Taiwan University, No. 1, Section 4, Roosevelt Rd, Taipei, 10617, Taiwan
| | - Wan-Yi Chiou
- Institute of Plant and Microbial Biology, Academia Sinica, No. 128, Section 2, Yien-Chu-Yuan Road, Taipei, 11529, Taiwan
| | - Vicki Hsieh-Feng
- Department of Agronomy, National Taiwan University, No. 1, Section 4, Roosevelt Rd, Taipei, 10617, Taiwan
| | - Cheng-Han Chung
- Institute of Plant and Microbial Biology, Academia Sinica, No. 128, Section 2, Yien-Chu-Yuan Road, Taipei, 11529, Taiwan
| | - Su-May Yu
- Institute of Molecular Biology, Academia Sinica, No. 128, Section 2, Yien-Chu-Yuan Road, Taipei, 11529, Taiwan
| | - Lan-Ying Lee
- Department of Biological Sciences, Purdue University, 201 South University St., West Lafayette, IN, 47907-1392, USA
| | - Stanton B Gelvin
- Department of Biological Sciences, Purdue University, 201 South University St., West Lafayette, IN, 47907-1392, USA
| | - Yue-Ie C Hsing
- Institute of Plant and Microbial Biology, Academia Sinica, No. 128, Section 2, Yien-Chu-Yuan Road, Taipei, 11529, Taiwan
| |
Collapse
|
12
|
Köhl K, Gremmels J. A software tool for the input and management of phenotypic data using personal digital assistants and other mobile devices. PLANT METHODS 2015; 11:25. [PMID: 25866550 PMCID: PMC4393613 DOI: 10.1186/s13007-015-0069-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 03/19/2015] [Indexed: 05/29/2023]
Abstract
BACKGROUND Plant breeding and genetics demand fast, exact and reproducible phenotyping. Efficient statistical evaluation of phenotyping data requires standardised data storage ensuring long-term data availability while maintaining intellectual property rights. This is state of the art at phenomics centres, which, however, are unavailable for most scientists. For them we developed a simple and cost-efficient system, the Phenotyper, which employs mobile devices or personal digital assistants (PDA) for on-site data entry and open-source software for data management. RESULTS A graphical user interface (GUI) on a PDA replaces paper-based form sheet and data entry on a desktop. The user can define his phenotyping schemes in a web tool without in-depth knowledge of the system and thus adjust it more easily to new research aspects than in a classical laboratory information management system (LIMS). In the Phenotyper, schemes are built from controlled vocabulary gained from published ontologies. Vocabulary and schemes are stored in a database that also manages the user access. From the web page, schemes are downloaded as extended markup language (XML) files for the transfer to the PDA and the exchange between users. On the PDA, the GUI displays the schemes and stores data in comma separated value format and XML format. After manual quality control, data are uploaded via a web page to an independently hosted results database, in which data are stored in an entity-attribute-value structure to provide maximum flexibility. Datasets are linked to the original and curated data files stored on a file server. The ownership stamp, project affiliation and date stamp of a dataset are used to regulate data access, which is restricted to data belonging to the user or to his projects and data, for which the embargo period has ended. By export of standardised ASCII reports to long-term data storage facility, long-term accessibility allows searching, citing and use of raw data beyond the lifetime of the database. The Phenotyper is available to the scientific community for use and further development. CONCLUSIONS The Phenotyper provides a well-structured, but flexible data acquisition and management structure for mobile on-site measurements for efficient evaluation and shared use of data.
Collapse
Affiliation(s)
- Karin Köhl
- Max-Planck-Institute of Molecular Plant Physiology, 14424 Potsdam-Golm, Germany
| | - Jürgen Gremmels
- Max-Planck-Institute of Molecular Plant Physiology, 14424 Potsdam-Golm, Germany
| |
Collapse
|
13
|
Schnell J, Steele M, Bean J, Neuspiel M, Girard C, Dormann N, Pearson C, Savoie A, Bourbonnière L, Macdonald P. A comparative analysis of insertional effects in genetically engineered plants: considerations for pre-market assessments. Transgenic Res 2014; 24:1-17. [PMID: 25344849 PMCID: PMC4274372 DOI: 10.1007/s11248-014-9843-7] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Accepted: 10/16/2014] [Indexed: 01/20/2023]
Abstract
During genetic engineering, DNA is inserted into a plant’s genome, and such insertions are often accompanied by the insertion of additional DNA, deletions and/or rearrangements. These genetic changes are collectively known as insertional effects, and they have the potential to give rise to unintended traits in plants. In addition, there are many other genetic changes that occur in plants both spontaneously and as a result of conventional breeding practices. Genetic changes similar to insertional effects occur in plants, namely as a result of the movement of transposable elements, the repair of double-strand breaks by non-homologous end-joining, and the intracellular transfer of organelle DNA. Based on this similarity, insertional effects should present a similar level of risk as these other genetic changes in plants, and it is within the context of these genetic changes that insertional effects must be considered. Increased familiarity with genetic engineering techniques and advances in molecular analysis techniques have provided us with a greater understanding of the nature and impact of genetic changes in plants, and this can be used to refine pre-market assessments of genetically engineered plants and food and feeds derived from genetically engineered plants.
Collapse
Affiliation(s)
- Jaimie Schnell
- Plant and Biotechnology Risk Assessment Unit, Canadian Food Inspection Agency, 1400 Merivale Road, Ottawa, ON, K1A 0Y9, Canada,
| | | | | | | | | | | | | | | | | | | |
Collapse
|
14
|
A review of imaging techniques for plant phenotyping. SENSORS 2014; 14:20078-111. [PMID: 25347588 PMCID: PMC4279472 DOI: 10.3390/s141120078] [Citation(s) in RCA: 360] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Revised: 10/09/2014] [Accepted: 10/10/2014] [Indexed: 11/29/2022]
Abstract
Given the rapid development of plant genomic technologies, a lack of access to plant phenotyping capabilities limits our ability to dissect the genetics of quantitative traits. Effective, high-throughput phenotyping platforms have recently been developed to solve this problem. In high-throughput phenotyping platforms, a variety of imaging methodologies are being used to collect data for quantitative studies of complex traits related to the growth, yield and adaptation to biotic or abiotic stress (disease, insects, drought and salinity). These imaging techniques include visible imaging (machine vision), imaging spectroscopy (multispectral and hyperspectral remote sensing), thermal infrared imaging, fluorescence imaging, 3D imaging and tomographic imaging (MRT, PET and CT). This paper presents a brief review on these imaging techniques and their applications in plant phenotyping. The features used to apply these imaging techniques to plant phenotyping are described and discussed in this review.
Collapse
|
15
|
Feldman AB, Murchie EH, Leung H, Baraoidan M, Coe R, Yu SM, Lo SF, Quick WP. Increasing leaf vein density by mutagenesis: laying the foundations for C4 rice. PLoS One 2014; 9:e94947. [PMID: 24760084 PMCID: PMC3997395 DOI: 10.1371/journal.pone.0094947] [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: 11/22/2013] [Accepted: 03/21/2014] [Indexed: 11/24/2022] Open
Abstract
A high leaf vein density is both an essential feature of C4 photosynthesis and a foundation trait to C4 evolution, ensuring the optimal proportion and proximity of mesophyll and bundle sheath cells for permitting the rapid exchange of photosynthates. Two rice mutant populations, a deletion mutant library with a cv. IR64 background (12,470 lines) and a T-DNA insertion mutant library with a cv. Tainung 67 background (10,830 lines), were screened for increases in vein density. A high throughput method with handheld microscopes was developed and its accuracy was supported by more rigorous microscopy analysis. Eight lines with significantly increased leaf vein densities were identified to be used as genetic stock for the global C4 Rice Consortium. The candidate population was shown to include both shared and independent mutations and so more than one gene controlled the high vein density phenotype. The high vein density trait was found to be linked to a narrow leaf width trait but the linkage was incomplete. The more genetically robust narrow leaf width trait was proposed to be used as a reliable phenotypic marker for finding high vein density variants in rice in future screens.
Collapse
Affiliation(s)
- Aryo B. Feldman
- School of Biosciences, University of Nottingham Malaysia Campus, Semenyih, Selangor Darul Ehsan, Malaysia
| | - Erik H. Murchie
- School of Biosciences, University of Nottingham Sutton Bonington Campus, Sutton Bonington, Leicestershire, United Kingdom
- * E-mail:
| | - Hei Leung
- Plant Breeding, Genetics and Biotechnology, the International Rice Research Institute, Los Baños, Philippines
| | - Marietta Baraoidan
- Plant Breeding, Genetics and Biotechnology, the International Rice Research Institute, Los Baños, Philippines
| | - Robert Coe
- The C4 Rice Center, the International Rice Research Institute, Los Baños, Philippines
| | - Su-May Yu
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, Taiwan
| | - Shuen-Fang Lo
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, Taiwan
| | - William P. Quick
- The C4 Rice Center, the International Rice Research Institute, Los Baños, Philippines
| |
Collapse
|
16
|
Wei FJ, Droc G, Guiderdoni E, Hsing YIC. International Consortium of Rice Mutagenesis: resources and beyond. RICE (NEW YORK, N.Y.) 2013; 6:39. [PMID: 24341871 PMCID: PMC3946042 DOI: 10.1186/1939-8433-6-39] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Accepted: 12/04/2013] [Indexed: 05/20/2023]
Abstract
Rice is one of the most important crops in the world. The rice community needs to cooperate and share efforts and resources so that we can understand the functions of rice genes, especially those with a role in important agronomical traits, for application in agricultural production. Mutation is a major source of genetic variation that can be used for studying gene function. We will present here the status of mutant collections affected in a random manner by physical/chemical and insertion mutageneses.As of early September 2013, a total of 447, 919 flanking sequence tags from rice mutant libraries with T-DNA, Ac/Ds, En/Spm, Tos17, nDART/aDART insertions have been collected and publicly available. From these, 336,262 sequences are precisely positioned on the japonica rice chromosomes, and 67.5% are in gene interval. We discuss the genome coverage and preference of the insertion, issues limiting the exchange and use of the current collections, as well as new and improved resources. We propose a call to renew all mutant populations as soon as possible. We also suggest that a common web portal should be established for ordering seeds.
Collapse
Affiliation(s)
- Fu-Jin Wei
- Institute of Plant and Microbial Biology, Academia Sinica, Hsing: Rm312, IPMB, Academia Sinica, Nankang District, Taipei 11529 Taiwan
| | - Gaëtan Droc
- CIRAD, Centre de coopération Internationale en Recherche Agronomique pour le Développement, Cirad - av. Agropolis -TA A-108/03, 34398 Montpellier Cedex 5, France
| | - Emmanuel Guiderdoni
- CIRAD, Centre de coopération Internationale en Recherche Agronomique pour le Développement, Cirad - av. Agropolis -TA A-108/03, 34398 Montpellier Cedex 5, France
| | - Yue-ie C Hsing
- Institute of Plant and Microbial Biology, Academia Sinica, Hsing: Rm312, IPMB, Academia Sinica, Nankang District, Taipei 11529 Taiwan
| |
Collapse
|
17
|
Kim SL, Choi M, Jung KH, An G. Analysis of the early-flowering mechanisms and generation of T-DNA tagging lines in Kitaake, a model rice cultivar. JOURNAL OF EXPERIMENTAL BOTANY 2013; 64:4169-82. [PMID: 23966593 PMCID: PMC3808308 DOI: 10.1093/jxb/ert226] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
As an extremely early flowering cultivar, rice cultivar Kitaake is a suitable model system for molecular studies. Expression analyses revealed that transcript levels of the flowering repressor Ghd7 were decreased while those of its downstream genes, Ehd1, Hd3a, and RFT1, were increased. Sequencing the known flowering-regulator genes revealed mutations in Ghd7 and OsPRR37 that cause early translation termination and amino acid substitutions, respectively. Genetic analysis of F2 progeny from a cross between cv. Kitaake and cv. Dongjin indicated that those mutations additively contribute to the early-flowering phenotype in cv. Kitaake. Because the short life cycle facilitates genetics research, this study generated 10 000 T-DNA tagging lines and deduced 6758 flanking sequence tags (FSTs), in which 3122 were genic and 3636 were intergenic. Among the genic lines, 367 (11.8%) were inserted into new genes that were not previously tagged. Because the lines were generated by T-DNA that contained the promoterless GUS reporter gene, which had an intron with triple splicing donors/acceptors in the right border region, a high efficiency of GUS expression was shown in various organs. Sequencing of the GUS-positive lines demonstrated that the third splicing donor and the first splicing acceptor of the vector were extensively used. The FST data have now been released into the public domain for seed distribution and facilitation of rice research.
Collapse
Affiliation(s)
- Song Lim Kim
- Crop Biotech Institute, Kyung Hee University, Yongin 446-701, Korea
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 790-784, Korea
| | - Minkyung Choi
- Crop Biotech Institute, Kyung Hee University, Yongin 446-701, Korea
- Department of Plant Molecular Systems Biotechnology, Kyung Hee University, Yongin 446-701, Korea
| | - Ki-Hong Jung
- Crop Biotech Institute, Kyung Hee University, Yongin 446-701, Korea
- Department of Plant Molecular Systems Biotechnology, Kyung Hee University, Yongin 446-701, Korea
| | - Gynheung An
- Crop Biotech Institute, Kyung Hee University, Yongin 446-701, Korea
- Department of Plant Molecular Systems Biotechnology, Kyung Hee University, Yongin 446-701, Korea
| |
Collapse
|
18
|
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.
Collapse
Affiliation(s)
- Nili Wang
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China
| | | | | | | | | | | |
Collapse
|
19
|
Yamamoto E, Yonemaru JI, Yamamoto T, Yano M. OGRO: The Overview of functionally characterized Genes in Rice online database. ACTA ACUST UNITED AC 2012; 5:26. [PMID: 27234245 PMCID: PMC5520837 DOI: 10.1186/1939-8433-5-26] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Accepted: 09/13/2012] [Indexed: 12/14/2022]
Abstract
Background The high-quality sequence information and rich bioinformatics tools available for rice have contributed to remarkable advances in functional genomics. To facilitate the application of gene function information to the study of natural variation in rice, we comprehensively searched for articles related to rice functional genomics and extracted information on functionally characterized genes. Results As of 31 March 2012, 702 functionally characterized genes were annotated. This number represents about 1.6% of the predicted loci in the Rice Annotation Project Database. The compiled gene information is organized to facilitate direct comparisons with quantitative trait locus (QTL) information in the Q-TARO database. Comparison of genomic locations between functionally characterized genes and the QTLs revealed that QTL clusters were often co-localized with high-density gene regions, and that the genes associated with the QTLs in these clusters were different genes, suggesting that these QTL clusters are likely to be explained by tightly linked but distinct genes. Information on the functionally characterized genes compiled during this study is now available in the O verview of Functionally Characterized G enes in R ice O nline database (OGRO) on the Q-TARO website (http://qtaro.abr.affrc.go.jp/ogro). The database has two interfaces: a table containing gene information, and a genome viewer that allows users to compare the locations of QTLs and functionally characterized genes. Conclusions OGRO on Q-TARO will facilitate a candidate-gene approach to identifying the genes responsible for QTLs. Because the QTL descriptions in Q-TARO contain information on agronomic traits, such comparisons will also facilitate the annotation of functionally characterized genes in terms of their effects on traits important for rice breeding. The increasing amount of information on rice gene function being generated from mutant panels and other types of studies will make the OGRO database even more valuable in the future. Electronic supplementary material The online version of this article (doi:10.1186/1939-8433-5-26) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Eiji Yamamoto
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan
| | - Jun-Ichi Yonemaru
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan.
| | - Toshio Yamamoto
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan
| | - Masahiro Yano
- National Institute of Agrobiological Sciences, 1-2 Ohwashi, Tsukuba, Ibaraki, 305-8634, Japan
| |
Collapse
|
20
|
Lorieux M, Blein M, Lozano J, Bouniol M, Droc G, Diévart A, Périn C, Mieulet D, Lanau N, Bès M, Rouvière C, Gay C, Piffanelli P, Larmande P, Michel C, Barnola I, Biderre-Petit C, Sallaud C, Perez P, Bourgis F, Ghesquière A, Gantet P, Tohme J, Morel JB, Guiderdoni E. In-depth molecular and phenotypic characterization in a rice insertion line library facilitates gene identification through reverse and forward genetics approaches. PLANT BIOTECHNOLOGY JOURNAL 2012; 10:555-68. [PMID: 22369597 DOI: 10.1111/j.1467-7652.2012.00689.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
We report here the molecular and phenotypic features of a library of 31,562 insertion lines generated in the model japonica cultivar Nipponbare of rice (Oryza sativa L.), called Oryza Tag Line (OTL). Sixteen thousand eight hundred and fourteen T-DNA and 12,410 Tos17 discrete insertion sites have been characterized in these lines. We estimate that 8686 predicted gene intervals--i.e. one-fourth to one-fifth of the estimated rice nontransposable element gene complement--are interrupted by sequence-indexed T-DNA (6563 genes) and/or Tos17 (2755 genes) inserts. Six hundred and forty-three genes are interrupted by both T-DNA and Tos17 inserts. High quality of the sequence indexation of the T2 seed samples was ascertained by several approaches. Field evaluation under agronomic conditions of 27,832 OTL has revealed that 18.2% exhibit at least one morphophysiological alteration in the T1 progeny plants. Screening 10,000 lines for altered response to inoculation by the fungal pathogen Magnaporthe oryzae allowed to observe 71 lines (0.7%) developing spontaneous lesions simulating disease mutants and 43 lines (0.4%) exhibiting an enhanced disease resistance or susceptibility. We show here that at least 3.5% (four of 114) of these alterations are tagged by the mutagens. The presence of allelic series of sequence-indexed mutations in a gene among OTL that exhibit a convergent phenotype clearly increases the chance of establishing a linkage between alterations and inserts. This convergence approach is illustrated by the identification of the rice ortholog of AtPHO2, the disruption of which causes a lesion-mimic phenotype owing to an over-accumulation of phosphate, in nine lines bearing allelic insertions.
Collapse
Affiliation(s)
- Mathias Lorieux
- IRD, UMR DIADE, CIAT, Agrobiodiversity and Biotechnology Project, Cali, Colombia
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
21
|
Rizal G, Karki S, Thakur V, Chatterjee J, A. Coe R, Wanchana S, Quick WP. Towards a C4 Rice. ACTA ACUST UNITED AC 2012. [DOI: 10.3923/ajcb.2012.13.31] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
|
22
|
Abstract
Genome walking is a molecular procedure for the direct identification of nucleotide sequences from purified genomes. The only requirement is the availability of a known nucleotide sequence from which to start. Several genome walking methods have been developed in the last 20 years, with continuous improvements added to the first basic strategies, including the recent coupling with next generation sequencing technologies. This review focuses on the use of genome walking strategies in several aspects of the study of eukaryotic genomes. In a first part, the analysis of the numerous strategies available is reported. The technical aspects involved in genome walking are particularly intriguing, also because they represent the synthesis of the talent, the fantasy and the intelligence of several scientists. Applications in which genome walking can be employed are systematically examined in the second part of the review, showing the large potentiality of this technique, including not only the simple identification of nucleotide sequences but also the analysis of large collections of mutants obtained from the insertion of DNA of viral origin, transposons and transfer DNA (T-DNA) constructs. The enormous amount of data obtained indicates that genome walking, with its large range of applicability, multiplicity of strategies and recent developments, will continue to have much to offer for the rapid identification of unknown sequences in several fields of genomic research.
Collapse
Affiliation(s)
- Claudia Leoni
- Department of Biochemistry and Molecular Biology, University of Bari, Bari, Italy
| | | | | | | | | |
Collapse
|
23
|
Kim SR, Jeon JS, An G. Development of an efficient inverse PCR method for isolating gene tags from T-DNA insertional mutants in rice. Methods Mol Biol 2011; 678:139-46. [PMID: 20931378 DOI: 10.1007/978-1-60761-682-5_11] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023]
Abstract
The central goal of current genomics research in plants, as in other organisms, is to elucidate the functions of every gene. Insertional mutagenesis using known DNA sequences such as T-DNA is a powerful tool in functional genomics. Development of efficient methods for isolating the genomic sequences flanking insertion elements accelerates the systematic cataloging of insertional mutants, and thus allows functions to be assigned to uncharacterized genes via reverse genetic approaches. In our current study, we report a rapid and efficient inverse PCR (iPCR) method for the isolation of gene tags in T-DNA mutant lines of rice (Oryza sativa), a model monocot plant.
Collapse
Affiliation(s)
- Sung-Ryul Kim
- National Research Laboratory of Plant Functional Genomics, Division of Molecular and Life Sciences, POSTECH Biotech Center, Pohang University of Science and Technology, Pohang, Korea
| | | | | |
Collapse
|
24
|
Chern CG, Fan MJ, Huang SC, Yu SM, Wei FJ, Wu CC, Trisiriroj A, Lai MH, Chen S, Hsing YIC. Methods for rice phenomics studies. Methods Mol Biol 2011; 678:129-138. [PMID: 20931377 DOI: 10.1007/978-1-60761-682-5_10] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
With the completion of the rice genome sequencing project, the next major challenge is the large-scale determination of gene function. A systematic phenotypic profiling of mutant collections will provide major insights into gene functions important for crop growth or production. Thus, detailed phenomics analysis is the key to functional genomics. Currently, the two major types of rice mutant collections are insertional mutants and chemical or irradiation-induced mutants. Here we describe how to manipulate a rice mutant population, including conducting phenomics studies and the subsequent propagation and seed storage. We list the phenotypes screened and also describe how to collect data systematically for a database of the qualitative and quantitative phenotypic traits. Thus, data on mutant lines, phenotypes, and segregation rate for all kinds of mutant populations, as well as integration sites for insertional mutant populations, would be searchable, and the collection would be a good resource for rice functional genomics study.
Collapse
Affiliation(s)
- Chyr-Guan Chern
- Taiwan Agricultural Research Institute, Wufeng, Taichung, Taiwan
| | | | | | | | | | | | | | | | | | | |
Collapse
|
25
|
Huang CK, Yu SM, Lu CA. A rice DEAD-box protein, OsRH36, can complement an Arabidopsis atrh36 mutant, but cannot functionally replace its yeast homolog Dbp8p. PLANT MOLECULAR BIOLOGY 2010; 74:119-28. [PMID: 20607362 DOI: 10.1007/s11103-010-9659-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2010] [Accepted: 06/18/2010] [Indexed: 05/25/2023]
Abstract
DEAD-box proteins comprise a large family and function in RNA metabolism. Although DEAD-box proteins are highly conserved among eukaryotes, little is known about the role of DEAD-box proteins in rice. In this study, we identified a rice DEAD-box protein, OsRH36, and demonstrated that OsRH36 and AtRH36 are functional orthologs. OsRH36 was expressed ubiquitously throughout the plant and the OsRH36-GFP fusion protein was localized to the nucleus and nucleolus. Furthermore, functional complementation tests among three homologous DEAD-box protein genes indicated that OsRH36 can restore segregation distortion in the Arabidopsis atrh36-1 mutant, but cannot complement the lethal phenotype in the yeast dbp8p mutant. Moreover, mutation of osrh36 also led to defective transmission of the osrh36 allele, as shown for the atrh36 mutants of Arabidopsis. Previously, we have shown that AtRH36 is involved at an early stage of rRNA maturation and is required for synchronous development of female gametophytes in Arabidopsis. Therefore, we suggest that OsRH36 is required for rRNA biogenesis and megagametogenesis in rice, consistent with the function of AtRH36 in Arabidopsis.
Collapse
Affiliation(s)
- Chun-Kai Huang
- Department of Life Science, National Central University, Zhongli, Taoyuan County, Taiwan, ROC
| | | | | |
Collapse
|
26
|
Assigning biological functions to rice genes by genome annotation, expression analysis and mutagenesis. Biotechnol Lett 2010; 32:1753-63. [PMID: 20703802 DOI: 10.1007/s10529-010-0377-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2010] [Accepted: 07/28/2010] [Indexed: 12/17/2022]
Abstract
Rice is the first cereal genome to be completely sequenced. Since the completion of its genome sequencing, considerable progress has been made in multiple areas including the whole genome annotation, gene expression profiling, mutant collection, etc. Here, we summarize the current status of rice genome annotation and review the methodology of assigning biological functions to hundreds of thousands of rice genes as well as discuss the major limitations and the future perspective in rice functional genomics. Available data analysis shows that the rice genome encodes around 32,000 protein-coding genes. Expression analysis revealed at least 31,000 genes with expression evidence from full-length cDNA/EST collection or other transcript profiling. In addition, we have summarized various strategies to generate mutant population including natural, physical, chemical, T-DNA, transposon/retrotransposon or gene silencing based mutagenesis. Currently, more than 1 million of mutants have been generated and 27,551 of them have their flanking sequence tags. To assign biological functions to hundreds of thousands of rice genes, global co-operations are required, various genetic resources should be more easily accessible and diverse data from transcriptomics, proteomics, epigenetics, comparative genomics and bioinformatics should be integrated to better understand the functions of these genes and their regulatory mechanisms.
Collapse
|
27
|
Jiang SY, Ramachandran S. Natural and artificial mutants as valuable resources for functional genomics and molecular breeding. Int J Biol Sci 2010; 6:228-51. [PMID: 20440406 PMCID: PMC2862397 DOI: 10.7150/ijbs.6.228] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2010] [Accepted: 04/20/2010] [Indexed: 12/31/2022] Open
Abstract
With the completion of rice genome sequencing, large collection of expression data and the great efforts in annotating rice genomes, the next challenge is to systematically assign functions to all predicted genes in the genome. The generations and collections of mutants at the genome-wide level form technological platform of functional genomics. In this study, we have reviewed currently employed tools to generate such mutant populations. These tools include natural, physical, chemical, tissue culture, T-DNA, transposon or gene silencing based mutagenesis. We also reviewed how these tools were used to generate a large collection of mutants and how these mutants can be screened and detected for functional analysis of a gene. The data suggested that the current population of mutants might be large enough to tag all predicted genes. However, the collection of flanking sequencing tags (FSTs) is limited due to the relatively higher cost. Thus, we have proposed a new strategy to generate gene-silencing mutants at the genome-wide level. Due to the large collection of insertion mutants, the next step to rice functional genomics should be focusing on functional characterization of tagged genes by detailed survey of corresponding mutants. Additionally, we also evaluated the utilization of these mutants as valuable resources for molecular breeding.
Collapse
Affiliation(s)
| | - Srinivasan Ramachandran
- Rice Functional Genomics Group, Temasek Life Sciences Laboratory, 1 Research Link, Singapore 117604
| |
Collapse
|
28
|
Kondou Y, Higuchi M, Matsui M. High-throughput characterization of plant gene functions by using gain-of-function technology. ANNUAL REVIEW OF PLANT BIOLOGY 2010; 61:373-93. [PMID: 20192750 DOI: 10.1146/annurev-arplant-042809-112143] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Gain-of-function approaches have been used as an alternative or complementary method to loss-of-function approaches as well as to confer new functions to plants. Gain-of-function is achieved by increasing gene expression levels through the random activation of endogenous genes by transcriptional enhancers or the expression of individual transgenes by transformation. The advantages of gain-of-function approaches compared to loss-of-function approaches for the characterization of gene functions include the abilities to (a) analyze individual gene family members, (b) characterize the function of genes from nonmodel plants using a heterologous expression system, and (c) identify genes that confer stress tolerance to plants that result from the introduction of transgenes. In this review, we describe the current status of gain-of-function mutagenesis and provide several examples of how gene functions have been characterized via high-throughput screening using gain-of-function technology.
Collapse
Affiliation(s)
- Youichi Kondou
- Plant Functional Genomics Research Team, RIKEN Plant Science Center, Tsurumi-ku, Yokohama, Japan.
| | | | | |
Collapse
|
29
|
Ayliffe MA, Pryor AJ. Transposon-based activation tagging in cereals. FUNCTIONAL PLANT BIOLOGY : FPB 2009; 36:915-921. [PMID: 32688702 DOI: 10.1071/fp09130] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2009] [Accepted: 08/14/2009] [Indexed: 06/11/2023]
Abstract
Advances in DNA sequencing technologies have produced an ever increasing number of sequenced genomes. However, many of the genes identified in these sequencing efforts have unknown functions or functions inferred based upon sequence homology, highlighting the necessity for functional gene analysis. Mutagenesis combined with phenotypic analyses remains a key mechanism for identifying and establishing gene function. Activation tagging is a mutagenic process that uses altered gene expression, usually gene overexpression, to generate mutant phenotypes. We have developed an activation tagging system in barley (Hordeum vulgare L.) based upon a maize (Zea mays L.) transposable element that carries two highly expressed cereal promoters. Insertion of this mobile genetic element in the genome can lead to insertional gene inactivation, gene overexpression and gene silencing through the production of antisense transcripts. This transposable element system has also been introduced into both wheat (Triticum aestivum L.) and maize and transposon mobility observed.
Collapse
Affiliation(s)
- M A Ayliffe
- CSIRO Plant Industry, Box 1600, Clunies Ross Street, Canberra, ACT 2601, Australia
| | - A J Pryor
- CSIRO Plant Industry, Box 1600, Clunies Ross Street, Canberra, ACT 2601, Australia
| |
Collapse
|
30
|
Papdi C, Joseph MP, Salamó IP, Vidal S, Szabados L. Genetic technologies for the identification of plant genes controlling environmental stress responses. FUNCTIONAL PLANT BIOLOGY : FPB 2009; 36:696-720. [PMID: 32688681 DOI: 10.1071/fp09047] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2009] [Accepted: 06/11/2009] [Indexed: 06/11/2023]
Abstract
Abiotic conditions such as light, temperature, water availability and soil parameters determine plant growth and development. The adaptation of plants to extreme environments or to sudden changes in their growth conditions is controlled by a well balanced, genetically determined signalling system, which is still far from being understood. The identification and characterisation of plant genes which control responses to environmental stresses is an essential step to elucidate the complex regulatory network, which determines stress tolerance. Here, we review the genetic approaches, which have been used with success to identify plant genes which control responses to different abiotic stress factors. We describe strategies and concepts for forward and reverse genetic screens, conventional and insertion mutagenesis, TILLING, gene tagging, promoter trapping, activation mutagenesis and cDNA library transfer. The utility of the various genetic approaches in plant stress research we review is illustrated by several published examples.
Collapse
Affiliation(s)
- Csaba Papdi
- Institute of Plant Biology, Biological Research Centre, 6726-Szeged, Temesvári krt. 62, Hungary
| | - Mary Prathiba Joseph
- Institute of Plant Biology, Biological Research Centre, 6726-Szeged, Temesvári krt. 62, Hungary
| | - Imma Pérez Salamó
- Institute of Plant Biology, Biological Research Centre, 6726-Szeged, Temesvári krt. 62, Hungary
| | - Sabina Vidal
- Facultad de Ciencias, Universidad de la República, Iguá 4225, CP 11400, Montevideo, Uruguay
| | - László Szabados
- Institute of Plant Biology, Biological Research Centre, 6726-Szeged, Temesvári krt. 62, Hungary
| |
Collapse
|
31
|
Kuromori T, Takahashi S, Kondou Y, Shinozaki K, Matsui M. Phenome analysis in plant species using loss-of-function and gain-of-function mutants. PLANT & CELL PHYSIOLOGY 2009; 50:1215-31. [PMID: 19502383 PMCID: PMC2709550 DOI: 10.1093/pcp/pcp078] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2009] [Accepted: 05/29/2009] [Indexed: 05/20/2023]
Abstract
Analysis of genetic mutations is one of the most effective ways to investigate gene function. We now have methods that allow for mass production of mutant lines and cells in a variety of model species. Recently, large numbers of mutant lines have been generated by both 'loss-of-function' and 'gain-of-function' techniques. In parallel, phenotypic information covering various mutant resources has been acquired and released in web-based databases. As a result, significant progress in comprehensive phenotype analysis is being made through the use of these tools. Arabidopsis and rice are two major model plant species in which genome sequencing projects have been completed. Arabidopsis is the most widely used experimental plant, with a large number of mutant resources and several examples of systematic phenotype analysis. Rice is a major crop species and is used as a model plant, with an increasing number of mutant resources. Other plant species are also being employed in functional genetics research. In this review, the present status of mutant resources for large-scale studies of gene function in plant research and the current perspective on using loss-of-function and gain-of-function mutants in phenome research will be discussed.
Collapse
Affiliation(s)
- Takashi Kuromori
- Gene Discovery Research Group, RIKEN Plant Science Center, Yokohama, Kanagawa, 230-0045 Japan
| | - Shinya Takahashi
- Plant Functional Genomics Research Group, RIKEN Plant Science Center, Yokohama, Kanagawa, 230-0045 Japan
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Noda, Chiba, 278-8510 Japan
| | - Youichi Kondou
- Plant Functional Genomics Research Group, RIKEN Plant Science Center, Yokohama, Kanagawa, 230-0045 Japan
| | - Kazuo Shinozaki
- Gene Discovery Research Group, RIKEN Plant Science Center, Yokohama, Kanagawa, 230-0045 Japan
| | - Minami Matsui
- Plant Functional Genomics Research Group, RIKEN Plant Science Center, Yokohama, Kanagawa, 230-0045 Japan
- *Corresponding author: E-mail, ; Fax, +81-45-503-9584
| |
Collapse
|
32
|
Molecular analysis of rice plants harboring a multi-functional T-DNA tagging system. J Genet Genomics 2009; 36:267-76. [DOI: 10.1016/s1673-8527(08)60114-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2008] [Revised: 02/23/2009] [Accepted: 02/26/2009] [Indexed: 11/21/2022]
|
33
|
Fu FF, Ye R, Xu SP, Xue HW. Studies on rice seed quality through analysis of a large-scale T-DNA insertion population. Cell Res 2009; 19:380-91. [PMID: 19223856 DOI: 10.1038/cr.2009.15] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
A rice (Oryza sativa) T-DNA insertion population, which included more than 63 000 independent transgenic lines and 8 840 identified flanking sequence tags (FSTs) that were mapped onto the rice genome, was developed to systemically study the rice seed quality control. Genome-wide analysis of the FST distribution showed that T-DNA insertions were positively correlated with expressed genes, but negatively with transposable elements and small RNAs. In addition, the recovered T-DNAs were preferentially located at the untranslated region of the expressed genes. More than 11 000 putative homozygous lines were obtained through multi-generations of planting and resistance screening, and measurement of seed quality of around half of them, including the contents of starch, amylose, protein and fat, with a nondestructive near-infrared spectroscopy method, identified 551 mutants with unique or multiple altered parameters of seed quality. Analysis of the corresponding FSTs showed that genes participating in diverse functions, including metabolic processes and transcriptional regulation, were involved, indicating that seed quality is regulated by a complex network.
Collapse
Affiliation(s)
- Fang-Fang Fu
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Science (SIBS), Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, China
| | | | | | | |
Collapse
|
34
|
Micol JL. Leaf development: time to turn over a new leaf? CURRENT OPINION IN PLANT BIOLOGY 2009; 12:9-16. [PMID: 19109050 DOI: 10.1016/j.pbi.2008.11.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2008] [Revised: 10/30/2008] [Accepted: 11/01/2008] [Indexed: 05/18/2023]
Abstract
Molecular cloning of mutations affecting the morphology of plant leaves has proven to be useful for the causal analysis of leaf development. Studies of leaf mutants have produced a wealth of biologically meaningful information on the genes that participate in leaf initiation, leaf polarity specification and maintenance, and leaf expansion and maturation. The availability of collections of gene-indexed insertional mutants, automated platforms for high-throughput imaging, and new morphometry software is making genome-wide leaf phenomics possible and complements classical forward genetics approaches. Large-scale phenomic studies will further our understanding, among others, of two intriguing phenomena that recently reentered the leaf scenario. One is the unexpected relationship between translation and leaf dorsoventrality, recently confirmed by the severe abaxialization of double mutants involving loss-of-function alleles of the developmental selector genes AS1 and AS2 and some genes encoding ribosomal proteins. The second unexplained phenomenon is the compensatory cell enlargement experienced by some leaf mutants, in which a reduced cell number is compensated by their increased cell size compared with the wild type. This compensation suggests that cell cycling and cell enlargement are integrated in leaf primordia via cell-to-cell communication.
Collapse
Affiliation(s)
- José Luis Micol
- División de Genética and Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, Elche, Alicante, Spain.
| |
Collapse
|
35
|
Wan S, Wu J, Zhang Z, Sun X, Lv Y, Gao C, Ning Y, Ma J, Guo Y, Zhang Q, Zheng X, Zhang C, Ma Z, Lu T. Activation tagging, an efficient tool for functional analysis of the rice genome. PLANT MOLECULAR BIOLOGY 2009; 69:69-80. [PMID: 18830797 DOI: 10.1007/s11103-008-9406-5] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2007] [Accepted: 09/17/2008] [Indexed: 05/19/2023]
Abstract
Over the past 6 years, we have generated about 50,000 individual transgenic rice plants by an Agrobacterium-mediated transformation approach with the pER38 activation tagging vector. The vector contains tandemly arranged double 35S enhancers next to the right border of T-DNA. Expression analysis by reverse transcription-PCR indicates that the activation efficiency is high if the genes are located within 7 kb of the inserted double 35S enhancers. Comparative field phenotyping of part of the activation tagging and enhancer trapping populations in two generations (6,000 and 6,400 lines, respectively, in the T(0) generation, and 36,000 and 32,000 lines, respectively, in the T(1) generation) identified about four hundred dominant mutants. Characterization of a dominant mutant with a large leaf angle (M107) suggests that this mutant phenotype is caused by enhanced expression of CYP724B1/D11. The activation tagging pool described in this paper is a valuable alternative tool for functional analysis of the rice genome.
Collapse
Affiliation(s)
- Shuyan Wan
- Biotechnology Research Institute/National Key Facility for Gene Resources and Gene Improvement, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
36
|
Krishnan A, Guiderdoni E, An G, Hsing YIC, Han CD, Lee MC, Yu SM, Upadhyaya N, Ramachandran S, Zhang Q, Sundaresan V, Hirochika H, Leung H, Pereira A. Mutant resources in rice for functional genomics of the grasses. PLANT PHYSIOLOGY 2009; 149:165-70. [PMID: 19126710 PMCID: PMC2613728 DOI: 10.1104/pp.108.128918] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2008] [Accepted: 11/04/2008] [Indexed: 05/18/2023]
Affiliation(s)
- Arjun Krishnan
- Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, Virginia 24061, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
37
|
Pogorelko GV, Fursova OV, Ogarkova OA, Tarasov VA. A new technique for activation tagging in Arabidopsis. Gene 2008; 414:67-75. [DOI: 10.1016/j.gene.2008.02.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2007] [Revised: 02/07/2008] [Accepted: 02/11/2008] [Indexed: 10/22/2022]
|