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Vishwakarma C, Krishna GK, Kapoor RT, Mathur K, Dalal M, Singh NK, Mohapatra T, Chinnusamy V. Physiological Analysis of Source-Sink Relationship in Rice Genotypes with Contrasting Grain Yields. PLANTS (BASEL, SWITZERLAND) 2023; 13:62. [PMID: 38202369 PMCID: PMC10780537 DOI: 10.3390/plants13010062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 11/19/2023] [Accepted: 11/22/2023] [Indexed: 01/12/2024]
Abstract
Rice is a major staple food, and, hence, doubling its productivity is critical to sustain future food security. Improving photosynthesis, source-sink relationships and grain-filling mechanisms are promising traits for improvement in grain yield. To understand the source-sink relationship and grain yield, a set of contrasting rice genotypes differing in yield and biomass were studied for physiological, biochemical and gene-expression differences. The physiological and yield component traits of selected rice genotypes were analyzed in 2016 and 2017 under field conditions. This led to the categorization of genotypes as high yielding (HY) and high biomass, viz., Dular, Gontra Bidhan 3, Way Rarem, Patchai Perumal, Sahbhagi Dhan, Indira Barani Dhan-1, MTU1010, and Maudamani; while, low yielding (LY) and low biomass, viz. Anjali, Ghanteswari, Parijat, Khao Daw Tai, RKVY-104, Ghati Kamma Nangarhar, BAM4510 and BAM5850. The HY genotypes in general had relatively better values of yield component traits, higher photosynthetic rate (Pn) and chlorophyll (Chl) content. The study revealed that leaf area per plant and whole plant photosynthesis are the key traits contributing to high biomass production. We selected two good-performing (Sahbhagi Dhan and Maudamani) and two poor-performing (Ghanteswari and Parijat) rice genotypes for a detailed expression analysis of selected genes involved in photosynthesis, sucrose synthesis, transport, and starch synthesis in the leaf and starch metabolism in grain. Some of the HY genotypes had a relatively high level of expression of key photosynthesis genes, such as RbcS, RCA, FBPase, and ZEP over LY genotypes. This study suggests that traits, such as leaf area, photosynthesis and grain number, contribute to high grain yield in rice. These good-performing genotypes can be used as a donor in a breeding program aimed at high yields in rice.
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Affiliation(s)
- Chandrapal Vishwakarma
- Division of Plant Physiology, Indian Council of Agricultural Research-Indian Agricultural Research Institute (IARI), New Delhi 110012, India;
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida 201313, Uttar Pradesh, India; (R.T.K.); (K.M.)
| | - Gopinathan Kumar Krishna
- Department of Plant Physiology, College of Agriculture, Vellanikkara, Kerala Agricultural University, Thrissur 680656, Kerala, India;
| | - Riti Thapar Kapoor
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida 201313, Uttar Pradesh, India; (R.T.K.); (K.M.)
| | - Komal Mathur
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida 201313, Uttar Pradesh, India; (R.T.K.); (K.M.)
| | - Monika Dalal
- Indian Council of Agricultural Research-National Institute for Plant Biotechnology, New Delhi 110012, India; (M.D.); (N.K.S.)
| | - Nagendra Kumar Singh
- Indian Council of Agricultural Research-National Institute for Plant Biotechnology, New Delhi 110012, India; (M.D.); (N.K.S.)
| | - Trilochan Mohapatra
- Protection of Plant Varieties and Farmers’ Rights Authority, New Delhi 110012, India;
| | - Viswanathan Chinnusamy
- Division of Plant Physiology, Indian Council of Agricultural Research-Indian Agricultural Research Institute (IARI), New Delhi 110012, India;
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Xiong H, Guo H, Fu M, Xie Y, Zhao L, Gu J, Zhao S, Ding Y, Du Q, Zhang J, Qiu L, Xie X, Zhou L, Chen Z, Liu L. A large-scale whole-exome sequencing mutant resource for functional genomics in wheat. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:2047-2056. [PMID: 37401008 PMCID: PMC10502753 DOI: 10.1111/pbi.14111] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 06/01/2023] [Accepted: 06/15/2023] [Indexed: 07/05/2023]
Abstract
Hexaploid wheat (Triticum aestivum), a major staple crop, has a remarkably large genome of ~14.4 Gb (containing 106 913 high-confidence [HC] and 159 840 low-confidence [LC] genes in the Chinese Spring v2.1 reference genome), which poses a major challenge for functional genomics studies. To overcome this hurdle, we performed whole-exome sequencing to generate a nearly saturated wheat mutant database containing 18 025 209 mutations induced by ethyl methanesulfonate (EMS), carbon (C)-ion beams, or γ-ray mutagenesis. This database contains an average of 47.1 mutations per kb in each gene-coding sequence: the potential functional mutations were predicted to cover 96.7% of HC genes and 70.5% of LC genes. Comparative analysis of mutations induced by EMS, γ-rays, or C-ion beam irradiation revealed that γ-ray and C-ion beam mutagenesis induced a more diverse array of variations than EMS, including large-fragment deletions, small insertions/deletions, and various non-synonymous single nucleotide polymorphisms. As a test case, we combined mutation analysis with phenotypic screening and rapidly mapped the candidate gene responsible for the phenotype of a yellow-green leaf mutant to a 2.8-Mb chromosomal region. Furthermore, a proof-of-concept reverse genetics study revealed that mutations in gibberellic acid biosynthesis and signalling genes could be associated with negative impacts on plant height. Finally, we built a publically available database of these mutations with the corresponding germplasm (seed stock) repository to facilitate advanced functional genomics studies in wheat for the broad plant research community.
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Affiliation(s)
- Hongchun Xiong
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences/National Engineering Laboratory for Crop Molecular BreedingNational Center of Space Mutagenesis for Crop ImprovementBeijingChina
| | - Huijun Guo
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences/National Engineering Laboratory for Crop Molecular BreedingNational Center of Space Mutagenesis for Crop ImprovementBeijingChina
| | - Meiyu Fu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences/National Engineering Laboratory for Crop Molecular BreedingNational Center of Space Mutagenesis for Crop ImprovementBeijingChina
| | - Yongdun Xie
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences/National Engineering Laboratory for Crop Molecular BreedingNational Center of Space Mutagenesis for Crop ImprovementBeijingChina
| | - Linshu Zhao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences/National Engineering Laboratory for Crop Molecular BreedingNational Center of Space Mutagenesis for Crop ImprovementBeijingChina
| | - Jiayu Gu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences/National Engineering Laboratory for Crop Molecular BreedingNational Center of Space Mutagenesis for Crop ImprovementBeijingChina
| | - Shirong Zhao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences/National Engineering Laboratory for Crop Molecular BreedingNational Center of Space Mutagenesis for Crop ImprovementBeijingChina
| | - Yuping Ding
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences/National Engineering Laboratory for Crop Molecular BreedingNational Center of Space Mutagenesis for Crop ImprovementBeijingChina
| | - Qidi Du
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences/National Engineering Laboratory for Crop Molecular BreedingNational Center of Space Mutagenesis for Crop ImprovementBeijingChina
| | - Jiazi Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences/National Engineering Laboratory for Crop Molecular BreedingNational Center of Space Mutagenesis for Crop ImprovementBeijingChina
| | - Lin Qiu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences/National Engineering Laboratory for Crop Molecular BreedingNational Center of Space Mutagenesis for Crop ImprovementBeijingChina
| | - Xiaomei Xie
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences/National Engineering Laboratory for Crop Molecular BreedingNational Center of Space Mutagenesis for Crop ImprovementBeijingChina
| | - Libin Zhou
- Biophysics GroupInstitute of Modern Physics, Chinese Academy of SciencesLanzhouChina
| | - Zhongxu Chen
- Department of Life ScienceTcuni Inc.ChengduChina
| | - Luxiang Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences/National Engineering Laboratory for Crop Molecular BreedingNational Center of Space Mutagenesis for Crop ImprovementBeijingChina
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3
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Ahmad M. Genomics and transcriptomics to protect rice ( Oryza sativa. L.) from abiotic stressors: -pathways to achieving zero hunger. FRONTIERS IN PLANT SCIENCE 2022; 13:1002596. [PMID: 36340401 PMCID: PMC9630331 DOI: 10.3389/fpls.2022.1002596] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 09/29/2022] [Indexed: 06/16/2023]
Abstract
More over half of the world's population depends on rice as a major food crop. Rice (Oryza sativa L.) is vulnerable to abiotic challenges including drought, cold, and salinity since it grown in semi-aquatic, tropical, or subtropical settings. Abiotic stress resistance has bred into rice plants since the earliest rice cultivation techniques. Prior to the discovery of the genome, abiotic stress-related genes were identified using forward genetic methods, and abiotic stress-tolerant lines have developed using traditional breeding methods. Dynamic transcriptome expression represents the degree of gene expression in a specific cell, tissue, or organ of an individual organism at a specific point in its growth and development. Transcriptomics can reveal the expression at the entire genome level during stressful conditions from the entire transcriptional level, which can be helpful in understanding the intricate regulatory network relating to the stress tolerance and adaptability of plants. Rice (Oryza sativa L.) gene families found comparatively using the reference genome sequences of other plant species, allowing for genome-wide identification. Transcriptomics via gene expression profiling which have recently dominated by RNA-seq complements genomic techniques. The identification of numerous important qtl,s genes, promoter elements, transcription factors and miRNAs involved in rice response to abiotic stress was made possible by all of these genomic and transcriptomic techniques. The use of several genomes and transcriptome methodologies to comprehend rice (Oryza sativa, L.) ability to withstand abiotic stress have been discussed in this review.
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Affiliation(s)
- Mushtaq Ahmad
- Visiting Scientist Plant Sciences, University of Nebraska, Lincoln, NE, United States
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Zhang YC, Zhou YF, Cheng Y, Huang JH, Lian JP, Yang L, He RR, Lei MQ, Liu YW, Yuan C, Zhao WL, Xiao S, Chen YQ. Genome-wide analysis and functional annotation of chromatin-enriched noncoding RNAs in rice during somatic cell regeneration. Genome Biol 2022; 23:28. [PMID: 35045887 PMCID: PMC8772118 DOI: 10.1186/s13059-022-02608-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 01/12/2022] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Plants have the remarkable ability to generate callus, a pluripotent cell mass that acquires competence for subsequent tissue regeneration. Global chromatin remodeling is required for this cell fate transition, but how the process is regulated is not fully understood. Chromatin-enriched noncoding RNAs (cheRNAs) are thought to play important roles in maintaining chromatin state. However, whether cheRNAs participate in somatic cell regeneration in plants has not yet been clarified. RESULTS To uncover the characteristics and functions of cheRNAs during somatic cell reprogramming in plants, we systematically investigate cheRNAs during callus induction, proliferation and regeneration in rice. We identify 2284 cheRNAs, most of which are novel long non-coding RNAs or small nucleolar RNAs. These cheRNAs, which are highly conserved across plant species, shuttle between chromatin and the nucleoplasm during somatic cell regeneration. They positively regulate the expression of neighboring genes via specific RNA motifs, which may interact with DNA motifs around cheRNA loci. Large-scale mutant analysis shows that cheRNAs are associated with plant size and seed morphology. Further detailed functional investigation of two che-lncRNAs demonstrates that their loss of function impairs cell dedifferentiation and plant regeneration, highlighting the functions of cheRNAs in regulating the expression of neighboring genes via specific motifs. These findings support cis- regulatory roles of cheRNAs in influencing a variety of rice traits. CONCLUSIONS cheRNAs are a distinct subclass of regulatory non-coding RNAs that are required for somatic cell regeneration and regulate rice traits. Targeting cheRNAs has great potential for crop trait improvement and breeding in future.
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Affiliation(s)
- Yu-Chan Zhang
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.
- MOE Key Laboratory of Gene Function and Regulation, Sun Yat-sen University, Guangzhou, 510275, People's Republic of China.
| | - Yan-Fei Zhou
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Yu Cheng
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Jia-Hui Huang
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Jian-Ping Lian
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Lu Yang
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Rui-Rui He
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Meng-Qi Lei
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Yu-Wei Liu
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Chao Yuan
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Wen-Long Zhao
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Shi Xiao
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Yue-Qin Chen
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.
- MOE Key Laboratory of Gene Function and Regulation, Sun Yat-sen University, Guangzhou, 510275, People's Republic of China.
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Zhang X, Hu Y, Smith DR. HSDFinder: A BLAST-Based Strategy for Identifying Highly Similar Duplicated Genes in Eukaryotic Genomes. FRONTIERS IN BIOINFORMATICS 2021; 1:803176. [PMID: 36303740 PMCID: PMC9580922 DOI: 10.3389/fbinf.2021.803176] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 11/25/2021] [Indexed: 01/01/2023] Open
Abstract
Gene duplication is an important evolutionary mechanism capable of providing new genetic material for adaptive and nonadaptive evolution. However, bioinformatics tools for identifying duplicate genes are often limited to the detection of paralogs in multiple species or to specific types of gene duplicates, such as retrocopies. Here, we present a user-friendly, BLAST-based web tool, called HSDFinder, which can identify, annotate, categorize, and visualize highly similar duplicate genes (HSDs) in eukaryotic nuclear genomes. HSDFinder includes an online heatmap plotting option, allowing users to compare HSDs among different species and visualize the results in different Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway functional categories. The external software requirements are BLAST, InterProScan, and KEGG. The utility of HSDFinder was tested on various model eukaryotic species, including Chlamydomonas reinhardtii, Arabidopsis thaliana, Oryza sativa, and Zea mays as well as the psychrophilic green alga Chlamydomonas sp. UWO241, and was proven to be a practical and accurate tool for gene duplication analyses. The web tool is free to use at http://hsdfinder.com. Documentation and tutorials can be found via the GitHub: https://github.com/zx0223winner/HSDFinder.
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Affiliation(s)
- Xi Zhang
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada
- Institute for Comparative Genomics, Dalhousie University, Halifax, NS, Canada
- *Correspondence: Xi Zhang, ; David Roy Smith,
| | - Yining Hu
- Department of Computer Science, Western University, London, ON, Canada
| | - David Roy Smith
- Department of Biology, Western University, London, ON, Canada
- *Correspondence: Xi Zhang, ; David Roy Smith,
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Iqbal Z, Iqbal MS, Khan MIR, Ansari MI. Toward Integrated Multi-Omics Intervention: Rice Trait Improvement and Stress Management. FRONTIERS IN PLANT SCIENCE 2021; 12:741419. [PMID: 34721467 PMCID: PMC8554098 DOI: 10.3389/fpls.2021.741419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 09/20/2021] [Indexed: 05/04/2023]
Abstract
Rice (Oryza sativa) is an imperative staple crop for nearly half of the world's population. Challenging environmental conditions encompassing abiotic and biotic stresses negatively impact the quality and yield of rice. To assure food supply for the unprecedented ever-growing world population, the improvement of rice as a crop is of utmost importance. In this era, "omics" techniques have been comprehensively utilized to decipher the regulatory mechanisms and cellular intricacies in rice. Advancements in omics technologies have provided a strong platform for the reliable exploration of genetic resources involved in rice trait development. Omics disciplines like genomics, transcriptomics, proteomics, and metabolomics have significantly contributed toward the achievement of desired improvements in rice under optimal and stressful environments. The present review recapitulates the basic and applied multi-omics technologies in providing new orchestration toward the improvement of rice desirable traits. The article also provides a catalog of current scenario of omics applications in comprehending this imperative crop in relation to yield enhancement and various environmental stresses. Further, the appropriate databases in the field of data science to analyze big data, and retrieve relevant information vis-à-vis rice trait improvement and stress management are described.
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Affiliation(s)
- Zahra Iqbal
- Molecular Crop Research Unit, Department of Biochemistry, Chulalongkorn University, Bangkok, Thailand
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Hu W, Figueroa‐Balderas R, Chi‐Ham C, Lagarias JC. Regulation of monocot and dicot plant development with constitutively active alleles of phytochrome B. PLANT DIRECT 2020; 4:e00210. [PMID: 32346668 PMCID: PMC7184922 DOI: 10.1002/pld3.210] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 02/03/2020] [Accepted: 02/25/2020] [Indexed: 05/31/2023]
Abstract
The constitutively active missense allele of Arabidopsis phytochrome B, AtPHYBY276H or AtYHB, encodes a polypeptide that adopts a light-insensitive, physiologically active conformation capable of sustaining photomorphogenesis in darkness. Here, we show that the orthologous OsYHB allele of rice phytochrome B (OsPHYBY283H ) also encodes a dominant "constitutively active" photoreceptor through comparative phenotypic analyses of AtYHB and OsYHB transgenic lines of four eudicot species, Arabidopsis thaliana, Nicotiana tabacum (tobacco), Nicotiana sylvestris and Solanum lycopersicum cv. MicroTom (tomato), and of two monocot species, Oryza sativa ssp. japonica and Brachypodium distachyon. Reciprocal transformation experiments show that the gain-of-function constitutive photomorphogenic (cop) phenotypes by YHB expression are stronger in host plants within the same class than across classes. Our studies also reveal additional YHB-dependent traits in adult plants, which include extreme shade tolerance, both early and late flowering behaviors, delayed leaf senescence, reduced tillering, and even viviparous seed germination. However, the strength of these gain-of-function phenotypes depends on the specific combination of YHB allele and species/cultivar transformed. Flowering and tillering of OsYHB- and OsPHYB-expressing lines of rice Nipponbare and Kitaake cultivars were compared, also revealing differences in YHB/PHYB allele versus genotype interaction on the phenotypic behavior of the two rice cultivars. In view of recent evidence that the regulatory activity of AtYHB is not only light insensitive but also temperature insensitive, selective YHB expression is expected to yield improved agronomic performance of both dicot and monocot crop plant species not possible with wild-type PHYB alleles.
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Affiliation(s)
- Wei Hu
- Department of Molecular and Cellular BiologyUniversity of CaliforniaDavisCAUSA
| | - Rosa Figueroa‐Balderas
- Public Intellectual Property Resource for Agriculture (PIPRA)University of CaliforniaDavisCAUSA
- Department of Viticulture and EnologyUniversity of CaliforniaDavisCAUSA
| | - Cecilia Chi‐Ham
- Public Intellectual Property Resource for Agriculture (PIPRA)University of CaliforniaDavisCAUSA
| | - J. Clark Lagarias
- Department of Molecular and Cellular BiologyUniversity of CaliforniaDavisCAUSA
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Hong WJ, Kim YJ, Chandran AKN, Jung KH. Infrastructures of systems biology that facilitate functional genomic study in rice. RICE (NEW YORK, N.Y.) 2019; 12:15. [PMID: 30874968 PMCID: PMC6419666 DOI: 10.1186/s12284-019-0276-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Accepted: 03/06/2019] [Indexed: 05/08/2023]
Abstract
Rice (Oryza sativa L.) is both a major staple food for the worldwide population and a model crop plant for studying the mode of action of agronomically valuable traits, providing information that can be applied to other crop plants. Due to the development of high-throughput technologies such as next generation sequencing and mass spectrometry, a huge mass of multi-omics data in rice has been accumulated. Through the integration of those data, systems biology in rice is becoming more advanced.To facilitate such systemic approaches, we have summarized current resources, such as databases and tools, for systems biology in rice. In this review, we categorize the resources using six omics levels: genomics, transcriptomics, proteomics, metabolomics, integrated omics, and functional genomics. We provide the names, websites, references, working states, and number of citations for each individual database or tool and discuss future prospects for the integrated understanding of rice gene functions.
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Affiliation(s)
- Woo-Jong Hong
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Korea
| | - Yu-Jin Kim
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Korea
| | | | - Ki-Hong Jung
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Korea.
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Mieulet D, Aubert G, Bres C, Klein A, Droc G, Vieille E, Rond-Coissieux C, Sanchez M, Dalmais M, Mauxion JP, Rothan C, Guiderdoni E, Mercier R. Unleashing meiotic crossovers in crops. NATURE PLANTS 2018. [PMID: 30478361 DOI: 10.1101/343509] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Improved plant varieties are important in our attempts to face the challenges of a growing human population and limited planet resources. Plant breeding relies on meiotic crossovers to combine favourable alleles into elite varieties1. However, meiotic crossovers are relatively rare, typically one to three per chromosome2, limiting the efficiency of the breeding process and related activities such as genetic mapping. Several genes that limit meiotic recombination were identified in the model species Arabidopsis thaliana2. Mutation of these genes in Arabidopsis induces a large increase in crossover frequency. However, it remained to be demonstrated whether crossovers could also be increased in crop species hybrids. We explored the effects of mutating the orthologues of FANCM3, RECQ44 or FIGL15 on recombination in three distant crop species, rice (Oryza sativa), pea (Pisum sativum) and tomato (Solanum lycopersicum). We found that the single recq4 mutation increases crossovers about three-fold in these crops, suggesting that manipulating RECQ4 may be a universal tool for increasing recombination in plants. Enhanced recombination could be used with other state-of-the-art technologies such as genomic selection, genome editing or speed breeding6 to enhance the pace and efficiency of plant improvement.
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Affiliation(s)
- Delphine Mieulet
- CIRAD, UMR AGAP, Montpellier, France
- Université Montpellier, CIRAD, INRA Montpellier SupAgro, Montpellier, France
| | - Gregoire Aubert
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté, Dijon, France
| | - Cecile Bres
- UMR 1332 BFP, INRA, Université Bordeaux, Villenave d'Ornon, France
| | - Anthony Klein
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté, Dijon, France
| | - Gaëtan Droc
- CIRAD, UMR AGAP, Montpellier, France
- Université Montpellier, CIRAD, INRA Montpellier SupAgro, Montpellier, France
| | - Emilie Vieille
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté, Dijon, France
| | - Celine Rond-Coissieux
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté, Dijon, France
| | - Myriam Sanchez
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté, Dijon, France
| | - Marion Dalmais
- Institute of Plant Sciences, Paris-Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Orsay, France
| | | | | | - Emmanuel Guiderdoni
- CIRAD, UMR AGAP, Montpellier, France
- Université Montpellier, CIRAD, INRA Montpellier SupAgro, Montpellier, France
| | - Raphael Mercier
- Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech, Université Paris-Saclay, Versailles, France.
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10
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Mieulet D, Aubert G, Bres C, Klein A, Droc G, Vieille E, Rond-Coissieux C, Sanchez M, Dalmais M, Mauxion JP, Rothan C, Guiderdoni E, Mercier R. Unleashing meiotic crossovers in crops. NATURE PLANTS 2018; 4:1010-1016. [PMID: 30478361 DOI: 10.1038/s41477-018-0311-x] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 10/17/2018] [Indexed: 05/21/2023]
Abstract
Improved plant varieties are important in our attempts to face the challenges of a growing human population and limited planet resources. Plant breeding relies on meiotic crossovers to combine favourable alleles into elite varieties1. However, meiotic crossovers are relatively rare, typically one to three per chromosome2, limiting the efficiency of the breeding process and related activities such as genetic mapping. Several genes that limit meiotic recombination were identified in the model species Arabidopsis thaliana2. Mutation of these genes in Arabidopsis induces a large increase in crossover frequency. However, it remained to be demonstrated whether crossovers could also be increased in crop species hybrids. We explored the effects of mutating the orthologues of FANCM3, RECQ44 or FIGL15 on recombination in three distant crop species, rice (Oryza sativa), pea (Pisum sativum) and tomato (Solanum lycopersicum). We found that the single recq4 mutation increases crossovers about three-fold in these crops, suggesting that manipulating RECQ4 may be a universal tool for increasing recombination in plants. Enhanced recombination could be used with other state-of-the-art technologies such as genomic selection, genome editing or speed breeding6 to enhance the pace and efficiency of plant improvement.
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Affiliation(s)
- Delphine Mieulet
- CIRAD, UMR AGAP, Montpellier, France
- Université Montpellier, CIRAD, INRA Montpellier SupAgro, Montpellier, France
| | - Gregoire Aubert
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté, Dijon, France
| | - Cecile Bres
- UMR 1332 BFP, INRA, Université Bordeaux, Villenave d'Ornon, France
| | - Anthony Klein
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté, Dijon, France
| | - Gaëtan Droc
- CIRAD, UMR AGAP, Montpellier, France
- Université Montpellier, CIRAD, INRA Montpellier SupAgro, Montpellier, France
| | - Emilie Vieille
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté, Dijon, France
| | - Celine Rond-Coissieux
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté, Dijon, France
| | - Myriam Sanchez
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté, Dijon, France
| | - Marion Dalmais
- Institute of Plant Sciences, Paris-Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Orsay, France
| | | | | | - Emmanuel Guiderdoni
- CIRAD, UMR AGAP, Montpellier, France
- Université Montpellier, CIRAD, INRA Montpellier SupAgro, Montpellier, France
| | - Raphael Mercier
- Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech, Université Paris-Saclay, Versailles, France.
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11
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Venkatesan A, Tagny Ngompe G, Hassouni NE, Chentli I, Guignon V, Jonquet C, Ruiz M, Larmande P. Agronomic Linked Data (AgroLD): A knowledge-based system to enable integrative biology in agronomy. PLoS One 2018; 13:e0198270. [PMID: 30500839 PMCID: PMC6269127 DOI: 10.1371/journal.pone.0198270] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 09/03/2018] [Indexed: 12/22/2022] Open
Abstract
Recent advances in high-throughput technologies have resulted in a tremendous increase in the amount of omics data produced in plant science. This increase, in conjunction with the heterogeneity and variability of the data, presents a major challenge to adopt an integrative research approach. We are facing an urgent need to effectively integrate and assimilate complementary datasets to understand the biological system as a whole. The Semantic Web offers technologies for the integration of heterogeneous data and their transformation into explicit knowledge thanks to ontologies. We have developed the Agronomic Linked Data (AgroLD- www.agrold.org), a knowledge-based system relying on Semantic Web technologies and exploiting standard domain ontologies, to integrate data about plant species of high interest for the plant science community e.g., rice, wheat, arabidopsis. We present some integration results of the project, which initially focused on genomics, proteomics and phenomics. AgroLD is now an RDF (Resource Description Format) knowledge base of 100M triples created by annotating and integrating more than 50 datasets coming from 10 data sources-such as Gramene.org and TropGeneDB-with 10 ontologies-such as the Gene Ontology and Plant Trait Ontology. Our evaluation results show users appreciate the multiple query modes which support different use cases. AgroLD's objective is to offer a domain specific knowledge platform to solve complex biological and agronomical questions related to the implication of genes/proteins in, for instances, plant disease resistance or high yield traits. We expect the resolution of these questions to facilitate the formulation of new scientific hypotheses to be validated with a knowledge-oriented approach.
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Affiliation(s)
- Aravind Venkatesan
- Institut de Biologie Computationnelle (IBC), Univ. of Montpellier, Montpellier, France
- LIRMM, Univ. of Montpellier & CNRS, Montpellier, France
| | - Gildas Tagny Ngompe
- Institut de Biologie Computationnelle (IBC), Univ. of Montpellier, Montpellier, France
- LIRMM, Univ. of Montpellier & CNRS, Montpellier, France
| | - Nordine El Hassouni
- Institut de Biologie Computationnelle (IBC), Univ. of Montpellier, Montpellier, France
- UMR AGAP, CIRAD, Montpellier, France
- South Green Bioinformatics Platform, Montpellier, France
| | - Imene Chentli
- Institut de Biologie Computationnelle (IBC), Univ. of Montpellier, Montpellier, France
- LIRMM, Univ. of Montpellier & CNRS, Montpellier, France
| | - Valentin Guignon
- South Green Bioinformatics Platform, Montpellier, France
- Bioversity International, Montpellier, France
| | - Clement Jonquet
- Institut de Biologie Computationnelle (IBC), Univ. of Montpellier, Montpellier, France
- LIRMM, Univ. of Montpellier & CNRS, Montpellier, France
| | - Manuel Ruiz
- Institut de Biologie Computationnelle (IBC), Univ. of Montpellier, Montpellier, France
- UMR AGAP, CIRAD, Montpellier, France
- South Green Bioinformatics Platform, Montpellier, France
- AGAP, Univ. of Montpellier, CIRAD, INRA, INRIA, SupAgro, Montpellier, France
| | - Pierre Larmande
- Institut de Biologie Computationnelle (IBC), Univ. of Montpellier, Montpellier, France
- LIRMM, Univ. of Montpellier & CNRS, Montpellier, France
- South Green Bioinformatics Platform, Montpellier, France
- DIADE, IRD, Univ. of Montpellier, Montpellier, France
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12
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Giri J, Bhosale R, Huang G, Pandey BK, Parker H, Zappala S, Yang J, Dievart A, Bureau C, Ljung K, Price A, Rose T, Larrieu A, Mairhofer S, Sturrock CJ, White P, Dupuy L, Hawkesford M, Perin C, Liang W, Peret B, Hodgman CT, Lynch J, Wissuwa M, Zhang D, Pridmore T, Mooney SJ, Guiderdoni E, Swarup R, Bennett MJ. Rice auxin influx carrier OsAUX1 facilitates root hair elongation in response to low external phosphate. Nat Commun 2018; 9:1408. [PMID: 29650967 PMCID: PMC5897452 DOI: 10.1038/s41467-018-03850-4] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 03/16/2018] [Indexed: 11/09/2022] Open
Abstract
Root traits such as root angle and hair length influence resource acquisition particularly for immobile nutrients like phosphorus (P). Here, we attempted to modify root angle in rice by disrupting the OsAUX1 auxin influx transporter gene in an effort to improve rice P acquisition efficiency. We show by X-ray microCT imaging that root angle is altered in the osaux1 mutant, causing preferential foraging in the top soil where P normally accumulates, yet surprisingly, P acquisition efficiency does not improve. Through closer investigation, we reveal that OsAUX1 also promotes root hair elongation in response to P limitation. Reporter studies reveal that auxin response increases in the root hair zone in low P environments. We demonstrate that OsAUX1 functions to mobilize auxin from the root apex to the differentiation zone where this signal promotes hair elongation when roots encounter low external P. We conclude that auxin and OsAUX1 play key roles in promoting root foraging for P in rice. Plant root architecture can adapt to different nutrient conditions in the soil. Here Giri et al. show that the rice auxin influx carrier AUX1 mobilizes auxin from the root apex to the differentiation zone and promotes root hair elongation when roots encounter low external phosphate.
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Affiliation(s)
- Jitender Giri
- Centre for Plant Integrative Biology (CPIB), School of Biosciences, University of Nottingham, Nottingham, LE12 5RD, UK.,National Institute of Plant Genome Research (NIPGR), New Delhi, India
| | - Rahul Bhosale
- Centre for Plant Integrative Biology (CPIB), School of Biosciences, University of Nottingham, Nottingham, LE12 5RD, UK
| | - Guoqiang Huang
- Centre for Plant Integrative Biology (CPIB), School of Biosciences, University of Nottingham, Nottingham, LE12 5RD, UK.,State Key Laboratory of Hybrid Rice, Shanghai Jiao Tong University, Shanghai, China
| | - Bipin K Pandey
- Centre for Plant Integrative Biology (CPIB), School of Biosciences, University of Nottingham, Nottingham, LE12 5RD, UK.,National Institute of Plant Genome Research (NIPGR), New Delhi, India
| | - Helen Parker
- Centre for Plant Integrative Biology (CPIB), School of Biosciences, University of Nottingham, Nottingham, LE12 5RD, UK
| | - Susan Zappala
- Centre for Plant Integrative Biology (CPIB), School of Biosciences, University of Nottingham, Nottingham, LE12 5RD, UK
| | - Jing Yang
- Centre for Plant Integrative Biology (CPIB), School of Biosciences, University of Nottingham, Nottingham, LE12 5RD, UK.,State Key Laboratory of Hybrid Rice, Shanghai Jiao Tong University, Shanghai, China
| | - Anne Dievart
- CIRAD, UMR AGAP, F34398, Montpellier, Cedex 5, France
| | | | - Karin Ljung
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-901 83, Umeå, Sweden
| | - Adam Price
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, AB24 2TZ, UK
| | - Terry Rose
- Japan International Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki, 305-8686, Japan.,Southern Cross Plant Science, Southern Cross University, Lismore, NSW, 2480, Australia
| | - Antoine Larrieu
- Centre for Plant Integrative Biology (CPIB), School of Biosciences, University of Nottingham, Nottingham, LE12 5RD, UK
| | - Stefan Mairhofer
- Centre for Plant Integrative Biology (CPIB), School of Biosciences, University of Nottingham, Nottingham, LE12 5RD, UK.,School of Computer Science, University of Nottingham, Jubilee Campus, Nottingham, NG8 1BB, UK
| | - Craig J Sturrock
- Centre for Plant Integrative Biology (CPIB), School of Biosciences, University of Nottingham, Nottingham, LE12 5RD, UK
| | - Philip White
- Ecological Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Lionel Dupuy
- Ecological Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | | | | | - Wanqi Liang
- Centre for Plant Integrative Biology (CPIB), School of Biosciences, University of Nottingham, Nottingham, LE12 5RD, UK.,State Key Laboratory of Hybrid Rice, Shanghai Jiao Tong University, Shanghai, China
| | - Benjamin Peret
- Centre for Plant Integrative Biology (CPIB), School of Biosciences, University of Nottingham, Nottingham, LE12 5RD, UK
| | - Charlie T Hodgman
- Centre for Plant Integrative Biology (CPIB), School of Biosciences, University of Nottingham, Nottingham, LE12 5RD, UK
| | - Jonathan Lynch
- Centre for Plant Integrative Biology (CPIB), School of Biosciences, University of Nottingham, Nottingham, LE12 5RD, UK.,Department of Plant Science, The Pennsylvania State University, 102 Tyson Building, University Park, PA, 16802, USA
| | - Matthias Wissuwa
- Japan International Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki, 305-8686, Japan
| | - Dabing Zhang
- State Key Laboratory of Hybrid Rice, Shanghai Jiao Tong University, Shanghai, China.,University of Adelaide-SJTU Joint Centre for Agriculture and Health, University of Adelaide, Waite Campus, Urrbrae, SA, Australia
| | - Tony Pridmore
- Centre for Plant Integrative Biology (CPIB), School of Biosciences, University of Nottingham, Nottingham, LE12 5RD, UK.,School of Computer Science, University of Nottingham, Jubilee Campus, Nottingham, NG8 1BB, UK
| | - Sacha J Mooney
- Centre for Plant Integrative Biology (CPIB), School of Biosciences, University of Nottingham, Nottingham, LE12 5RD, UK
| | | | - Ranjan Swarup
- Centre for Plant Integrative Biology (CPIB), School of Biosciences, University of Nottingham, Nottingham, LE12 5RD, UK
| | - Malcolm J Bennett
- Centre for Plant Integrative Biology (CPIB), School of Biosciences, University of Nottingham, Nottingham, LE12 5RD, UK.
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13
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Sandhu M, Sureshkumar V, Prakash C, Dixit R, Solanke AU, Sharma TR, Mohapatra T, S V AM. RiceMetaSys for salt and drought stress responsive genes in rice: a web interface for crop improvement. BMC Bioinformatics 2017; 18:432. [PMID: 28964253 PMCID: PMC5622590 DOI: 10.1186/s12859-017-1846-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Accepted: 09/21/2017] [Indexed: 11/17/2022] Open
Abstract
Background Genome-wide microarray has enabled development of robust databases for functional genomics studies in rice. However, such databases do not directly cater to the needs of breeders. Here, we have attempted to develop a web interface which combines the information from functional genomic studies across different genetic backgrounds with DNA markers so that they can be readily deployed in crop improvement. In the current version of the database, we have included drought and salinity stress studies since these two are the major abiotic stresses in rice. Results RiceMetaSys, a user-friendly and freely available web interface provides comprehensive information on salt responsive genes (SRGs) and drought responsive genes (DRGs) across genotypes, crop development stages and tissues, identified from multiple microarray datasets. ‘Physical position search’ is an attractive tool for those using QTL based approach for dissecting tolerance to salt and drought stress since it can provide the list of SRGs and DRGs in any physical interval. To identify robust candidate genes for use in crop improvement, the ‘common genes across varieties’ search tool is useful. Graphical visualization of expression profiles across genes and rice genotypes has been enabled to facilitate the user and to make the comparisons more impactful. Simple Sequence Repeat (SSR) search in the SRGs and DRGs is a valuable tool for fine mapping and marker assisted selection since it provides primers for survey of polymorphism. An external link to intron specific markers is also provided for this purpose. Bulk retrieval of data without any limit has been enabled in case of locus and SSR search. Conclusions The aim of this database is to facilitate users with a simple and straight-forward search options for identification of robust candidate genes from among thousands of SRGs and DRGs so as to facilitate linking variation in expression profiles to variation in phenotype. Database URL: http://14.139.229.201 Electronic supplementary material The online version of this article (10.1186/s12859-017-1846-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Maninder Sandhu
- ICAR-National Research Centre on Plant Biotechnology, LBS Building, Pusa Campus, New Delhi, 110012, India.,Shobhit University, Modipuram, Meerut, 250110, Uttar Pradesh, India
| | - V Sureshkumar
- ICAR-National Research Centre on Plant Biotechnology, LBS Building, Pusa Campus, New Delhi, 110012, India.,Department of Plant Molecular Biology and Bioinformatics, Tamil Nadu Agricultural University, Coimbatore, 641003, India
| | - Chandra Prakash
- ICAR-National Research Centre on Plant Biotechnology, LBS Building, Pusa Campus, New Delhi, 110012, India
| | - Rekha Dixit
- Shobhit University, Modipuram, Meerut, 250110, Uttar Pradesh, India.,Current address: Department of biotechnology, Keralverma faculty of science, Swami Vivekanand Subharti University, Meerut, 250005, Uttar Pradesh, India
| | - Amolkumar U Solanke
- ICAR-National Research Centre on Plant Biotechnology, LBS Building, Pusa Campus, New Delhi, 110012, India
| | - Tilak Raj Sharma
- ICAR-National Research Centre on Plant Biotechnology, LBS Building, Pusa Campus, New Delhi, 110012, India
| | - Trilochan Mohapatra
- Indian Council of Agricultural Research, Krishi Bhawan, New Delhi, 110001, India
| | - Amitha Mithra S V
- ICAR-National Research Centre on Plant Biotechnology, LBS Building, Pusa Campus, New Delhi, 110012, India.
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14
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Li G, Jain R, Chern M, Pham NT, Martin JA, Wei T, Schackwitz WS, Lipzen AM, Duong PQ, Jones KC, Jiang L, Ruan D, Bauer D, Peng Y, Barry KW, Schmutz J, Ronald PC. The Sequences of 1504 Mutants in the Model Rice Variety Kitaake Facilitate Rapid Functional Genomic Studies. THE PLANT CELL 2017; 29:1218-1231. [PMID: 28576844 PMCID: PMC5502455 DOI: 10.1105/tpc.17.00154] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 05/16/2017] [Accepted: 06/01/2017] [Indexed: 05/19/2023]
Abstract
The availability of a whole-genome sequenced mutant population and the cataloging of mutations of each line at a single-nucleotide resolution facilitate functional genomic analysis. To this end, we generated and sequenced a fast-neutron-induced mutant population in the model rice cultivar Kitaake (Oryza sativa ssp japonica), which completes its life cycle in 9 weeks. We sequenced 1504 mutant lines at 45-fold coverage and identified 91,513 mutations affecting 32,307 genes, i.e., 58% of all rice genes. We detected an average of 61 mutations per line. Mutation types include single-base substitutions, deletions, insertions, inversions, translocations, and tandem duplications. We observed a high proportion of loss-of-function mutations. We identified an inversion affecting a single gene as the causative mutation for the short-grain phenotype in one mutant line. This result reveals the usefulness of the resource for efficient, cost-effective identification of genes conferring specific phenotypes. To facilitate public access to this genetic resource, we established an open access database called KitBase that provides access to sequence data and seed stocks. This population complements other available mutant collections and gene-editing technologies. This work demonstrates how inexpensive next-generation sequencing can be applied to generate a high-density catalog of mutations.
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Affiliation(s)
- Guotian Li
- Department of Plant Pathology and the Genome Center, University of California, Davis, California 95616
- Grass Genetics, Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Rashmi Jain
- Department of Plant Pathology and the Genome Center, University of California, Davis, California 95616
- Grass Genetics, Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Mawsheng Chern
- Department of Plant Pathology and the Genome Center, University of California, Davis, California 95616
- Grass Genetics, Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Nikki T Pham
- Department of Plant Pathology and the Genome Center, University of California, Davis, California 95616
- Grass Genetics, Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Joel A Martin
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, California 94598
| | - Tong Wei
- Department of Plant Pathology and the Genome Center, University of California, Davis, California 95616
- Grass Genetics, Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Wendy S Schackwitz
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, California 94598
| | - Anna M Lipzen
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, California 94598
| | - Phat Q Duong
- Department of Plant Pathology and the Genome Center, University of California, Davis, California 95616
| | - Kyle C Jones
- Department of Plant Pathology and the Genome Center, University of California, Davis, California 95616
- Grass Genetics, Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Liangrong Jiang
- Department of Plant Pathology and the Genome Center, University of California, Davis, California 95616
- School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Deling Ruan
- Department of Plant Pathology and the Genome Center, University of California, Davis, California 95616
- Grass Genetics, Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Diane Bauer
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, California 94598
| | - Yi Peng
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, California 94598
| | - Kerrie W Barry
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, California 94598
| | - Jeremy Schmutz
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, California 94598
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806
| | - Pamela C Ronald
- Department of Plant Pathology and the Genome Center, University of California, Davis, California 95616
- Grass Genetics, Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, California 94720
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15
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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.
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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
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16
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Mieulet D, Jolivet S, Rivard M, Cromer L, Vernet A, Mayonove P, Pereira L, Droc G, Courtois B, Guiderdoni E, Mercier R. Turning rice meiosis into mitosis. Cell Res 2016; 26:1242-1254. [PMID: 27767093 DOI: 10.1038/cr.2016.117] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Revised: 08/09/2016] [Accepted: 08/30/2016] [Indexed: 11/09/2022] Open
Abstract
Introduction of clonal reproduction through seeds (apomixis) in crops has the potential to revolutionize agriculture by allowing self-propagation of any elite variety, in particular F1 hybrids. In the sexual model plant Arabidopsis thaliana synthetic clonal reproduction through seeds can be artificially implemented by (i) combining three mutations to turn meiosis into mitosis (MiMe) and (ii) crossing the obtained clonal gametes with a line expressing modified CENH3 and whose genome is eliminated in the zygote. Here we show that additional combinations of mutations can turn Arabidopsis meiosis into mitosis and that a combination of three mutations in rice (Oryza sativa) efficiently turns meiosis into mitosis, leading to the production of male and female clonal diploid gametes in this major crop. Successful implementation of the MiMe technology in the phylogenetically distant eudicot Arabidopsis and monocot rice opens doors for its application to any flowering plant and paves the way for introducing apomixis in crop species.
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Affiliation(s)
| | - Sylvie Jolivet
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78000 Versailles, France
| | - Maud Rivard
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78000 Versailles, France
| | - Laurence Cromer
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78000 Versailles, France
| | | | | | - Lucie Pereira
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78000 Versailles, France
| | - Gaëtan Droc
- CIRAD, UMR AGAP, 34398 Montpellier Cedex 5, France
| | | | | | - Raphael Mercier
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78000 Versailles, France
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17
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Dievart A, Perin C, Hirsch J, Bettembourg M, Lanau N, Artus F, Bureau C, Noel N, Droc G, Peyramard M, Pereira S, Courtois B, Morel JB, Guiderdoni E. The phenome analysis of mutant alleles in Leucine-Rich Repeat Receptor-Like Kinase genes in rice reveals new potential targets for stress tolerant cereals. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2016; 242:240-249. [PMID: 26566841 DOI: 10.1016/j.plantsci.2015.06.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Revised: 06/17/2015] [Accepted: 06/22/2015] [Indexed: 05/08/2023]
Abstract
Plants are constantly exposed to a variety of biotic and abiotic stresses that reduce their fitness and performance. At the molecular level, the perception of extracellular stimuli and the subsequent activation of defense responses require a complex interplay of signaling cascades, in which protein phosphorylation plays a central role. Several studies have shown that some members of the Leucine-Rich Repeat Receptor-Like Kinase (LRR-RLK) family are involved in stress and developmental pathways. We report here a systematic analysis of the role of the members of this gene family by mutant phenotyping in the monocotyledon model plant rice, Oryza sativa. We have then targeted 176 of the ∼320 LRR-RLK genes (55.7%) and genotyped 288 mutant lines. Position of the insertion was confirmed in 128 lines corresponding to 100 LRR-RLK genes (31.6% of the entire family). All mutant lines harboring homozygous insertions have been screened for phenotypes under normal conditions and under various abiotic stresses. Mutant plants have been observed at several stages of growth, from seedlings in Petri dishes to flowering and grain filling under greenhouse conditions. Our results show that 37 of the LRR-RLK rice genes are potential targets for improvement especially in the generation of abiotic stress tolerant cereals.
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Affiliation(s)
- Anne Dievart
- CIRAD, UMR AGAP, 34398 Montpellier cedex 5, France.
| | | | - Judith Hirsch
- INRA, UMR BGPI, INRA-CIRAD-SupAgro, TA 54/K, Campus International de Baillarguet, 34398 Montpellier cedex 5, France
| | | | - Nadège Lanau
- CIRAD, UMR AGAP, 34398 Montpellier cedex 5, France
| | | | | | - Nicolas Noel
- CIRAD, UMR AGAP, 34398 Montpellier cedex 5, France
| | - Gaétan Droc
- CIRAD, UMR AGAP, 34398 Montpellier cedex 5, France
| | | | - Serge Pereira
- INRA, UMR BGPI, INRA-CIRAD-SupAgro, TA 54/K, Campus International de Baillarguet, 34398 Montpellier cedex 5, France
| | | | - Jean-Benoit Morel
- INRA, UMR BGPI, INRA-CIRAD-SupAgro, TA 54/K, Campus International de Baillarguet, 34398 Montpellier cedex 5, France
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Khong GN, Pati PK, Richaud F, Parizot B, Bidzinski P, Mai CD, Bès M, Bourrié I, Meynard D, Beeckman T, Selvaraj MG, Manabu I, Genga AM, Brugidou C, Nang Do V, Guiderdoni E, Morel JB, Gantet P. OsMADS26 Negatively Regulates Resistance to Pathogens and Drought Tolerance in Rice. PLANT PHYSIOLOGY 2015; 169:2935-49. [PMID: 26424158 PMCID: PMC4677910 DOI: 10.1104/pp.15.01192] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 09/28/2015] [Indexed: 05/19/2023]
Abstract
Functional analyses of MADS-box transcription factors in plants have unraveled their role in major developmental programs (e.g. flowering and floral organ identity) as well as stress-related developmental processes, such as abscission, fruit ripening, and senescence. Overexpression of the rice (Oryza sativa) MADS26 gene in rice has revealed a possible function related to stress response. Here, we show that OsMADS26-down-regulated plants exhibit enhanced resistance against two major rice pathogens: Magnaporthe oryzae and Xanthomonas oryzae. Despite this enhanced resistance to biotic stresses, OsMADS26-down-regulated plants also displayed enhanced tolerance to water deficit. These phenotypes were observed in both controlled and field conditions. Interestingly, alteration of OsMADS26 expression does not have a strong impact on plant development. Gene expression profiling revealed that a majority of genes misregulated in overexpresser and down-regulated OsMADS26 lines compared with control plants are associated to biotic or abiotic stress response. Altogether, our data indicate that OsMADS26 acts as an upstream regulator of stress-associated genes and thereby, a hub to modulate the response to various stresses in the rice plant.
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Affiliation(s)
- Giang Ngan Khong
- Université de Montpellier, Unité Mixte de Recherche Diversité, Adaptation, et Développement des Plantes, 34095 Montpellier cedex 5, France (G.N.K., I.B., P.G.);Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Unité Mixte de Recherche Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales, 34398 Montpellier cedex 5, France (G.N.K., P.K.P., F.R., M.B., D.M., E.G.);Department of Biotechnology, Guru Nanak Dev University, Amritsar 143 005, India (P.K.P.);Department of Plant Systems Biology, Flanders Institute for Biotechnology, 9052 Ghent, Belgium (B.P., T.B.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (B.P., T.B.);Institut National de la Recherche Agronomique, Unité Mixte de Recherche Biologie et Génétique des Interactions Plante-Parasite, 34398 Montpellier, France (P.B., J.-B.M.);Laboratoire Mixte International Rice Functional Genomics and Plant Biotechnology, Institut de Recherche pour le Développement, University of Science and Technology of Hanoi, Agricultural Genetics Institute, 00 000 Hanoi, Vietnam (C.D.M., V.N.D., P.G.);International Center for Tropical Agriculture, 6713 Cali, Colombia (M.G.S., I.M.);Consiglio Nazionale delle Ricerche, Institute of Agricultural Biology and Biotechnology, 20133 Milan, Italy (A.-M.G.); andInstitut de Recherche pour le Développement, Unité Mixte de Recherche Interactions Plantes Microorganismes et Environnement, 34398 Montpellier cedex, France (C.B.)
| | - Pratap Kumar Pati
- Université de Montpellier, Unité Mixte de Recherche Diversité, Adaptation, et Développement des Plantes, 34095 Montpellier cedex 5, France (G.N.K., I.B., P.G.);Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Unité Mixte de Recherche Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales, 34398 Montpellier cedex 5, France (G.N.K., P.K.P., F.R., M.B., D.M., E.G.);Department of Biotechnology, Guru Nanak Dev University, Amritsar 143 005, India (P.K.P.);Department of Plant Systems Biology, Flanders Institute for Biotechnology, 9052 Ghent, Belgium (B.P., T.B.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (B.P., T.B.);Institut National de la Recherche Agronomique, Unité Mixte de Recherche Biologie et Génétique des Interactions Plante-Parasite, 34398 Montpellier, France (P.B., J.-B.M.);Laboratoire Mixte International Rice Functional Genomics and Plant Biotechnology, Institut de Recherche pour le Développement, University of Science and Technology of Hanoi, Agricultural Genetics Institute, 00 000 Hanoi, Vietnam (C.D.M., V.N.D., P.G.);International Center for Tropical Agriculture, 6713 Cali, Colombia (M.G.S., I.M.);Consiglio Nazionale delle Ricerche, Institute of Agricultural Biology and Biotechnology, 20133 Milan, Italy (A.-M.G.); andInstitut de Recherche pour le Développement, Unité Mixte de Recherche Interactions Plantes Microorganismes et Environnement, 34398 Montpellier cedex, France (C.B.)
| | - Frédérique Richaud
- Université de Montpellier, Unité Mixte de Recherche Diversité, Adaptation, et Développement des Plantes, 34095 Montpellier cedex 5, France (G.N.K., I.B., P.G.);Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Unité Mixte de Recherche Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales, 34398 Montpellier cedex 5, France (G.N.K., P.K.P., F.R., M.B., D.M., E.G.);Department of Biotechnology, Guru Nanak Dev University, Amritsar 143 005, India (P.K.P.);Department of Plant Systems Biology, Flanders Institute for Biotechnology, 9052 Ghent, Belgium (B.P., T.B.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (B.P., T.B.);Institut National de la Recherche Agronomique, Unité Mixte de Recherche Biologie et Génétique des Interactions Plante-Parasite, 34398 Montpellier, France (P.B., J.-B.M.);Laboratoire Mixte International Rice Functional Genomics and Plant Biotechnology, Institut de Recherche pour le Développement, University of Science and Technology of Hanoi, Agricultural Genetics Institute, 00 000 Hanoi, Vietnam (C.D.M., V.N.D., P.G.);International Center for Tropical Agriculture, 6713 Cali, Colombia (M.G.S., I.M.);Consiglio Nazionale delle Ricerche, Institute of Agricultural Biology and Biotechnology, 20133 Milan, Italy (A.-M.G.); andInstitut de Recherche pour le Développement, Unité Mixte de Recherche Interactions Plantes Microorganismes et Environnement, 34398 Montpellier cedex, France (C.B.)
| | - Boris Parizot
- Université de Montpellier, Unité Mixte de Recherche Diversité, Adaptation, et Développement des Plantes, 34095 Montpellier cedex 5, France (G.N.K., I.B., P.G.);Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Unité Mixte de Recherche Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales, 34398 Montpellier cedex 5, France (G.N.K., P.K.P., F.R., M.B., D.M., E.G.);Department of Biotechnology, Guru Nanak Dev University, Amritsar 143 005, India (P.K.P.);Department of Plant Systems Biology, Flanders Institute for Biotechnology, 9052 Ghent, Belgium (B.P., T.B.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (B.P., T.B.);Institut National de la Recherche Agronomique, Unité Mixte de Recherche Biologie et Génétique des Interactions Plante-Parasite, 34398 Montpellier, France (P.B., J.-B.M.);Laboratoire Mixte International Rice Functional Genomics and Plant Biotechnology, Institut de Recherche pour le Développement, University of Science and Technology of Hanoi, Agricultural Genetics Institute, 00 000 Hanoi, Vietnam (C.D.M., V.N.D., P.G.);International Center for Tropical Agriculture, 6713 Cali, Colombia (M.G.S., I.M.);Consiglio Nazionale delle Ricerche, Institute of Agricultural Biology and Biotechnology, 20133 Milan, Italy (A.-M.G.); andInstitut de Recherche pour le Développement, Unité Mixte de Recherche Interactions Plantes Microorganismes et Environnement, 34398 Montpellier cedex, France (C.B.)
| | - Przemyslaw Bidzinski
- Université de Montpellier, Unité Mixte de Recherche Diversité, Adaptation, et Développement des Plantes, 34095 Montpellier cedex 5, France (G.N.K., I.B., P.G.);Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Unité Mixte de Recherche Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales, 34398 Montpellier cedex 5, France (G.N.K., P.K.P., F.R., M.B., D.M., E.G.);Department of Biotechnology, Guru Nanak Dev University, Amritsar 143 005, India (P.K.P.);Department of Plant Systems Biology, Flanders Institute for Biotechnology, 9052 Ghent, Belgium (B.P., T.B.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (B.P., T.B.);Institut National de la Recherche Agronomique, Unité Mixte de Recherche Biologie et Génétique des Interactions Plante-Parasite, 34398 Montpellier, France (P.B., J.-B.M.);Laboratoire Mixte International Rice Functional Genomics and Plant Biotechnology, Institut de Recherche pour le Développement, University of Science and Technology of Hanoi, Agricultural Genetics Institute, 00 000 Hanoi, Vietnam (C.D.M., V.N.D., P.G.);International Center for Tropical Agriculture, 6713 Cali, Colombia (M.G.S., I.M.);Consiglio Nazionale delle Ricerche, Institute of Agricultural Biology and Biotechnology, 20133 Milan, Italy (A.-M.G.); andInstitut de Recherche pour le Développement, Unité Mixte de Recherche Interactions Plantes Microorganismes et Environnement, 34398 Montpellier cedex, France (C.B.)
| | - Chung Duc Mai
- Université de Montpellier, Unité Mixte de Recherche Diversité, Adaptation, et Développement des Plantes, 34095 Montpellier cedex 5, France (G.N.K., I.B., P.G.);Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Unité Mixte de Recherche Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales, 34398 Montpellier cedex 5, France (G.N.K., P.K.P., F.R., M.B., D.M., E.G.);Department of Biotechnology, Guru Nanak Dev University, Amritsar 143 005, India (P.K.P.);Department of Plant Systems Biology, Flanders Institute for Biotechnology, 9052 Ghent, Belgium (B.P., T.B.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (B.P., T.B.);Institut National de la Recherche Agronomique, Unité Mixte de Recherche Biologie et Génétique des Interactions Plante-Parasite, 34398 Montpellier, France (P.B., J.-B.M.);Laboratoire Mixte International Rice Functional Genomics and Plant Biotechnology, Institut de Recherche pour le Développement, University of Science and Technology of Hanoi, Agricultural Genetics Institute, 00 000 Hanoi, Vietnam (C.D.M., V.N.D., P.G.);International Center for Tropical Agriculture, 6713 Cali, Colombia (M.G.S., I.M.);Consiglio Nazionale delle Ricerche, Institute of Agricultural Biology and Biotechnology, 20133 Milan, Italy (A.-M.G.); andInstitut de Recherche pour le Développement, Unité Mixte de Recherche Interactions Plantes Microorganismes et Environnement, 34398 Montpellier cedex, France (C.B.)
| | - Martine Bès
- Université de Montpellier, Unité Mixte de Recherche Diversité, Adaptation, et Développement des Plantes, 34095 Montpellier cedex 5, France (G.N.K., I.B., P.G.);Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Unité Mixte de Recherche Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales, 34398 Montpellier cedex 5, France (G.N.K., P.K.P., F.R., M.B., D.M., E.G.);Department of Biotechnology, Guru Nanak Dev University, Amritsar 143 005, India (P.K.P.);Department of Plant Systems Biology, Flanders Institute for Biotechnology, 9052 Ghent, Belgium (B.P., T.B.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (B.P., T.B.);Institut National de la Recherche Agronomique, Unité Mixte de Recherche Biologie et Génétique des Interactions Plante-Parasite, 34398 Montpellier, France (P.B., J.-B.M.);Laboratoire Mixte International Rice Functional Genomics and Plant Biotechnology, Institut de Recherche pour le Développement, University of Science and Technology of Hanoi, Agricultural Genetics Institute, 00 000 Hanoi, Vietnam (C.D.M., V.N.D., P.G.);International Center for Tropical Agriculture, 6713 Cali, Colombia (M.G.S., I.M.);Consiglio Nazionale delle Ricerche, Institute of Agricultural Biology and Biotechnology, 20133 Milan, Italy (A.-M.G.); andInstitut de Recherche pour le Développement, Unité Mixte de Recherche Interactions Plantes Microorganismes et Environnement, 34398 Montpellier cedex, France (C.B.)
| | - Isabelle Bourrié
- Université de Montpellier, Unité Mixte de Recherche Diversité, Adaptation, et Développement des Plantes, 34095 Montpellier cedex 5, France (G.N.K., I.B., P.G.);Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Unité Mixte de Recherche Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales, 34398 Montpellier cedex 5, France (G.N.K., P.K.P., F.R., M.B., D.M., E.G.);Department of Biotechnology, Guru Nanak Dev University, Amritsar 143 005, India (P.K.P.);Department of Plant Systems Biology, Flanders Institute for Biotechnology, 9052 Ghent, Belgium (B.P., T.B.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (B.P., T.B.);Institut National de la Recherche Agronomique, Unité Mixte de Recherche Biologie et Génétique des Interactions Plante-Parasite, 34398 Montpellier, France (P.B., J.-B.M.);Laboratoire Mixte International Rice Functional Genomics and Plant Biotechnology, Institut de Recherche pour le Développement, University of Science and Technology of Hanoi, Agricultural Genetics Institute, 00 000 Hanoi, Vietnam (C.D.M., V.N.D., P.G.);International Center for Tropical Agriculture, 6713 Cali, Colombia (M.G.S., I.M.);Consiglio Nazionale delle Ricerche, Institute of Agricultural Biology and Biotechnology, 20133 Milan, Italy (A.-M.G.); andInstitut de Recherche pour le Développement, Unité Mixte de Recherche Interactions Plantes Microorganismes et Environnement, 34398 Montpellier cedex, France (C.B.)
| | - Donaldo Meynard
- Université de Montpellier, Unité Mixte de Recherche Diversité, Adaptation, et Développement des Plantes, 34095 Montpellier cedex 5, France (G.N.K., I.B., P.G.);Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Unité Mixte de Recherche Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales, 34398 Montpellier cedex 5, France (G.N.K., P.K.P., F.R., M.B., D.M., E.G.);Department of Biotechnology, Guru Nanak Dev University, Amritsar 143 005, India (P.K.P.);Department of Plant Systems Biology, Flanders Institute for Biotechnology, 9052 Ghent, Belgium (B.P., T.B.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (B.P., T.B.);Institut National de la Recherche Agronomique, Unité Mixte de Recherche Biologie et Génétique des Interactions Plante-Parasite, 34398 Montpellier, France (P.B., J.-B.M.);Laboratoire Mixte International Rice Functional Genomics and Plant Biotechnology, Institut de Recherche pour le Développement, University of Science and Technology of Hanoi, Agricultural Genetics Institute, 00 000 Hanoi, Vietnam (C.D.M., V.N.D., P.G.);International Center for Tropical Agriculture, 6713 Cali, Colombia (M.G.S., I.M.);Consiglio Nazionale delle Ricerche, Institute of Agricultural Biology and Biotechnology, 20133 Milan, Italy (A.-M.G.); andInstitut de Recherche pour le Développement, Unité Mixte de Recherche Interactions Plantes Microorganismes et Environnement, 34398 Montpellier cedex, France (C.B.)
| | - Tom Beeckman
- Université de Montpellier, Unité Mixte de Recherche Diversité, Adaptation, et Développement des Plantes, 34095 Montpellier cedex 5, France (G.N.K., I.B., P.G.);Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Unité Mixte de Recherche Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales, 34398 Montpellier cedex 5, France (G.N.K., P.K.P., F.R., M.B., D.M., E.G.);Department of Biotechnology, Guru Nanak Dev University, Amritsar 143 005, India (P.K.P.);Department of Plant Systems Biology, Flanders Institute for Biotechnology, 9052 Ghent, Belgium (B.P., T.B.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (B.P., T.B.);Institut National de la Recherche Agronomique, Unité Mixte de Recherche Biologie et Génétique des Interactions Plante-Parasite, 34398 Montpellier, France (P.B., J.-B.M.);Laboratoire Mixte International Rice Functional Genomics and Plant Biotechnology, Institut de Recherche pour le Développement, University of Science and Technology of Hanoi, Agricultural Genetics Institute, 00 000 Hanoi, Vietnam (C.D.M., V.N.D., P.G.);International Center for Tropical Agriculture, 6713 Cali, Colombia (M.G.S., I.M.);Consiglio Nazionale delle Ricerche, Institute of Agricultural Biology and Biotechnology, 20133 Milan, Italy (A.-M.G.); andInstitut de Recherche pour le Développement, Unité Mixte de Recherche Interactions Plantes Microorganismes et Environnement, 34398 Montpellier cedex, France (C.B.)
| | - Michael Gomez Selvaraj
- Université de Montpellier, Unité Mixte de Recherche Diversité, Adaptation, et Développement des Plantes, 34095 Montpellier cedex 5, France (G.N.K., I.B., P.G.);Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Unité Mixte de Recherche Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales, 34398 Montpellier cedex 5, France (G.N.K., P.K.P., F.R., M.B., D.M., E.G.);Department of Biotechnology, Guru Nanak Dev University, Amritsar 143 005, India (P.K.P.);Department of Plant Systems Biology, Flanders Institute for Biotechnology, 9052 Ghent, Belgium (B.P., T.B.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (B.P., T.B.);Institut National de la Recherche Agronomique, Unité Mixte de Recherche Biologie et Génétique des Interactions Plante-Parasite, 34398 Montpellier, France (P.B., J.-B.M.);Laboratoire Mixte International Rice Functional Genomics and Plant Biotechnology, Institut de Recherche pour le Développement, University of Science and Technology of Hanoi, Agricultural Genetics Institute, 00 000 Hanoi, Vietnam (C.D.M., V.N.D., P.G.);International Center for Tropical Agriculture, 6713 Cali, Colombia (M.G.S., I.M.);Consiglio Nazionale delle Ricerche, Institute of Agricultural Biology and Biotechnology, 20133 Milan, Italy (A.-M.G.); andInstitut de Recherche pour le Développement, Unité Mixte de Recherche Interactions Plantes Microorganismes et Environnement, 34398 Montpellier cedex, France (C.B.)
| | - Ishitani Manabu
- Université de Montpellier, Unité Mixte de Recherche Diversité, Adaptation, et Développement des Plantes, 34095 Montpellier cedex 5, France (G.N.K., I.B., P.G.);Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Unité Mixte de Recherche Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales, 34398 Montpellier cedex 5, France (G.N.K., P.K.P., F.R., M.B., D.M., E.G.);Department of Biotechnology, Guru Nanak Dev University, Amritsar 143 005, India (P.K.P.);Department of Plant Systems Biology, Flanders Institute for Biotechnology, 9052 Ghent, Belgium (B.P., T.B.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (B.P., T.B.);Institut National de la Recherche Agronomique, Unité Mixte de Recherche Biologie et Génétique des Interactions Plante-Parasite, 34398 Montpellier, France (P.B., J.-B.M.);Laboratoire Mixte International Rice Functional Genomics and Plant Biotechnology, Institut de Recherche pour le Développement, University of Science and Technology of Hanoi, Agricultural Genetics Institute, 00 000 Hanoi, Vietnam (C.D.M., V.N.D., P.G.);International Center for Tropical Agriculture, 6713 Cali, Colombia (M.G.S., I.M.);Consiglio Nazionale delle Ricerche, Institute of Agricultural Biology and Biotechnology, 20133 Milan, Italy (A.-M.G.); andInstitut de Recherche pour le Développement, Unité Mixte de Recherche Interactions Plantes Microorganismes et Environnement, 34398 Montpellier cedex, France (C.B.)
| | - Anna-Maria Genga
- Université de Montpellier, Unité Mixte de Recherche Diversité, Adaptation, et Développement des Plantes, 34095 Montpellier cedex 5, France (G.N.K., I.B., P.G.);Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Unité Mixte de Recherche Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales, 34398 Montpellier cedex 5, France (G.N.K., P.K.P., F.R., M.B., D.M., E.G.);Department of Biotechnology, Guru Nanak Dev University, Amritsar 143 005, India (P.K.P.);Department of Plant Systems Biology, Flanders Institute for Biotechnology, 9052 Ghent, Belgium (B.P., T.B.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (B.P., T.B.);Institut National de la Recherche Agronomique, Unité Mixte de Recherche Biologie et Génétique des Interactions Plante-Parasite, 34398 Montpellier, France (P.B., J.-B.M.);Laboratoire Mixte International Rice Functional Genomics and Plant Biotechnology, Institut de Recherche pour le Développement, University of Science and Technology of Hanoi, Agricultural Genetics Institute, 00 000 Hanoi, Vietnam (C.D.M., V.N.D., P.G.);International Center for Tropical Agriculture, 6713 Cali, Colombia (M.G.S., I.M.);Consiglio Nazionale delle Ricerche, Institute of Agricultural Biology and Biotechnology, 20133 Milan, Italy (A.-M.G.); andInstitut de Recherche pour le Développement, Unité Mixte de Recherche Interactions Plantes Microorganismes et Environnement, 34398 Montpellier cedex, France (C.B.)
| | - Christophe Brugidou
- Université de Montpellier, Unité Mixte de Recherche Diversité, Adaptation, et Développement des Plantes, 34095 Montpellier cedex 5, France (G.N.K., I.B., P.G.);Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Unité Mixte de Recherche Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales, 34398 Montpellier cedex 5, France (G.N.K., P.K.P., F.R., M.B., D.M., E.G.);Department of Biotechnology, Guru Nanak Dev University, Amritsar 143 005, India (P.K.P.);Department of Plant Systems Biology, Flanders Institute for Biotechnology, 9052 Ghent, Belgium (B.P., T.B.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (B.P., T.B.);Institut National de la Recherche Agronomique, Unité Mixte de Recherche Biologie et Génétique des Interactions Plante-Parasite, 34398 Montpellier, France (P.B., J.-B.M.);Laboratoire Mixte International Rice Functional Genomics and Plant Biotechnology, Institut de Recherche pour le Développement, University of Science and Technology of Hanoi, Agricultural Genetics Institute, 00 000 Hanoi, Vietnam (C.D.M., V.N.D., P.G.);International Center for Tropical Agriculture, 6713 Cali, Colombia (M.G.S., I.M.);Consiglio Nazionale delle Ricerche, Institute of Agricultural Biology and Biotechnology, 20133 Milan, Italy (A.-M.G.); andInstitut de Recherche pour le Développement, Unité Mixte de Recherche Interactions Plantes Microorganismes et Environnement, 34398 Montpellier cedex, France (C.B.)
| | - Vinh Nang Do
- Université de Montpellier, Unité Mixte de Recherche Diversité, Adaptation, et Développement des Plantes, 34095 Montpellier cedex 5, France (G.N.K., I.B., P.G.);Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Unité Mixte de Recherche Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales, 34398 Montpellier cedex 5, France (G.N.K., P.K.P., F.R., M.B., D.M., E.G.);Department of Biotechnology, Guru Nanak Dev University, Amritsar 143 005, India (P.K.P.);Department of Plant Systems Biology, Flanders Institute for Biotechnology, 9052 Ghent, Belgium (B.P., T.B.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (B.P., T.B.);Institut National de la Recherche Agronomique, Unité Mixte de Recherche Biologie et Génétique des Interactions Plante-Parasite, 34398 Montpellier, France (P.B., J.-B.M.);Laboratoire Mixte International Rice Functional Genomics and Plant Biotechnology, Institut de Recherche pour le Développement, University of Science and Technology of Hanoi, Agricultural Genetics Institute, 00 000 Hanoi, Vietnam (C.D.M., V.N.D., P.G.);International Center for Tropical Agriculture, 6713 Cali, Colombia (M.G.S., I.M.);Consiglio Nazionale delle Ricerche, Institute of Agricultural Biology and Biotechnology, 20133 Milan, Italy (A.-M.G.); andInstitut de Recherche pour le Développement, Unité Mixte de Recherche Interactions Plantes Microorganismes et Environnement, 34398 Montpellier cedex, France (C.B.)
| | - Emmanuel Guiderdoni
- Université de Montpellier, Unité Mixte de Recherche Diversité, Adaptation, et Développement des Plantes, 34095 Montpellier cedex 5, France (G.N.K., I.B., P.G.);Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Unité Mixte de Recherche Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales, 34398 Montpellier cedex 5, France (G.N.K., P.K.P., F.R., M.B., D.M., E.G.);Department of Biotechnology, Guru Nanak Dev University, Amritsar 143 005, India (P.K.P.);Department of Plant Systems Biology, Flanders Institute for Biotechnology, 9052 Ghent, Belgium (B.P., T.B.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (B.P., T.B.);Institut National de la Recherche Agronomique, Unité Mixte de Recherche Biologie et Génétique des Interactions Plante-Parasite, 34398 Montpellier, France (P.B., J.-B.M.);Laboratoire Mixte International Rice Functional Genomics and Plant Biotechnology, Institut de Recherche pour le Développement, University of Science and Technology of Hanoi, Agricultural Genetics Institute, 00 000 Hanoi, Vietnam (C.D.M., V.N.D., P.G.);International Center for Tropical Agriculture, 6713 Cali, Colombia (M.G.S., I.M.);Consiglio Nazionale delle Ricerche, Institute of Agricultural Biology and Biotechnology, 20133 Milan, Italy (A.-M.G.); andInstitut de Recherche pour le Développement, Unité Mixte de Recherche Interactions Plantes Microorganismes et Environnement, 34398 Montpellier cedex, France (C.B.)
| | - Jean-Benoit Morel
- Université de Montpellier, Unité Mixte de Recherche Diversité, Adaptation, et Développement des Plantes, 34095 Montpellier cedex 5, France (G.N.K., I.B., P.G.);Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Unité Mixte de Recherche Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales, 34398 Montpellier cedex 5, France (G.N.K., P.K.P., F.R., M.B., D.M., E.G.);Department of Biotechnology, Guru Nanak Dev University, Amritsar 143 005, India (P.K.P.);Department of Plant Systems Biology, Flanders Institute for Biotechnology, 9052 Ghent, Belgium (B.P., T.B.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (B.P., T.B.);Institut National de la Recherche Agronomique, Unité Mixte de Recherche Biologie et Génétique des Interactions Plante-Parasite, 34398 Montpellier, France (P.B., J.-B.M.);Laboratoire Mixte International Rice Functional Genomics and Plant Biotechnology, Institut de Recherche pour le Développement, University of Science and Technology of Hanoi, Agricultural Genetics Institute, 00 000 Hanoi, Vietnam (C.D.M., V.N.D., P.G.);International Center for Tropical Agriculture, 6713 Cali, Colombia (M.G.S., I.M.);Consiglio Nazionale delle Ricerche, Institute of Agricultural Biology and Biotechnology, 20133 Milan, Italy (A.-M.G.); andInstitut de Recherche pour le Développement, Unité Mixte de Recherche Interactions Plantes Microorganismes et Environnement, 34398 Montpellier cedex, France (C.B.)
| | - Pascal Gantet
- Université de Montpellier, Unité Mixte de Recherche Diversité, Adaptation, et Développement des Plantes, 34095 Montpellier cedex 5, France (G.N.K., I.B., P.G.);Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Unité Mixte de Recherche Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales, 34398 Montpellier cedex 5, France (G.N.K., P.K.P., F.R., M.B., D.M., E.G.);Department of Biotechnology, Guru Nanak Dev University, Amritsar 143 005, India (P.K.P.);Department of Plant Systems Biology, Flanders Institute for Biotechnology, 9052 Ghent, Belgium (B.P., T.B.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (B.P., T.B.);Institut National de la Recherche Agronomique, Unité Mixte de Recherche Biologie et Génétique des Interactions Plante-Parasite, 34398 Montpellier, France (P.B., J.-B.M.);Laboratoire Mixte International Rice Functional Genomics and Plant Biotechnology, Institut de Recherche pour le Développement, University of Science and Technology of Hanoi, Agricultural Genetics Institute, 00 000 Hanoi, Vietnam (C.D.M., V.N.D., P.G.);International Center for Tropical Agriculture, 6713 Cali, Colombia (M.G.S., I.M.);Consiglio Nazionale delle Ricerche, Institute of Agricultural Biology and Biotechnology, 20133 Milan, Italy (A.-M.G.); andInstitut de Recherche pour le Développement, Unité Mixte de Recherche Interactions Plantes Microorganismes et Environnement, 34398 Montpellier cedex, France (C.B.)
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Ishikawa T, Aki T, Yanagisawa S, Uchimiya H, Kawai-Yamada M. Overexpression of BAX INHIBITOR-1 Links Plasma Membrane Microdomain Proteins to Stress. PLANT PHYSIOLOGY 2015; 169:1333-43. [PMID: 26297139 PMCID: PMC4587443 DOI: 10.1104/pp.15.00445] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 08/17/2015] [Indexed: 05/22/2023]
Abstract
BAX INHIBITOR-1 (BI-1) is a cell death suppressor widely conserved in plants and animals. Overexpression of BI-1 enhances tolerance to stress-induced cell death in plant cells, although the molecular mechanism behind this enhancement is unclear. We recently found that Arabidopsis (Arabidopsis thaliana) BI-1 is involved in the metabolism of sphingolipids, such as the synthesis of 2-hydroxy fatty acids, suggesting the involvement of sphingolipids in the cell death regulatory mechanism downstream of BI-1. Here, we show that BI-1 affects cell death-associated components localized in sphingolipid-enriched microdomains of the plasma membrane in rice (Oryza sativa) cells. The amount of 2-hydroxy fatty acid-containing glucosylceramide increased in the detergent-resistant membrane (DRM; a biochemical counterpart of plasma membrane microdomains) fraction obtained from BI-1-overexpressing rice cells. Comparative proteomics analysis showed quantitative changes of DRM proteins in BI-1-overexpressing cells. In particular, the protein abundance of FLOTILLIN HOMOLOG (FLOT) and HYPERSENSITIVE-INDUCED REACTION PROTEIN3 (HIR3) markedly decreased in DRM of BI-1-overexpressing cells. Loss-of-function analysis demonstrated that FLOT and HIR3 are required for cell death by oxidative stress and salicylic acid, suggesting that the decreased levels of these proteins directly contribute to the stress-tolerant phenotypes in BI-1-overexpressing rice cells. These findings provide a novel biological implication of plant membrane microdomains in stress-induced cell death, which is negatively modulated by BI-1 overexpression via decreasing the abundance of a set of key proteins involved in cell death.
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Affiliation(s)
- Toshiki Ishikawa
- Graduate School of Science and Engineering (T.I., M.K.-Y.) and Institute for Environmental Science and Technology (H.U., M.K.-Y.), Saitama University, Saitama City, Saitama 338-8570, Japan; andGraduate School of Agricultural and Life Sciences (T.A., S.Y.) and Biotechnology Research Center (S.Y.), University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Toshihiko Aki
- Graduate School of Science and Engineering (T.I., M.K.-Y.) and Institute for Environmental Science and Technology (H.U., M.K.-Y.), Saitama University, Saitama City, Saitama 338-8570, Japan; andGraduate School of Agricultural and Life Sciences (T.A., S.Y.) and Biotechnology Research Center (S.Y.), University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Shuichi Yanagisawa
- Graduate School of Science and Engineering (T.I., M.K.-Y.) and Institute for Environmental Science and Technology (H.U., M.K.-Y.), Saitama University, Saitama City, Saitama 338-8570, Japan; andGraduate School of Agricultural and Life Sciences (T.A., S.Y.) and Biotechnology Research Center (S.Y.), University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Hirofumi Uchimiya
- Graduate School of Science and Engineering (T.I., M.K.-Y.) and Institute for Environmental Science and Technology (H.U., M.K.-Y.), Saitama University, Saitama City, Saitama 338-8570, Japan; andGraduate School of Agricultural and Life Sciences (T.A., S.Y.) and Biotechnology Research Center (S.Y.), University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Maki Kawai-Yamada
- Graduate School of Science and Engineering (T.I., M.K.-Y.) and Institute for Environmental Science and Technology (H.U., M.K.-Y.), Saitama University, Saitama City, Saitama 338-8570, Japan; andGraduate School of Agricultural and Life Sciences (T.A., S.Y.) and Biotechnology Research Center (S.Y.), University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
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20
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Coudert Y, Le VAT, Adam H, Bès M, Vignols F, Jouannic S, Guiderdoni E, Gantet P. Identification of CROWN ROOTLESS1-regulated genes in rice reveals specific and conserved elements of postembryonic root formation. THE NEW PHYTOLOGIST 2015; 206:243-254. [PMID: 25442012 DOI: 10.1111/nph.13196] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Accepted: 10/22/2014] [Indexed: 05/22/2023]
Abstract
In monocotyledons, the root system is mostly composed of postembryonic shoot-borne roots called crown roots. In rice (Oryza sativa), auxin promotes crown root initiation via the LOB-domain transcription factor (LBD) transcription factor CROWN ROOTLESS1 (CRL1); however, the gene regulatory network downstream of CRL1 remains largely unknown. We tested CRL1 transcriptional activity in yeast and in planta, identified CRL1-regulated genes using an inducible gene expression system and a transcriptome analysis, and used in situ hybridization to demonstrate coexpression of a sample of CRL1-regulated genes with CRL1 in crown root primordia. We show that CRL1 positively regulates 277 genes, including key genes involved in meristem patterning (such as QUIESCENT-CENTER SPECIFIC HOMEOBOX; QHB), cell proliferation and hormone homeostasis. Many genes are homologous to Arabidopsis genes involved in lateral root formation, but about a quarter are rice-specific. Our study reveals that several genes acting downstream of LBD transcription factors controlling postembryonic root formation are conserved between monocots and dicots. It also provides evidence that specific genes are involved in the formation of shoot-derived roots in rice.
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Affiliation(s)
| | - Van Anh Thi Le
- Université Montpellier 2, Montpellier, France
- IRD, UMR DIADE, Montpellier, France
- University of Science and Technology of Hanoi, LMI RICE, Agricultural Genetics Institute, Hanoi, Vietnam
| | | | | | | | | | | | - Pascal Gantet
- Université Montpellier 2, Montpellier, France
- IRD, UMR DIADE, Montpellier, France
- University of Science and Technology of Hanoi, LMI RICE, Agricultural Genetics Institute, Hanoi, Vietnam
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21
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Zhang YC, Liao JY, Li ZY, Yu Y, Zhang JP, Li QF, Qu LH, Shu WS, Chen YQ. Genome-wide screening and functional analysis identify a large number of long noncoding RNAs involved in the sexual reproduction of rice. Genome Biol 2014; 15:512. [PMID: 25517485 PMCID: PMC4253996 DOI: 10.1186/s13059-014-0512-1] [Citation(s) in RCA: 362] [Impact Index Per Article: 36.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Accepted: 10/28/2014] [Indexed: 01/09/2023] Open
Abstract
Background Long noncoding RNAs (lncRNAs) play important roles in a wide range of biological processes in mammals and plants. However, the systematic examination of lncRNAs in plants lags behind that in mammals. Recently, lncRNAs have been identified in Arabidopsis and wheat; however, no systematic screening of potential lncRNAs has been reported for the rice genome. Results In this study, we perform whole transcriptome strand-specific RNA sequencing (ssRNA-seq) of samples from rice anthers, pistils, and seeds 5 days after pollination and from shoots 14 days after germination. Using these data, together with 40 available rice RNA-seq datasets, we systematically analyze rice lncRNAs and definitively identify lncRNAs that are involved in the reproductive process. The results show that rice lncRNAs have some different characteristics compared to those of Arabidopsis and mammals and are expressed in a highly tissue-specific or stage-specific manner. We further verify the functions of a set of lncRNAs that are preferentially expressed in reproductive stages and identify several lncRNAs as competing endogenous RNAs (ceRNAs), which sequester miR160 or miR164 in a type of target mimicry. More importantly, one lncRNA, XLOC_057324, is demonstrated to play a role in panicle development and fertility. We also develop a source of rice lncRNA-associated insertional mutants. Conclusions Genome-wide screening and functional analysis enabled the identification of a set of lncRNAs that are involved in the sexual reproduction of rice. The results also provide a source of lncRNAs and associated insertional mutants in rice. Electronic supplementary material The online version of this article (doi:10.1186/s13059-014-0512-1) contains supplementary material, which is available to authorized users.
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Cesari S, Thilliez G, Ribot C, Chalvon V, Michel C, Jauneau A, Rivas S, Alaux L, Kanzaki H, Okuyama Y, Morel JB, Fournier E, Tharreau D, Terauchi R, Kroj T. The rice resistance protein pair RGA4/RGA5 recognizes the Magnaporthe oryzae effectors AVR-Pia and AVR1-CO39 by direct binding. THE PLANT CELL 2013; 25:1463-81. [PMID: 23548743 PMCID: PMC3663280 DOI: 10.1105/tpc.112.107201] [Citation(s) in RCA: 341] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Resistance (R) proteins recognize pathogen avirulence (Avr) proteins by direct or indirect binding and are multidomain proteins generally carrying a nucleotide binding (NB) and a leucine-rich repeat (LRR) domain. Two NB-LRR protein-coding genes from rice (Oryza sativa), RGA4 and RGA5, were found to be required for the recognition of the Magnaporthe oryzae effector AVR1-CO39. RGA4 and RGA5 also mediate recognition of the unrelated M. oryzae effector AVR-Pia, indicating that the corresponding R proteins possess dual recognition specificity. For RGA5, two alternative transcripts, RGA5-A and RGA5-B, were identified. Genetic analysis showed that only RGA5-A confers resistance, while RGA5-B is inactive. Yeast two-hybrid, coimmunoprecipitation, and fluorescence resonance energy transfer-fluorescence lifetime imaging experiments revealed direct binding of AVR-Pia and AVR1-CO39 to RGA5-A, providing evidence for the recognition of multiple Avr proteins by direct binding to a single R protein. Direct binding seems to be required for resistance as an inactive AVR-Pia allele did not bind RGA5-A. A small Avr interaction domain with homology to the Avr recognition domain in the rice R protein Pik-1 was identified in the C terminus of RGA5-A. This reveals a mode of Avr protein recognition through direct binding to a novel, non-LRR interaction domain.
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Affiliation(s)
- Stella Cesari
- INRA, UMR 385 Biologie et Génétique des Interactions Plante-Parasite, F-34398 Montpellier, France
- CIRAD, UMR Biologie et Génétique des Interactions Plante-Parasite, F-34398 Montpellier, France
| | - Gaëtan Thilliez
- INRA, UMR 385 Biologie et Génétique des Interactions Plante-Parasite, F-34398 Montpellier, France
- CIRAD, UMR Biologie et Génétique des Interactions Plante-Parasite, F-34398 Montpellier, France
| | - Cécile Ribot
- INRA, UMR 385 Biologie et Génétique des Interactions Plante-Parasite, F-34398 Montpellier, France
- CIRAD, UMR Biologie et Génétique des Interactions Plante-Parasite, F-34398 Montpellier, France
| | - Véronique Chalvon
- INRA, UMR 385 Biologie et Génétique des Interactions Plante-Parasite, F-34398 Montpellier, France
- CIRAD, UMR Biologie et Génétique des Interactions Plante-Parasite, F-34398 Montpellier, France
| | - Corinne Michel
- INRA, UMR 385 Biologie et Génétique des Interactions Plante-Parasite, F-34398 Montpellier, France
- CIRAD, UMR Biologie et Génétique des Interactions Plante-Parasite, F-34398 Montpellier, France
| | - Alain Jauneau
- CNRS, Plateforme Imagerie-Microscopie, Fédération de Recherche FR3450, 31326 Castanet-Tolosan, France
| | - Susana Rivas
- INRA, UMR 441 Laboratoire des Interactions Plantes-Microorganismes, F-31326 Castanet-Tolosan, France
- CNRS, UMR 2594 Laboratoire des Interactions Plantes-Microorganismes, F-31326 Castanet-Tolosan, France
| | - Ludovic Alaux
- INRA, UMR 385 Biologie et Génétique des Interactions Plante-Parasite, F-34398 Montpellier, France
- CIRAD, UMR Biologie et Génétique des Interactions Plante-Parasite, F-34398 Montpellier, France
| | - Hiroyuki Kanzaki
- Iwate Biotechnology Research Center, Kitakami, Iwate 024-0003, Japan
| | - Yudai Okuyama
- Iwate Biotechnology Research Center, Kitakami, Iwate 024-0003, Japan
| | - Jean-Benoit Morel
- INRA, UMR 385 Biologie et Génétique des Interactions Plante-Parasite, F-34398 Montpellier, France
- CIRAD, UMR Biologie et Génétique des Interactions Plante-Parasite, F-34398 Montpellier, France
| | - Elisabeth Fournier
- INRA, UMR 385 Biologie et Génétique des Interactions Plante-Parasite, F-34398 Montpellier, France
- CIRAD, UMR Biologie et Génétique des Interactions Plante-Parasite, F-34398 Montpellier, France
| | - Didier Tharreau
- INRA, UMR 385 Biologie et Génétique des Interactions Plante-Parasite, F-34398 Montpellier, France
- CIRAD, UMR Biologie et Génétique des Interactions Plante-Parasite, F-34398 Montpellier, France
| | - Ryohei Terauchi
- Iwate Biotechnology Research Center, Kitakami, Iwate 024-0003, Japan
| | - Thomas Kroj
- INRA, UMR 385 Biologie et Génétique des Interactions Plante-Parasite, F-34398 Montpellier, France
- CIRAD, UMR Biologie et Génétique des Interactions Plante-Parasite, F-34398 Montpellier, France
- Address correspondence to
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Puig J, Meynard D, Khong GN, Pauluzzi G, Guiderdoni E, Gantet P. Analysis of the expression of the AGL17-like clade of MADS-box transcription factors in rice. Gene Expr Patterns 2013; 13:160-70. [PMID: 23466806 DOI: 10.1016/j.gep.2013.02.004] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Revised: 02/16/2013] [Accepted: 02/20/2013] [Indexed: 11/29/2022]
Abstract
In plants, MADS-box transcription factors are key regulators of floral and fruit development, organ dehiscence and stress responses. Nevertheless, the functions of most of them are still unknown. In Arabidopsis thaliana, the AGL17-like clade of MADS-box transcription factors comprises four members. AGL17 is involved in floral induction, whereas AGL44/ANR1 is involved in the adaptive development of roots in response to nitrate. AGL21 is primarily expressed in the roots and AGL16 in the leaves, suggesting that these transcription factors may be involved in the control of vegetative development. In Oryza sativa, the AGL17-like clade comprises five members, OsMADS23, OsMADS25, OsMADS27, OsMADS57 and OsMADS61. In a first attempt to characterize their functions, we used promoter::Gus reporter gene fusions and RT-qPCR to study the expression patterns of these genes and their regulation by different external stimuli. The OsMADS23, OsMADS25, OsMADS27 and OsMADS57 promoters were active in the root's central cylinder. In addition, the OsMADS57 promoter was active in leaves, whereas the OsMADS61 promoter was only active in the leaf tips and the stem base. OsMADS25 and OsMADS27 transcripts accumulated in response to osmotic stress, whereas the expression levels of OsMADS25, OsMADS27 and OsMADS57 were slightly induced by nitrate. Each of these five genes was responsive to various hormonal treatments. These distinct expression patterns indicate that these five genes have specific and non-redundant functions that likely differs from those of their A. thaliana homologs.
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Affiliation(s)
- Jérôme Puig
- Université Montpellier 2, Bat 15, CC 002, Place Eugène Bataillon, 34095 Montpellier Cedex 5, France
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Rawat N, Himabindu K, Neeraja CN, Nair S, Bentur JS. Suppressive subtraction hybridization reveals that rice gall midge attack elicits plant-pathogen-like responses in rice. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2013; 63:122-130. [PMID: 23257077 DOI: 10.1016/j.plaphy.2012.11.021] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2012] [Accepted: 11/22/2012] [Indexed: 05/28/2023]
Abstract
The Asian rice gall midge, Orseolia oryzae (Diptera: Cecidomyiidae), is the third most destructive insect pest of rice (Oryza sativa L.). Till date, 11 gall midge resistance gene loci have been characterized in different rice varieties. To elucidate molecular basis of incompatible (hypersensitive response plus [HR+] type) and compatible rice-gall midge interactions, two suppressive subtraction hybridization cDNA libraries were constructed. These were enriched for differentially expressed transcripts after gall midge infestation in two rice varieties (resistant Suraksha and susceptible TN1). In total, 2784 ESTs were generated and sequenced from the two libraries, of which 1536 were from the resistant Suraksha and 1248 were from the susceptible TN1. Majority (80%) of the ESTs was non-redundant sequences with known functions and was classified into three principal gene ontology (GO) categories and 12 groups. Upregulation of NBS-LRR, Cytochrome P450, heat shock proteins, phenylalanine ammonia lyase and OsPR10α genes from the Suraksha library, as revealed by real-time PCR, indicated that R gene mediated, salicylic acid related defense pathway is likely to be involved in gall midge resistance. Present study suggested that resistance in Suraksha against gall midge is similar in nature to the resistance observed in plants against pathogens. However, in TN1, genes related to primary metabolism and redox were induced abundantly. Results suggested that genes encoding translationally controlled tumor protein and NAC domain proteins are likely to be involved in the gall midge susceptibility.
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Affiliation(s)
- Nidhi Rawat
- Directorate of Rice Research, Rajendranagar, Hyderabad 500030, Andhra Pradesh, India
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25
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Abstract
Transposon of Oryza sativa 17 (Tos17), a Ty1-Copia Class I retroelement, is one of the few active retroelements identified in rice, the main cereal crop of human consumption and the model genome for cereals. Tos17 exists in two copies in the standard Nipponbare japonica genome (n = 12 and 379 Mb). Tos17 copies are inactive in the plant grown under normal conditions. However, the copy located on chromosome 7 can be activated upon tissue culture. Plants regenerated from 3- and 5-month-old tissue cultures harbor, respectively, an average of 3.5 and 8 newly transposed copies that are stably inserted at new positions in the genome. Due to its favorable features, Tos17 has been extensively used for insertion mutagenesis of the model genome and 31,403 sequence indexed inserts harbored by regenerants/T-DNA plants are available in the databases. The corresponding seed stocks can be ordered from the laboratories which generated them. Both forward genetics and reverse genetics approaches using these lines have allowed the deciphering of gene function in rice. We report here two protocols for ascertaining the presence of a Tos17 insertion in a gene of interest among R2/T2 seeds received from Tos17 mutant stock centers: The first protocol is PCR-based and allows the identification of azygous, heterozygous and homozygous plants among progenies segregating the insertion. The second protocol is based on DNA blot analysis and can be used to identify homozygous plants carrying the Tos17 copy responsible for gene disruption while cleaning the mutant background from other unwitting mutagen inserts.
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The screening and preliminary construction of quality mutant population for cultivar “Nipponbare” in japonica rice (Oryza sativa). Biologia (Bratisl) 2012. [DOI: 10.2478/s11756-012-0106-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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27
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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.
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Affiliation(s)
- Mathias Lorieux
- IRD, UMR DIADE, CIAT, Agrobiodiversity and Biotechnology Project, Cali, Colombia
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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]
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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.
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Affiliation(s)
- Claudia Leoni
- Department of Biochemistry and Molecular Biology, University of Bari, Bari, Italy
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Coudert Y, Bès M, Le TVA, Pré M, Guiderdoni E, Gantet P. Transcript profiling of crown rootless1 mutant stem base reveals new elements associated with crown root development in rice. BMC Genomics 2011; 12:387. [PMID: 21806801 PMCID: PMC3163228 DOI: 10.1186/1471-2164-12-387] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2010] [Accepted: 08/01/2011] [Indexed: 12/17/2022] Open
Abstract
Background In rice, the major part of the post-embryonic root system is made of stem-derived roots named crown roots (CR). Among the few characterized rice mutants affected in root development, crown rootless1 mutant is unable to initiate crown root primordia. CROWN ROOTLESS1 (CRL1) is induced by auxin and encodes an AS2/LOB-domain transcription factor that acts upstream of the gene regulatory network controlling CR development. Results To identify genes involved in CR development, we compared global gene expression profile in stem bases of crl1 mutant and wild-type (WT) plants. Our analysis revealed that 250 and 236 genes are down- and up-regulated respectively in the crl1 mutant. Auxin induces CRL1 expression and consequently it is expected that auxin also alters the expression of genes that are early regulated by CRL1. To identify genes under the early control of CRL1, we monitored the expression kinetics of a selected subset of genes, mainly chosen among those exhibiting differential expression, in crl1 and WT following exogenous auxin treatment. This analysis revealed that most of these genes, mainly related to hormone, water and nutrient, development and homeostasis, were likely not regulated directly by CRL1. We hypothesized that the differential expression for these genes observed in the crl1 mutant is likely a consequence of the absence of CR formation. Otherwise, three CRL1-dependent auxin-responsive genes: FSM (FLATENNED SHOOT MERISTEM)/FAS1 (FASCIATA1), GTE4 (GENERAL TRANSCRIPTION FACTOR GROUP E4) and MAP (MICROTUBULE-ASSOCIATED PROTEIN) were identified. FSM/FAS1 and GTE4 are known in rice and Arabidopsis to be involved in the maintenance of root meristem through chromatin remodelling and cell cycle regulation respectively. Conclusion Our data showed that the differential regulation of most genes in crl1 versus WT may be an indirect consequence of CRL1 inactivation resulting from the absence of CR in the crl1 mutant. Nevertheless some genes, FAS1/FSM, GTE4 and MAP, require CRL1 to be induced by auxin suggesting that they are likely directly regulated by CRL1. These genes have a function related to polarized cell growth, cell cycle regulation or chromatin remodelling. This suggests that these genes are controlled by CRL1 and involved in CR initiation in rice.
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Affiliation(s)
- Yoan Coudert
- Université Montpellier 2, UMR DAP, Place Eugène Bataillon, 34095 Montpellier Cedex 5, France
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Dèrozier S, Samson F, Tamby JP, Guichard C, Brunaud V, Grevet P, Gagnot S, Label P, Leplé JC, Lecharny A, Aubourg S. Exploration of plant genomes in the FLAGdb++ environment. PLANT METHODS 2011; 7:8. [PMID: 21447150 PMCID: PMC3073958 DOI: 10.1186/1746-4811-7-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2010] [Accepted: 03/29/2011] [Indexed: 05/04/2023]
Abstract
BACKGROUND In the contexts of genomics, post-genomics and systems biology approaches, data integration presents a major concern. Databases provide crucial solutions: they store, organize and allow information to be queried, they enhance the visibility of newly produced data by comparing them with previously published results, and facilitate the exploration and development of both existing hypotheses and new ideas. RESULTS The FLAGdb++ information system was developed with the aim of using whole plant genomes as physical references in order to gather and merge available genomic data from in silico or experimental approaches. Available through a JAVA application, original interfaces and tools assist the functional study of plant genes by considering them in their specific context: chromosome, gene family, orthology group, co-expression cluster and functional network. FLAGdb++ is mainly dedicated to the exploration of large gene groups in order to decipher functional connections, to highlight shared or specific structural or functional features, and to facilitate translational tasks between plant species (Arabidopsis thaliana, Oryza sativa, Populus trichocarpa and Vitis vinifera). CONCLUSION Combining original data with the output of experts and graphical displays that differ from classical plant genome browsers, FLAGdb++ presents a powerful complementary tool for exploring plant genomes and exploiting structural and functional resources, without the need for computer programming knowledge. First launched in 2002, a 15th version of FLAGdb++ is now available and comprises four model plant genomes and over eight million genomic features.
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Affiliation(s)
- Sandra Dèrozier
- Unité de Recherche en Génomique Végétale (URGV), UMR INRA 1165 - Université d'Evry Val d'Essonne - ERL CNRS 8196, 2 Rue Gaston Crémieux, CP 5708, F-91057 Evry Cedex, France
- Unité Mathématique Informatique et Génome (MIG), UR INRA 1077, Domaine de Vilvert, F-78352 Jouy-en-Josas Cedex, France
| | - Franck Samson
- Unité de Recherche en Génomique Végétale (URGV), UMR INRA 1165 - Université d'Evry Val d'Essonne - ERL CNRS 8196, 2 Rue Gaston Crémieux, CP 5708, F-91057 Evry Cedex, France
- Unité Mathématique Informatique et Génome (MIG), UR INRA 1077, Domaine de Vilvert, F-78352 Jouy-en-Josas Cedex, France
| | - Jean-Philippe Tamby
- Unité de Recherche en Génomique Végétale (URGV), UMR INRA 1165 - Université d'Evry Val d'Essonne - ERL CNRS 8196, 2 Rue Gaston Crémieux, CP 5708, F-91057 Evry Cedex, France
| | - Cécile Guichard
- Unité de Recherche en Génomique Végétale (URGV), UMR INRA 1165 - Université d'Evry Val d'Essonne - ERL CNRS 8196, 2 Rue Gaston Crémieux, CP 5708, F-91057 Evry Cedex, France
| | - Véronique Brunaud
- Unité de Recherche en Génomique Végétale (URGV), UMR INRA 1165 - Université d'Evry Val d'Essonne - ERL CNRS 8196, 2 Rue Gaston Crémieux, CP 5708, F-91057 Evry Cedex, France
| | - Philippe Grevet
- Unité de Recherche en Génomique Végétale (URGV), UMR INRA 1165 - Université d'Evry Val d'Essonne - ERL CNRS 8196, 2 Rue Gaston Crémieux, CP 5708, F-91057 Evry Cedex, France
| | - Séverine Gagnot
- Unité de Recherche en Génomique Végétale (URGV), UMR INRA 1165 - Université d'Evry Val d'Essonne - ERL CNRS 8196, 2 Rue Gaston Crémieux, CP 5708, F-91057 Evry Cedex, France
- Laboratoire de Chimie Bactérienne (LCB), UPR CNRS 9043 - IFR 88, 31 Chemin Joseph Aiguier, F-13009 Marseille, France
| | - Philippe Label
- Unité Amélioration, Génétique et Physiologie Forestières (UAGPF), UR INRA 588, 2163 avenue de la Pomme de Pin, CS 4001 Ardon, F-45075 Orléans, France
| | - Jean-Charles Leplé
- Unité Amélioration, Génétique et Physiologie Forestières (UAGPF), UR INRA 588, 2163 avenue de la Pomme de Pin, CS 4001 Ardon, F-45075 Orléans, France
| | - Alain Lecharny
- Unité de Recherche en Génomique Végétale (URGV), UMR INRA 1165 - Université d'Evry Val d'Essonne - ERL CNRS 8196, 2 Rue Gaston Crémieux, CP 5708, F-91057 Evry Cedex, France
| | - Sébastien Aubourg
- Unité de Recherche en Génomique Végétale (URGV), UMR INRA 1165 - Université d'Evry Val d'Essonne - ERL CNRS 8196, 2 Rue Gaston Crémieux, CP 5708, F-91057 Evry Cedex, France
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Zhang J, Nallamilli BR, Mujahid H, Peng Z. OsMADS6 plays an essential role in endosperm nutrient accumulation and is subject to epigenetic regulation in rice (Oryza sativa). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2010; 64:604-17. [PMID: 20822505 DOI: 10.1111/j.1365-313x.2010.04354.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
MADS-box transcription factors are known for their roles in plant growth and development. The regulatory mechanisms of spatial and temporal specific expression of MADS-box genes and the function of MADS-box genes in other biological processes are still to be explored. Here, we report that OsMADS6 is highly expressed in flower and endosperm in Oryza sativa (rice). In addition to displaying a homeotic organ identity phenotype in all the four whorls of the flowers, the endosperm development is severely affected in its mutant. At least 32% of the seeds lacked starch filling and aborted. For seeds that have starch filling and develop to maturity, the starch content is reduced by at least 13%. In addition, the seed shape changes from elliptical to roundish, and the protein content increases from 12.1 to 15.0% (P < 0.05). Further investigation shows that ADP-glucose pyrophosphorylase genes, encoding the rate-limiting step enzyme in the starch synthesis pathway, are subject to the regulation of OsMADS6. Chromatin immunoprecipitation (ChIP)-PCR analyses on the chromatin of the OsMADS6 gene find that H3K27 is trimethylated in tissues where OsMADS6 is silenced, and that H3K36 is trimethylated in tissues where OsMADS6 is highly activated. Point mutation analysis reveals that leucine at position 83 is critical to OsMADS6 function.
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Affiliation(s)
- Jian Zhang
- Department of Biochemistry and Molecular Biology, Mississippi State University, MS 39762, USA
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33
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Vergne E, Grand X, Ballini E, Chalvon V, Saindrenan P, Tharreau D, Nottéghem JL, Morel JB. Preformed expression of defense is a hallmark of partial resistance to rice blast fungal pathogen Magnaporthe oryzae. BMC PLANT BIOLOGY 2010; 10:206. [PMID: 20849575 PMCID: PMC2956555 DOI: 10.1186/1471-2229-10-206] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2009] [Accepted: 09/17/2010] [Indexed: 05/09/2023]
Abstract
BACKGROUND Partial resistance to plant pathogens is extensively used in breeding programs since it could contribute to resistance durability. Partial resistance often builds up during plant development and confers quantitative and usually broad-spectrum resistance. However, very little is known on the mechanisms underlying partial resistance. Partial resistance is often explained by poorly effective induction of plant defense systems. By exploring rice natural diversity, we asked whether expression of defense systems before infection could explain partial resistance towards the major fungal pathogen Magnaporthe oryzae. The constitutive expression of 21 defense-related genes belonging to the defense system was monitored in 23 randomly sampled rice cultivars for which partial resistance was measured. RESULTS We identified a strong correlation between the expression of defense-related genes before infection and partial resistance. Only a weak correlation was found between the induction of defense genes and partial resistance. Increasing constitutive expression of defense-related genes also correlated with the establishment of partial resistance during plant development. Some rice genetic sub-groups displayed a particular pattern of constitutive expression, suggesting a strong natural polymorphism for constitutive expression of defense. Constitutive levels of hormones like salicylic acid and ethylene cannot explain constitutive expression of defense. We could identify an area of the genome that contributes to explain both preformed defense and partial resistance. CONCLUSION These results indicate that constitutive expression of defense-related genes is likely responsible for a large part of partial resistance in rice. The finding of this preformed defense system should help guide future breeding programs and open the possibility to identify the molecular mechanisms behind partial resistance.
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Affiliation(s)
- Emilie Vergne
- INRA, UMR BGPI INRA/CIRAD/SupAgro, Campus International de Baillarguet, TA A 54/K, 34398 Montpellier, France
| | - Xavier Grand
- INRA, UMR BGPI INRA/CIRAD/SupAgro, Campus International de Baillarguet, TA A 54/K, 34398 Montpellier, France
| | - Elsa Ballini
- Montpellier SUPAGRO, UMR BGPI INRA/CIRAD/SupAgro, Campus International de Baillarguet, TA A 54/K, 34398 Montpellier, France
| | - Véronique Chalvon
- INRA, UMR BGPI INRA/CIRAD/SupAgro, Campus International de Baillarguet, TA A 54/K, 34398 Montpellier, France
| | - P Saindrenan
- CNRS-Université Paris-Sud, Institut de Biotechnologie des Plantes, Physiopathologie Moléculaire Végétale, Bâtiment 630, 91405 Orsay Cedex, France
| | - D Tharreau
- CIRAD, UMR BGPI INRA/CIRAD/SupAgro, Campus International de Baillarguet, TA A 54/K, 34398 Montpellier, France
| | - J-L Nottéghem
- Montpellier SUPAGRO, UMR BGPI INRA/CIRAD/SupAgro, Campus International de Baillarguet, TA A 54/K, 34398 Montpellier, France
| | - J-B Morel
- INRA, UMR BGPI INRA/CIRAD/SupAgro, Campus International de Baillarguet, TA A 54/K, 34398 Montpellier, France
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The screening of mutants and construction of mutant library for Oryza sativa cv. Nipponbare via ethyl methane sulphonate inducing. Biologia (Bratisl) 2010. [DOI: 10.2478/s11756-010-0059-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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35
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Philippe R, Courtois B, McNally KL, Mournet P, El-Malki R, Le Paslier MC, Fabre D, Billot C, Brunel D, Glaszmann JC, This D. Structure, allelic diversity and selection of Asr genes, candidate for drought tolerance, in Oryza sativa L. and wild relatives. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2010; 121:769-787. [PMID: 20454772 DOI: 10.1007/s00122-010-1348-z] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2010] [Accepted: 04/19/2010] [Indexed: 05/29/2023]
Abstract
Asr (ABA, stress, ripening) genes represent a small gene family potentially involved in drought tolerance in several plant species. To analyze their interest for rice breeding for water-limited environments, this gene family was characterized further. Genomic organization of the gene family reveals six members located on four different chromosomes and with the same exon-intron structure. The maintenance of six members of the Asr gene family, which are the result of combination between tandem duplication and whole genome duplication, and their differential regulation under water stress, involves probably some sub-functionalization. The polymorphism of four members was studied in a worldwide collection of 204 accessions of Oryza sativa L. and 14 accessions of wild relatives (O. rufipogon and O. nivara). The nucleotide diversity of the Asr genes was globally low, but contrasted for the different genes, leading to different shapes of haplotype networks. Statistical tests for neutrality were used and compared to their distribution in a set of 111 reference genes spread across the genome, derived from another published study. Asr3 diversity exhibited a pattern concordant with a balancing selection at the species level and with a directional selection in the tropical japonica sub-group. This study provides a thorough description of the organization of the Asr family, and the nucleotide and haplotype diversity of four Asr in Oryza sativa species. Asr3 stood out as the best potential candidate. The polymorphism detected here represents a first step towards an association study between genetic polymorphisms of this gene family and variation in drought tolerance traits.
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Affiliation(s)
- Romain Philippe
- CIRAD, UMR Développement et Amélioration des Plantes, TA-A 96/03, 34398, Montpellier, France.
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Petit J, Bourgeois E, Stenger W, Bès M, Droc G, Meynard D, Courtois B, Ghesquière A, Sabot F, Panaud O, Guiderdoni E. Diversity of the Ty-1 copia retrotransposon Tos17 in rice (Oryza sativa L.) and the AA genome of the Oryza genus. Mol Genet Genomics 2009; 282:633-52. [PMID: 19856189 DOI: 10.1007/s00438-009-0493-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2009] [Accepted: 10/06/2009] [Indexed: 11/27/2022]
Abstract
Retrotransposons are mobile genetic elements, ubiquitous in Eukaryotic genomes, which have proven to be major genetic tools in determining phylogeny and structuring genetic diversity, notably in plants. We investigate here the diversity of the Ty1-copia retrotransposon Tos17 in the cultivated rice of Asian origin (Oryza sativa L.) and related AA genome species of the Oryza genus, to contribute understanding of the complex evolutionary history in this group of species through that of the element in the lineages. In that aim, we used a combination of Southern hybridization with a reverse transcriptase (RT) probe and an adapter-PCR mediated amplification, which allowed the sequencing of the genomic regions flanking Tos17 insertions. This analysis was carried out in a collection of 47 A-genome Oryza species accessions and 202 accessions of a core collection of Oryza sativa L. representative of the diversity of the species. Our Southern hybridization results show that Tos17 is present in all the accessions of the A-genome Oryza species, except for the South American species O. glumaepatula and the African species O. glaberrima and O. breviligulata. In O. sativa, the number of putative copies of Tos17 per accession ranged from 1 to 11 and multivariate analysis based on presence/absence of putative copies yielded a varietal clustering which is consistent with the isozyme classification of rice. Adapter PCR amplification and sequencing of flanking regions of Tos17 insertions in A-genome species other than O. sativa, followed by anchoring on the Nipponbare genome sequence, revealed 13 insertion sites of Tos17 in the surveyed O. rufipogon and O. longistaminata accessions, including one shared by both species. In O. sativa, the same approach revealed 25 insertions in the 6 varietal groups. Four insertion sites located on chromosomes 1, 2, 10, and 11 were found orthologous in O. rufipogon and O. sativa. The chromosome 1 insertion was also shared between O. rufipogon and O. longistaminata. The presence of Tos17 at three insertion sites was confirmed by retrotransposon-based insertion polymorphism (RBIP) in a sample of O. sativa accessions. The first insertion, located on chromosome 3 was only found in two japonica accessions from the Bhutan region while the second insertion, located on chromosome 10 was specific to the varietal groups 1, 2, and 5. The third insertion located on chromosome 7 corresponds to the only insertion shown active in rice so far, notably in cv. Nipponbare, where it has been extensively used for insertion mutagenesis. This copy was only found in a few varieties of the japonica group 6 and in one group 5 accession. Taken together, these results confirm that Tos17 was probably present in the ancestor of A-genome species and that some copies of the element remained active in some Oryza lineages--notably in O. rufipogon and O. longistaminata--as well as in the indica and japonica O. sativa L. lineages.
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Affiliation(s)
- Julie Petit
- CIRAD, UMR DAP, TAA96/03, 2477 Avenue Agropolis, 34398, Montpellier Cedex 5, France
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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.
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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
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Gu L, Guo R. Genome-wide detection and analysis of alternative splicing for nucleotide binding site-leucine-rich repeats sequences in rice. J Genet Genomics 2009; 34:247-57. [PMID: 17498622 DOI: 10.1016/s1673-8527(07)60026-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2006] [Accepted: 08/03/2006] [Indexed: 11/20/2022]
Abstract
Alternative splicing is a major contributor to genomic complexity and proteome diversity, yet the analysis of alternative splicing for the sequence containing nucleotide binding site and leucine-rich repeats (NBS-LRR) domain has not been explored in rice (Oryza sativa L.). Hidden Markov model (HMM) searches were performed for NBS-LRR domain. 875 NBS-LRR-encoding sequences were obtained from the Institute for Genomic Research (TIGR). All of them were used to blast Knowledge-based Oryza Molecular Biological Encyclopaedia (KOME), TIGR rice gene index (TGI), and Universal Protein Resource (UniProt) to obtain homologous full-length cDNAs (FL-cDNAs), tentative consensus sequences, and protein sequences. Alternative splicing events were detected from genomic alignment of FL-cDNAs, tentative consensus sequences, and protein sequences, which provide valuable information on splice variants of genes. These sequences were aligned to the corresponding BAC sequences using the Spidey and Sim4 programs and each of the proteins was aligned by tBLASTn. Of the 875 NBS-LRR sequences, 119 (13.6%) sequences had alternative splicing where multiple FL-cDNAs, TGI sequences and proteins corresponded to the same gene. 71 intron retention events, 20 exon skipping events, 16 alternative termination events, 25 alternative initiation events, 12 alternative 5' splicing events, and 16 alternative 3' splicing events were identified. Most of these alternative splices were supported by two or more transcripts. The data sets are available at http://www.bioinfor.org Furthermore, the bioinformatics analysis of splice boundaries showed that exon skipping and intron retention did not exhibit strong consensus. This implies a different regulation mechanism that guides the expression of splice isoforms. This article also presents the analysis of the effects of intron retention on proteins. The C-terminal regions of alternative proteins turned out to be more variable than the N-terminal regions. Finally, tissue distribution and protein localization of alternative splicing were explored. The largest categories of tissue distributions for alternative splicing were shoot and callus. More than one-thirds of protein localization for splice forms was plasma membrane and cytoplasm. All the NBS-LRR proteins for splice forms may have important function in disease resistance and activate downstream signaling pathways.
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Affiliation(s)
- Lianfeng Gu
- College of Agriculture, Guangdong Ocean University, Zhanjiang 524088, China
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Droc G, Périn C, Fromentin S, Larmande P. OryGenesDB 2008 update: database interoperability for functional genomics of rice. Nucleic Acids Res 2008; 37:D992-5. [PMID: 19036791 PMCID: PMC2686528 DOI: 10.1093/nar/gkn821] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
OryGenesDB (http://orygenesdb.cirad.fr/index.html) is a database developed for rice reverse genetics. OryGenesDB contains FSTs (flanking sequence tags) of various mutagens and functional genomics data, collected from both international insertion collections and the literature. The current release of OryGenesDB contains 171 000 FSTs, and annotations divided among 10 specific categories, totaling 78 annotation layers. Several additional tools have been added to the main interface; these tools enable the user to retrieve FSTs and design probes to analyze insertion lines. The major innovation of OryGenesDB 2008, besides updating the data and tools, is a new tool, Orylink, which was developed to speed up rice functional genomics by taking advantage of the resources developed in two related databases, Oryza Tag Line and GreenPhylDB. Orylink was designed to field complex queries across these three databases and store both the queries and their results in an intuitive manner. Orylink offers a simple and powerful virtual workbench for functional genomics. Alternatively, the Web services developed for Orylink can be used independently of its Web interface, increasing the interoperability between these different bioinformatics applications.
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Affiliation(s)
- Gaëtan Droc
- CIRAD Dept BIOS UMR DAP - TA40/03, 34398 Montpellier, France
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Cao PJ, Bartley LE, Jung KH, Ronald PC. Construction of a rice glycosyltransferase phylogenomic database and identification of rice-diverged glycosyltransferases. MOLECULAR PLANT 2008; 1:858-77. [PMID: 19825588 DOI: 10.1093/mp/ssn052] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Glycosyltransferases (GTs; EC 2.4.x.y) constitute a large group of enzymes that form glycosidic bonds through transfer of sugars from activated donor molecules to acceptor molecules. GTs are critical to the biosynthesis of plant cell walls, among other diverse functions. Based on the Carbohydrate-Active enZymes (CAZy) database and sequence similarity searches, we have identified 609 potential GT genes (loci) corresponding to 769 transcripts (gene models) in rice (Oryza sativa), the reference monocotyledonous species. Using domain composition and sequence similarity, these rice GTs were classified into 40 CAZy families plus an additional unknown class. We found that two Pfam domains of unknown function, PF04577 and PF04646, are associated with GT families GT61 and GT31, respectively. To facilitate functional analysis of this important and large gene family, we created a phylogenomic Rice GT Database (http://ricephylogenomics.ucdavis.edu/cellwalls/gt/). Through the database, several classes of functional genomic data, including mutant lines and gene expression data, can be displayed for each rice GT in the context of a phylogenetic tree, allowing for comparative analysis both within and between GT families. Comprehensive digital expression analysis of public gene expression data revealed that most ( approximately 80%) rice GTs are expressed. Based on analysis with Inparanoid, we identified 282 'rice-diverged' GTs that lack orthologs in sequenced dicots (Arabidopsis thaliana, Populus tricocarpa, Medicago truncatula, and Ricinus communis). Combining these analyses, we identified 33 rice-diverged GT genes (45 gene models) that are highly expressed in above-ground, vegetative tissues. From the literature and this analysis, 21 of these loci are excellent targets for functional examination toward understanding and manipulating grass cell wall qualities. Study of the remainder may reveal aspects of hormone and protein metabolism that are critical for rice biology. This list of 33 genes and the Rice GT Database will facilitate the study of GTs and cell wall synthesis in rice and other plants.
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Affiliation(s)
- Pei-Jian Cao
- Department of Plant Pathology, University of California, Davis, CA 95616, USA
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Vergne E, Ballini E, Droc G, Tharreau D, Nottéghem JL, Morel JB. ARCHIPELAGO: a dedicated resource for exploiting past, present, and future genomic data on disease resistance regulation in rice. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2008; 21:869-78. [PMID: 18533828 DOI: 10.1094/mpmi-21-7-0869] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Large amounts of expression data dealing with biotic stresses in rice have been produced in the past 5 years. Here, we extensively review approximately 70 publications and gather together information on more than 2,500 genes of the rice defense arsenal. This information was integrated into the OryGenesDB database. Several genes (e.g., metallothioneins and PBZ1) appear to be hallmarks of rice-pathogen interactions. Cross-referencing this information with the rice kinome highlighted some defense genes and kinases as possible central nodes of regulation. Cross referencing defense gene expression and quantitative trait loci (QTL) information identified some candidate genes for QTL. Overall, pathogenesis-related genes and disease regulators were found to be statistically associated with disease QTL. At the genomic level, we observed that some regions are richer than others and that some chromosomes (e.g., 11 and 12), which contain a lot of resistance gene analogs, have a low content of defense genes. Finally, we show that classical defense genes and defense-related genes such as resistance genes are preferentially organized in clusters. These clusters are not always coregulated and individual paralogs can show specific expression patterns. Thus, the rice defense arsenal has an ARCHIPELAGO-like genome structure at the macro and micro level. This resource opens new possibilities for marker-assisted selection and QTL cloning.
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Affiliation(s)
- E Vergne
- UMR BGPI INRA/CIRAD/Montpellier SupAgro, Campus International de Baillarguet, TA A54/K, 34398 Montpellier, France
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Vandenbussche M, Janssen A, Zethof J, van Orsouw N, Peters J, van Eijk MJT, Rijpkema AS, Schneiders H, Santhanam P, de Been M, van Tunen A, Gerats T. Generation of a 3D indexed Petunia insertion database for reverse genetics. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2008; 54:1105-14. [PMID: 18346192 DOI: 10.1111/j.1365-313x.2008.03482.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
BLAST searchable databases containing insertion flanking sequences have revolutionized reverse genetics in plant research. The development of such databases has so far been limited to a small number of model species and normally requires extensive labour input. Here we describe a highly efficient and widely applicable method that we adapted to identify unique transposon-flanking genomic sequences in Petunia. The procedure is based on a multi-dimensional pooling strategy for the collection of DNA samples; up to thousands of different templates are amplified from each of the DNA pools separately, and knowledge of their source is safeguarded by the use of pool-specific (sample) identification tags in one of the amplification primers. All products are combined into a single sample that is subsequently used as a template for unidirectional pyrosequencing. Computational analysis of the clustered sequence output allows automatic assignment of sequences to individual DNA sources. We have amplified and analysed transposon-flanking sequences from a Petunia transposon insertion library of 1000 individuals. Using 30 DNA isolations, 70 PCR reactions and two GS20 sequencing runs, we were able to allocate around 10 000 transposon flanking sequences to specific plants in the library. These sequences have been organized in a database that can be BLAST-searched for insertions into genes of interest. As a proof of concept, we have performed an in silico screen for insertions into members of the NAM/NAC transcription factor family. All in silico-predicted transposon insertions into members of this family could be confirmed in planta.
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Affiliation(s)
- Michiel Vandenbussche
- Radboud University, IWWR/Plant Genetics, Toernooiveld 1, 6525 ED Nijmegen, The Netherlands
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Conte MG, Gaillard S, Droc G, Perin C. Phylogenomics of plant genomes: a methodology for genome-wide searches for orthologs in plants. BMC Genomics 2008; 9:183. [PMID: 18426584 PMCID: PMC2377279 DOI: 10.1186/1471-2164-9-183] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2007] [Accepted: 04/21/2008] [Indexed: 12/04/2022] Open
Abstract
Background Gene ortholog identification is now a major objective for mining the increasing amount of sequence data generated by complete or partial genome sequencing projects. Comparative and functional genomics urgently need a method for ortholog detection to reduce gene function inference and to aid in the identification of conserved or divergent genetic pathways between several species. As gene functions change during evolution, reconstructing the evolutionary history of genes should be a more accurate way to differentiate orthologs from paralogs. Phylogenomics takes into account phylogenetic information from high-throughput genome annotation and is the most straightforward way to infer orthologs. However, procedures for automatic detection of orthologs are still scarce and suffer from several limitations. Results We developed a procedure for ortholog prediction between Oryza sativa and Arabidopsis thaliana. Firstly, we established an efficient method to cluster A. thaliana and O. sativa full proteomes into gene families. Then, we developed an optimized phylogenomics pipeline for ortholog inference. We validated the full procedure using test sets of orthologs and paralogs to demonstrate that our method outperforms pairwise methods for ortholog predictions. Conclusion Our procedure achieved a high level of accuracy in predicting ortholog and paralog relationships. Phylogenomic predictions for all validated gene families in both species were easily achieved and we can conclude that our methodology outperforms similarly based methods.
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Affiliation(s)
- Matthieu G Conte
- CIRAD, UMR 1096 TA40/03k, Avenue Agropolis, 34398 Montpellier, Cedex 5, France.
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Suzuki T, Eiguchi M, Kumamaru T, Satoh H, Matsusaka H, Moriguchi K, Nagato Y, Kurata N. MNU-induced mutant pools and high performance TILLING enable finding of any gene mutation in rice. Mol Genet Genomics 2008; 279:213-223. [PMID: 17952471 DOI: 10.1007/s00438-007-02932] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2007] [Revised: 09/12/2007] [Accepted: 09/17/2007] [Indexed: 05/26/2023]
Abstract
Mutant populations are indispensable genetic resources for functional genomics in all organisms. However, suitable rice mutant populations, induced either by chemicals or irradiation still have been rarely developed to date. To produce mutant pools and to launch a search system for rice gene mutations, we developed mutant populations of Oryza sativa japonica cv. Taichung 65, by treating single zygotic cells with N-methyl-N-nitrosourea (MNU). Mutagenesis in single zygotes can create mutations at a high frequency and rarely forms chimeric plants. A modified TILLING system using non-labeled primers and fast capillary gel electrophoresis was applied for high-throughput detection of single nucleotide substitution mutations. The mutation rate of an M(2) mutant population was calculated as 7.4 x 10(-6) per nucleotide representing one mutation in every 135 kb genome sequence. One can expect 7.4 single nucleotide substitution mutations in every 1 kb of gene region when using 1,000 M(2) mutant lines. The mutations were very evenly distributed over the regions examined. These results indicate that our rice mutant population generated by MNU-mutagenesis could be a promising resource for identifying mutations in any gene of rice. The modified TILLING method also proved very efficient and convenient in screening the mutant population.
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Affiliation(s)
- Tadzunu Suzuki
- Genetic Strains Research Center, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka, 411-8540, Japan
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45
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Ribot C, Hirsch J, Balzergue S, Tharreau D, Nottéghem JL, Lebrun MH, Morel JB. Susceptibility of rice to the blast fungus, Magnaporthe grisea. JOURNAL OF PLANT PHYSIOLOGY 2008; 165:114-24. [PMID: 17905473 DOI: 10.1016/j.jplph.2007.06.013] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2007] [Revised: 06/25/2007] [Accepted: 06/26/2007] [Indexed: 05/17/2023]
Abstract
The interaction between rice and the blast fungus Magnaporthe grisea is the focus of extensive studies on rice disease resistance and fungal infection mechanisms. Here, we review the characteristics of susceptible rice blast infections in terms of physiology, cytology and both host and pathogen transcriptional responses. The success of the infection and the type of disease symptoms strongly depend on environmental and developmental cues. After its penetration into a host cell, the fungus differentiates invasive hyphae that fill up the plant cell lumen and are in direct contact with the membrane of the infected cell. The infected plant cell is alive, displaying considerable vesicle accumulation near the fungus, which is consistent with the establishment of a biotrophic phase at this stage of the infection. Colonization of host tissues by the fungus occurs through the perforation of cell walls from adjacent cells, likely using plasmodesmata as breaking points, or through hyphal growth in the apoplasm. After a few days of biotrophic growth within rice tissues, the fungus switches to a necrotrophic-like phase associated with the onset of sporulation, leading to visible lesions. Genome-wide transcriptomic studies have shown that classical plant defence responses are triggered during a susceptible infection, although the kinetics and amplitude of these responses are slower and lower than in resistant interactions. Infected rice cells are submitted to an intense transcriptional reprogramming, where responses to hormones such as auxins, abscissic acid and jasmonates are likely involved. Consistent with the extensive plant-fungal exchanges during the biotrophic phase, many rice genes expressed during infection encode plasma membrane proteins. At the onset of lesion formation (5 days after the start of infection), M. grisea is actively reprogramming its transcription towards active DNA, RNA and protein syntheses to sustain its rapid growth in infected tissues. A striking characteristic of M. grisea genes expressed at this stage of the infection is the over-representation of genes encoding secreted proteins, mainly of unknown function. However, some of these secreted proteins are enzymes involved in cell wall, protein and lipid degradation, suggesting that the fungus is starting to degrade host polymers and cell walls or is remodelling its own cell wall. The next challenge will be to decipher the role of these induced plant and fungal genes in the susceptible interaction.
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Affiliation(s)
- Cécile Ribot
- UMR 5240 CNRS-UCB-INSA-BCS, Bayer CropScience, 14-20 rue Pierre Baizet BP9163, 69263 Lyon Cedex 09, France
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Collard BCY, Vera Cruz CM, McNally KL, Virk PS, Mackill DJ. Rice molecular breeding laboratories in the genomics era: Current status and future considerations. INTERNATIONAL JOURNAL OF PLANT GENOMICS 2008; 2008:524847. [PMID: 18528527 PMCID: PMC2408710 DOI: 10.1155/2008/524847] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2007] [Accepted: 03/15/2008] [Indexed: 05/20/2023]
Abstract
Using DNA markers in plant breeding with marker-assisted selection (MAS) could greatly improve the precision and efficiency of selection, leading to the accelerated development of new crop varieties. The numerous examples of MAS in rice have prompted many breeding institutes to establish molecular breeding labs. The last decade has produced an enormous amount of genomics research in rice, including the identification of thousands of QTLs for agronomically important traits, the generation of large amounts of gene expression data, and cloning and characterization of new genes, including the detection of single nucleotide polymorphisms. The pinnacle of genomics research has been the completion and annotation of genome sequences for indica and japonica rice. This information-coupled with the development of new genotyping methodologies and platforms, and the development of bioinformatics databases and software tools-provides even more exciting opportunities for rice molecular breeding in the 21st century. However, the great challenge for molecular breeders is to apply genomics data in actual breeding programs. Here, we review the current status of MAS in rice, current genomics projects and promising new genotyping methodologies, and evaluate the probable impact of genomics research. We also identify critical research areas to "bridge the application gap" between QTL identification and applied breeding that need to be addressed to realize the full potential of MAS, and propose ideas and guidelines for establishing rice molecular breeding labs in the postgenome sequence era to integrate molecular breeding within the context of overall rice breeding and research programs.
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Affiliation(s)
- Bert C. Y. Collard
- Hermitage Research Station, Queensland Department of Primary Industries & Fisheries, 604 Yangan Road, Warwick, Queensland 4370, Australia
| | - Casiana M. Vera Cruz
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
- *Casiana M. Vera Cruz:
| | - Kenneth L. McNally
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Parminder S. Virk
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - David J. Mackill
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
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Tanaka T, Antonio BA, Kikuchi S, Matsumoto T, Nagamura Y, Numa H, Sakai H, Wu J, Itoh T, Sasaki T, Aono R, Fujii Y, Habara T, Harada E, Kanno M, Kawahara Y, Kawashima H, Kubooka H, Matsuya A, Nakaoka H, Saichi N, Sanbonmatsu R, Sato Y, Shinso Y, Suzuki M, Takeda JI, Tanino M, Todokoro F, Yamaguchi K, Yamamoto N, Yamasaki C, Imanishi T, Okido T, Tada M, Ikeo K, Tateno Y, Gojobori T, Lin YC, Wei FJ, Hsing YI, Zhao Q, Han B, Kramer MR, McCombie RW, Lonsdale D, O'Donovan CC, Whitfield EJ, Apweiler R, Koyanagi KO, Khurana JP, Raghuvanshi S, Singh NK, Tyagi AK, Haberer G, Fujisawa M, Hosokawa S, Ito Y, Ikawa H, Shibata M, Yamamoto M, Bruskiewich RM, Hoen DR, Bureau TE, Namiki N, Ohyanagi H, Sakai Y, Nobushima S, Sakata K, Barrero RA, Sato Y, Souvorov A, Smith-White B, Tatusova T, An S, An G, OOta S, Fuks G, Fuks G, Messing J, Christie KR, Lieberherr D, Kim H, Zuccolo A, Wing RA, Nobuta K, Green PJ, Lu C, Meyers BC, Chaparro C, Piegu B, Panaud O, Echeverria M. The Rice Annotation Project Database (RAP-DB): 2008 update. Nucleic Acids Res 2007; 36:D1028-33. [PMID: 18089549 PMCID: PMC2238920 DOI: 10.1093/nar/gkm978] [Citation(s) in RCA: 195] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The Rice Annotation Project Database (RAP-DB) was created to provide the genome sequence assembly of the International Rice Genome Sequencing Project (IRGSP), manually curated annotation of the sequence, and other genomics information that could be useful for comprehensive understanding of the rice biology. Since the last publication of the RAP-DB, the IRGSP genome has been revised and reassembled. In addition, a large number of rice-expressed sequence tags have been released, and functional genomics resources have been produced worldwide. Thus, we have thoroughly updated our genome annotation by manual curation of all the functional descriptions of rice genes. The latest version of the RAP-DB contains a variety of annotation data as follows: clone positions, structures and functions of 31 439 genes validated by cDNAs, RNA genes detected by massively parallel signature sequencing (MPSS) technology and sequence similarity, flanking sequences of mutant lines, transposable elements, etc. Other annotation data such as Gnomon can be displayed along with those of RAP for comparison. We have also developed a new keyword search system to allow the user to access useful information. The RAP-DB is available at: http://rapdb.dna.affrc.go.jp/ and http://rapdb.lab.nig.ac.jp/.
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Affiliation(s)
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- National Institute of Agrobiological Sciences, Ibaraki 305-8602, Japan
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Conte MG, Gaillard S, Lanau N, Rouard M, Périn C. GreenPhylDB: a database for plant comparative genomics. Nucleic Acids Res 2007; 36:D991-8. [PMID: 17986457 PMCID: PMC2238940 DOI: 10.1093/nar/gkm934] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
GreenPhylDB (http://greenphyl.cirad.fr) is a comprehensive platform designed to facilitate comparative functional genomics in Oryza sativa and Arabidopsis thaliana genomes. The main functions of GreenPhylDB are to assign O. sativa and A. thaliana sequences to gene families using a semi-automatic clustering procedure and to create ‘orthologous’ groups using a phylogenomic approach. To date, GreenPhylDB comprises the most complete list of plant gene families, which have been manually curated (6421 families). GreenPhylDB also contains all of the phylogenomic relationships computed for 4375 families. A total of 492 TAIR, 1903 InterPro and 981 KEGG families and subfamilies were manually curated using the clusters created with the TribeMCL software. GreenPhylDB integrates information from several other databases including UniProt, KEGG, InterPro, TAIR and TIGR. Several entry points can be used to display phylogenomic relationships for A. thaliana or O. sativa sequences, using TAIR, TIGR gene ID, family name, InterPro, gene alias, UniProt or protein/nucleic sequence. Finally, a powerful phylogenomics tool, GreenPhyl Ortholog Search Tool (GOST), was incorporated into GreenPhylDB to predict orthologous relationships between O. sativa/A. thaliana protein(s) and sequences from other plant species.
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Affiliation(s)
- M G Conte
- CIRAD, Department BIOS, UMR DAP-TA40/03, 34398 Montpellier, France
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Piffanelli P, Droc G, Mieulet D, Lanau N, Bès M, Bourgeois E, Rouvière C, Gavory F, Cruaud C, Ghesquière A, Guiderdoni E. Large-scale characterization of Tos17 insertion sites in a rice T-DNA mutant library. PLANT MOLECULAR BIOLOGY 2007; 65:587-601. [PMID: 17874225 DOI: 10.1007/s11103-007-9222-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2007] [Accepted: 08/08/2007] [Indexed: 05/04/2023]
Abstract
We characterized the insertion sites of newly transposed copies of the tissue-culture-induced ty1-copia retrotransposon Tos17 in the Oryza Tag Line (OTL) T-DNA mutant library of rice cv. Nipponbare. While Nipponbare contains two native copies of Tos17 the number of additional copies, deduced from Southern blot analyses in a subset of 384 T-DNA lines and using a reverse transcriptase probe specific to the element, ranged from 1 to 8 and averaged 3.37. These copies were shown to be stably inherited and to segregate independently in the progenies of insertion lines. We took advantage of the absence of EcoRV restriction sites in the immediate vicinity of the 3' LTR of the native copies of Tos17 in the genome sequence of cv. Nipponbare, thereby preventing amplification of corresponding PCR fragments, to efficiently and selectively amplify and sequence flanking regions of newly transposed Tos17 inserts. From 25,286 T-DNA plants, we recovered 19,252 PCR products (76.1%), which were sequenced yielding 14,513 FSTs anchored on the rice pseudomolecules. Following elimination of redundant sequences due to the presence of T-DNA plants deriving from the same cell lineage, these FSTs corresponded to 11,689 unique insertion sites. These unique insertions exhibited higher densities in subtelomeric regions of the chromosomes and hot spots for integration, following a distribution that remarkably paralleled that of Tos17 sites in the National Institute for Agrobiological Sciences (NIAS) library. The insertion sites were mostly found in genic regions (77.5%) and preferably in coding sequences (68.8%) compared to unique T-DNA insertion sites in the same materials (49.1% and 28.3%, respectively). Predicted non- transposable element (TE) genes prone to a high frequency of Tos17 integration (i.e. from 5 to 121 inserts) in the OTL T-DNA collection were generally found to be also hot spots for integration in the NIAS library. The 9,060 Tos17 inserts inserted into non TE genes were found to disrupt a total of 2,773 genes with an average of 3.27 inserts per gene, similar to that in the NIAS library (3.28 inserts per gene on average) whereas the 4,472 T-DNA inserted into genes in the same materials disrupted a total of 3,911 genes (1.14 inserts per gene on average). Interestingly, genes disrupted by both Tos17 and T-DNA inserts in the library represented only 14.9% and 10.6% of the complement of genes interrupted by Tos17 and T-DNA inserts respectively while 52.1% of the genes tagged by Tos17 inserts in the OTL library were found to be tagged also in the NIAS Tos17 library. We concluded that the first advantage in characterizing Tos17 inserts in a rice T-DNA collection lies in a complementary tagging of novel genes and secondarily in finding other alleles in a same genetic background, thereby greatly enhancing the library genome coverage and its overall value for implementing forward and reverse genetics strategies.
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Affiliation(s)
- Pietro Piffanelli
- Biological Systems Department TAA96/03, CIRAD, UMR DAP 1098, 2477 Avenue Agropolis, Montpellier cedex 5 34398, France
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Suzuki T, Eiguchi M, Kumamaru T, Satoh H, Matsusaka H, Moriguchi K, Nagato Y, Kurata N. MNU-induced mutant pools and high performance TILLING enable finding of any gene mutation in rice. Mol Genet Genomics 2007; 279:213-23. [PMID: 17952471 DOI: 10.1007/s00438-007-0293-2] [Citation(s) in RCA: 102] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2007] [Revised: 09/12/2007] [Accepted: 09/17/2007] [Indexed: 02/07/2023]
Abstract
Mutant populations are indispensable genetic resources for functional genomics in all organisms. However, suitable rice mutant populations, induced either by chemicals or irradiation still have been rarely developed to date. To produce mutant pools and to launch a search system for rice gene mutations, we developed mutant populations of Oryza sativa japonica cv. Taichung 65, by treating single zygotic cells with N-methyl-N-nitrosourea (MNU). Mutagenesis in single zygotes can create mutations at a high frequency and rarely forms chimeric plants. A modified TILLING system using non-labeled primers and fast capillary gel electrophoresis was applied for high-throughput detection of single nucleotide substitution mutations. The mutation rate of an M(2) mutant population was calculated as 7.4 x 10(-6) per nucleotide representing one mutation in every 135 kb genome sequence. One can expect 7.4 single nucleotide substitution mutations in every 1 kb of gene region when using 1,000 M(2) mutant lines. The mutations were very evenly distributed over the regions examined. These results indicate that our rice mutant population generated by MNU-mutagenesis could be a promising resource for identifying mutations in any gene of rice. The modified TILLING method also proved very efficient and convenient in screening the mutant population.
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Affiliation(s)
- Tadzunu Suzuki
- Genetic Strains Research Center, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka, 411-8540, Japan
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