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Gottin C, Dievart A, Summo M, Droc G, Périn C, Ranwez V, Chantret N. A new comprehensive annotation of leucine-rich repeat-containing receptors in rice. Plant J 2021; 108:492-508. [PMID: 34382706 PMCID: PMC9292849 DOI: 10.1111/tpj.15456] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 07/23/2021] [Accepted: 07/30/2021] [Indexed: 06/13/2023]
Abstract
Oryza sativa (rice) plays an essential food security role for more than half of the world's population. Obtaining crops with high levels of disease resistance is a major challenge for breeders, especially today, given the urgent need for agriculture to be more sustainable. Plant resistance genes are mainly encoded by three large leucine-rich repeat (LRR)-containing receptor (LRR-CR) families: the LRR-receptor-like kinase (LRR-RLK), LRR-receptor-like protein (LRR-RLP) and nucleotide-binding LRR receptor (NLR). Using lrrprofiler, a pipeline that we developed to annotate and classify these proteins, we compared three publicly available annotations of the rice Nipponbare reference genome. The extended discrepancies that we observed for LRR-CR gene models led us to perform an in-depth manual curation of their annotations while paying special attention to nonsense mutations. We then transferred this manually curated annotation to Kitaake, a cultivar that is closely related to Nipponbare, using an optimized strategy. Here, we discuss the breakthrough achieved by manual curation when comparing genomes and, in addition to 'functional' and 'structural' annotations, we propose that the community adopts this approach, which we call 'comprehensive' annotation. The resulting data are crucial for further studies on the natural variability and evolution of LRR-CR genes in order to promote their use in breeding future resilient varieties.
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Affiliation(s)
- Céline Gottin
- UMR AGAP InstitutUniv MontpellierCIRAD, INRAEInstitut AgroF‐34398MontpellierFrance
- CIRADUMR AGAP InstitutF‐34398MontpellierFrance
| | - Anne Dievart
- UMR AGAP InstitutUniv MontpellierCIRAD, INRAEInstitut AgroF‐34398MontpellierFrance
- CIRADUMR AGAP InstitutF‐34398MontpellierFrance
| | - Marilyne Summo
- UMR AGAP InstitutUniv MontpellierCIRAD, INRAEInstitut AgroF‐34398MontpellierFrance
- CIRADUMR AGAP InstitutF‐34398MontpellierFrance
| | - Gaëtan Droc
- UMR AGAP InstitutUniv MontpellierCIRAD, INRAEInstitut AgroF‐34398MontpellierFrance
- CIRADUMR AGAP InstitutF‐34398MontpellierFrance
| | - Christophe Périn
- UMR AGAP InstitutUniv MontpellierCIRAD, INRAEInstitut AgroF‐34398MontpellierFrance
- CIRADUMR AGAP InstitutF‐34398MontpellierFrance
| | - Vincent Ranwez
- UMR AGAP InstitutUniv MontpellierCIRAD, INRAEInstitut AgroF‐34398MontpellierFrance
| | - Nathalie Chantret
- UMR AGAP InstitutUniv MontpellierCIRAD, INRAEInstitut AgroF‐34398MontpellierFrance
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Fayos I, Meunier AC, Vernet A, Navarro-Sanz S, Portefaix M, Lartaud M, Bastianelli G, Périn C, Nicolas A, Guiderdoni E. Assessment of the roles of SPO11-2 and SPO11-4 in meiosis in rice using CRISPR/Cas9 mutagenesis. J Exp Bot 2020; 71:7046-7058. [PMID: 32842152 DOI: 10.1093/jxb/eraa391] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 08/20/2020] [Indexed: 05/21/2023]
Abstract
In Arabidopsis, chromosomal double-strand breaks at meiosis are presumably catalyzed by two distinct SPO11 transesterases, AtSPO11-1 and AtSPO11-2, together with M-TOPVIB. To clarify the roles of the SPO11 paralogs in rice, we used CRISPR/Cas9 mutagenesis to produce null biallelic mutants in OsSPO11-1, OsSPO11-2, and OsSPO11-4. Similar to Osspo11-1, biallelic mutations in the first exon of OsSPO11-2 led to complete panicle sterility. Conversely, all Osspo11-4 biallelic mutants were fertile. To generate segregating Osspo11-2 mutant lines, we developed a strategy based on dual intron targeting. Similar to Osspo11-1, the pollen mother cells of Osspo11-2 progeny plants showed an absence of bivalent formation at metaphase I, aberrant segregation of homologous chromosomes, and formation of non-viable tetrads. In contrast, the chromosome behavior in Osspo11-4 male meiocytes was indistinguishable from that in the wild type. While similar numbers of OsDMC1 foci were revealed by immunostaining in wild-type and Osspo11-4 prophase pollen mother cells (114 and 101, respectively), a surprisingly high number (85) of foci was observed in the sterile Osspo11-2 mutant, indicative of a divergent function between OsSPO11-1 and OsSPO11-2. This study demonstrates that whereas OsSPO11-1 and OsSPO11-2 are the likely orthologs of AtSPO11-1 and AtSPO11-2, OsSPO11-4 has no major role in wild-type rice meiosis.
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Affiliation(s)
- Ian Fayos
- CIRAD, UMR AGAP, Montpellier Cedex, France
- Université de Montpellier, CIRAD-INRAe-Institut Agro, Montpellier, France
- Meiogenix, Paris, France
| | - Anne Cécile Meunier
- CIRAD, UMR AGAP, Montpellier Cedex, France
- Université de Montpellier, CIRAD-INRAe-Institut Agro, Montpellier, France
| | - Aurore Vernet
- CIRAD, UMR AGAP, Montpellier Cedex, France
- Université de Montpellier, CIRAD-INRAe-Institut Agro, Montpellier, France
| | - Sergi Navarro-Sanz
- CIRAD, UMR AGAP, Montpellier Cedex, France
- Université de Montpellier, CIRAD-INRAe-Institut Agro, Montpellier, France
| | - Murielle Portefaix
- CIRAD, UMR AGAP, Montpellier Cedex, France
- Université de Montpellier, CIRAD-INRAe-Institut Agro, Montpellier, France
| | - Marc Lartaud
- CIRAD, UMR AGAP, Montpellier Cedex, France
- Université de Montpellier, CIRAD-INRAe-Institut Agro, Montpellier, France
| | | | - Christophe Périn
- CIRAD, UMR AGAP, Montpellier Cedex, France
- Université de Montpellier, CIRAD-INRAe-Institut Agro, Montpellier, France
| | - Alain Nicolas
- Institut Curie, CNRS UMR 3244, PSL University, Paris Cedex, France
- Meiogenix, Paris, France
| | - Emmanuel Guiderdoni
- CIRAD, UMR AGAP, Montpellier Cedex, France
- Université de Montpellier, CIRAD-INRAe-Institut Agro, Montpellier, France
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Mounier T, Navarro-Sanz S, Bureau C, Antoine L, Varoquaux F, Durandet F, Périn C. A fast, efficient and high-throughput procedure involving laser microdissection and RT droplet digital PCR for tissue-specific expression profiling of rice roots. BMC Mol Cell Biol 2020; 21:92. [PMID: 33302866 PMCID: PMC7727186 DOI: 10.1186/s12860-020-00312-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 09/10/2020] [Indexed: 11/22/2022] Open
Abstract
Background In rice, the cortex and outer tissues play a key role in submergence tolerance. The cortex differentiates into aerenchyma, which are air-containing cavities that allow the flow of oxygen from shoots to roots, whereas exodermis suberification and sclerenchyma lignification limit oxygen loss from the mature parts of roots by forming a barrier to root oxygen loss (ROL). The genes and their networks involved in the cellular identity and differentiation of these tissues remain poorly understood. Identification and characterization of key regulators of aerenchyma and ROL barrier formation require determination of the specific expression profiles of these tissues. Results We optimized an approach combining laser microdissection (LM) and droplet digital RT-PCR (ddRT-PCR) for high-throughput identification of tissue-specific expression profiles. The developed protocol enables rapid (within 3 days) extraction of high-quality RNA from root tissues with a low contamination rate. We also demonstrated the possibility of extracting RNAs from paraffin blocks stored at 4 °C without any loss of quality. We included a detailed troubleshooting guide that should allow future users to adapt the proposed protocol to other tissues and/or species. We demonstrated that our protocol, which combines LM with ddRT-PCR, can be used as a complementary tool to in situ hybridization for tissue-specific characterization of gene expression even with a low RNA concentration input. We illustrated the efficiency of the proposed approach by validating three of four potential tissue-specific candidate genes detailed in the RiceXpro database. Conclusion The detailed protocol and the critical steps required to optimize its use for other species will democratize tissue-specific transcriptome approaches combining LM with ddRT-PCR for analyses of plants.
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Affiliation(s)
- Thibault Mounier
- CIRAD, UMR-AGAP, Université de Montpellier, Avenue Agropolis, F-34398, Montpellier Cedex 5, France
| | - Sergi Navarro-Sanz
- CIRAD, UMR-AGAP, Université de Montpellier, Avenue Agropolis, F-34398, Montpellier Cedex 5, France
| | - Charlotte Bureau
- CIRAD, UMR-AGAP, Université de Montpellier, Avenue Agropolis, F-34398, Montpellier Cedex 5, France
| | - Lefeuvre Antoine
- IAGE Company, Avenue Agropolis, F-34398, Montpellier Cedex 5, France
| | - Fabrice Varoquaux
- CIRAD, UMR-AGAP, Université de Montpellier, Avenue Agropolis, F-34398, Montpellier Cedex 5, France
| | - Franz Durandet
- IAGE Company, Avenue Agropolis, F-34398, Montpellier Cedex 5, France
| | - Christophe Périn
- CIRAD, UMR-AGAP, Université de Montpellier, Avenue Agropolis, F-34398, Montpellier Cedex 5, France.
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Yoon J, Cho LH, Yang W, Pasriga R, Wu Y, Hong WJ, Bureau C, Wi SJ, Zhang T, Wang R, Zhang D, Jung KH, Park KY, Périn C, Zhao Y, An G. Homeobox transcription factor OsZHD2 promotes root meristem activity in rice by inducing ethylene biosynthesis. J Exp Bot 2020; 71:5348-5364. [PMID: 32449922 PMCID: PMC7501826 DOI: 10.1093/jxb/eraa209] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Accepted: 04/27/2020] [Indexed: 05/11/2023]
Abstract
Root meristem activity is the most critical process influencing root development. Although several factors that regulate meristem activity have been identified in rice, studies on the enhancement of meristem activity in roots are limited. We identified a T-DNA activation tagging line of a zinc-finger homeobox gene, OsZHD2, which has longer seminal and lateral roots due to increased meristem activity. The phenotypes were confirmed in transgenic plants overexpressing OsZHD2. In addition, the overexpressing plants showed enhanced grain yield under low nutrient and paddy field conditions. OsZHD2 was preferentially expressed in the shoot apical meristem and root tips. Transcriptome analyses and quantitative real-time PCR experiments on roots from the activation tagging line and the wild type showed that genes for ethylene biosynthesis were up-regulated in the activation line. Ethylene levels were higher in the activation lines compared with the wild type. ChIP assay results suggested that OsZHD2 induces ethylene biosynthesis by controlling ACS5 directly. Treatment with ACC (1-aminocyclopropane-1-carboxylic acid), an ethylene precursor, induced the expression of the DR5 reporter at the root tip and stele, whereas treatment with an ethylene biosynthesis inhibitor, AVG (aminoethoxyvinylglycine), decreased that expression in both the wild type and the OsZHD2 overexpression line. These observations suggest that OsZHD2 enhances root meristem activity by influencing ethylene biosynthesis and, in turn, auxin.
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Affiliation(s)
- Jinmi Yoon
- Crop Biotech Institute and Graduate School of Biotechnology, Kyung Hee University, Yongin, Korea
| | - Lae-Hyeon Cho
- Crop Biotech Institute and Graduate School of Biotechnology, Kyung Hee University, Yongin, Korea
- Department of Plant Bioscience, Pusan National University, Miryang, Korea
| | - Wenzhu Yang
- Department of Crop Genomics and Genetic Improvement, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Richa Pasriga
- Crop Biotech Institute and Graduate School of Biotechnology, Kyung Hee University, Yongin, Korea
| | - Yunfei Wu
- Crop Biotech Institute and Graduate School of Biotechnology, Kyung Hee University, Yongin, Korea
| | - Woo-Jong Hong
- Crop Biotech Institute and Graduate School of Biotechnology, Kyung Hee University, Yongin, Korea
| | - Charlotte Bureau
- Agricultural Research Centre For International Development, Paris, France
| | - Soo Jin Wi
- Department of Biology, Sunchon National University, Sunchon, Chonnam, Korea
| | - Tao Zhang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Rongchen Wang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Dabing Zhang
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University–University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University Shanghai, China
- School of Agriculture, Food and Wine, University of Adelaide Urrbrae, SA, Australia
| | - Ki-Hong Jung
- Crop Biotech Institute and Graduate School of Biotechnology, Kyung Hee University, Yongin, Korea
| | - Ky Young Park
- Department of Biology, Sunchon National University, Sunchon, Chonnam, Korea
| | - Christophe Périn
- Agricultural Research Centre For International Development, Paris, France
| | - Yunde Zhao
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, USA
| | - Gynheung An
- Crop Biotech Institute and Graduate School of Biotechnology, Kyung Hee University, Yongin, Korea
- Correspondence:
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Abstract
Because of their high level of diversity and complex evolutionary histories, most studies on plant receptor-like kinase subfamilies have focused on their kinase domains. With the large amount of genome sequence data available today, particularly on basal land plants and Charophyta, more attention should be paid to primary events that shaped the diversity of the RLK gene family. We thus focus on the motifs and domains found in association with kinase domains to illustrate their origin, organization, and evolutionary dynamics. We discuss when these different domain associations first occurred and how they evolved, based on a literature review complemented by some of our unpublished results.
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Affiliation(s)
- Anne Dievart
- CIRAD, UMR AGAP, F-34398 Montpellier, France;
- AGAP, Université de Montpellier, CIRAD, INRA, Montpellier SupAgro, F-34060 Montpellier, France
| | - Céline Gottin
- CIRAD, UMR AGAP, F-34398 Montpellier, France;
- AGAP, Université de Montpellier, CIRAD, INRA, Montpellier SupAgro, F-34060 Montpellier, France
| | - Christophe Périn
- CIRAD, UMR AGAP, F-34398 Montpellier, France;
- AGAP, Université de Montpellier, CIRAD, INRA, Montpellier SupAgro, F-34060 Montpellier, France
| | - Vincent Ranwez
- AGAP, Université de Montpellier, CIRAD, INRA, Montpellier SupAgro, F-34060 Montpellier, France
| | - Nathalie Chantret
- AGAP, Université de Montpellier, CIRAD, INRA, Montpellier SupAgro, F-34060 Montpellier, France
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Herbert L, Meunier AC, Bes M, Vernet A, Portefaix M, Durandet F, Michel R, Chaine C, This P, Guiderdoni E, Périn C. Beyond Seek and Destroy: how to Generate Allelic Series Using Genome Editing Tools. Rice (N Y) 2020; 13:5. [PMID: 31993780 PMCID: PMC6987269 DOI: 10.1186/s12284-020-0366-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 01/14/2020] [Indexed: 05/11/2023]
Abstract
Genome editing tools have greatly facilitated the functional analysis of genes of interest by targeted mutagenesis. Many usable genome editing tools, including different site-specific nucleases and editor databases that allow single-nucleotide polymorphisms (SNPs) to be introduced at a given site, are now available. These tools can be used to generate high allelic diversity at a given locus to facilitate gene function studies, including examining the role of a specific protein domain or a single amino acid. We compared the effects, efficiencies and mutation types generated by our LbCPF1, SpCAS9 and base editor (BECAS9) constructs for the OsCAO1 gene. SpCAS9 and LbCPF1 have similar efficiencies in generating mutations but differ in the types of mutations induced, with the majority of changes being single-nucleotide insertions and short deletions for SpCAS9 and LbCPF1, respectively. The proportions of heterozygotes also differed, representing a majority in our LbCPF1, while with SpCAS9, we obtained a large number of biallelic mutants. Finally, we demonstrated that it is possible to specifically introduce stop codons using the BECAS9 with an acceptable efficiency of approximately 20%. Based on these results, a rational choice among these three alternatives may be made depending on the type of mutation that one wishes to introduce, the three systems being complementary. SpCAS9 remains the best choice to generate KO mutations in primary transformants, while if the desired gene mutation interferes with regeneration or viability, the use of our LbCPF1 construction will be preferred, because it produces mainly heterozygotes. LbCPF1 has been described in other studies as being as effective as SpCAS9 in generating homozygous and biallelic mutations. It will remain to be clarified in the future, whether the different LbCFP1 constructions have different efficiencies and determine the origin of these differences. Finally, if one wishes to specifically introduce stop codons, BECAS9 is a viable and efficient alternative, although it has a lower efficiency than SpCAS9 and LbCPF1 for creating KO mutations.
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Affiliation(s)
- Leo Herbert
- CIRAD, UMR-AGAP, F-34398, Montpellier, France
- Université de Montpellier, Cirad, Inra, Montpellier SupAgro, F-34000, Montpellier, France
| | - Anne-Cécile Meunier
- CIRAD, UMR-AGAP, F-34398, Montpellier, France
- Université de Montpellier, Cirad, Inra, Montpellier SupAgro, F-34000, Montpellier, France
| | - Martine Bes
- CIRAD, UMR-AGAP, F-34398, Montpellier, France
- Université de Montpellier, Cirad, Inra, Montpellier SupAgro, F-34000, Montpellier, France
| | - Aurore Vernet
- CIRAD, UMR-AGAP, F-34398, Montpellier, France
- Université de Montpellier, Cirad, Inra, Montpellier SupAgro, F-34000, Montpellier, France
| | - Murielle Portefaix
- CIRAD, UMR-AGAP, F-34398, Montpellier, France
- Université de Montpellier, Cirad, Inra, Montpellier SupAgro, F-34000, Montpellier, France
| | - Franz Durandet
- CIRAD, UMR-AGAP, F-34398, Montpellier, France
- Université de Montpellier, Cirad, Inra, Montpellier SupAgro, F-34000, Montpellier, France
| | - Remy Michel
- CIRAD, UMR-AGAP, F-34398, Montpellier, France
- Université de Montpellier, Cirad, Inra, Montpellier SupAgro, F-34000, Montpellier, France
| | - Christian Chaine
- CIRAD, UMR-AGAP, F-34398, Montpellier, France
- Université de Montpellier, Cirad, Inra, Montpellier SupAgro, F-34000, Montpellier, France
| | - Patrice This
- CIRAD, UMR-AGAP, F-34398, Montpellier, France
- Université de Montpellier, Cirad, Inra, Montpellier SupAgro, F-34000, Montpellier, France
| | - Emmanuel Guiderdoni
- CIRAD, UMR-AGAP, F-34398, Montpellier, France
- Université de Montpellier, Cirad, Inra, Montpellier SupAgro, F-34000, Montpellier, France
| | - Christophe Périn
- CIRAD, UMR-AGAP, F-34398, Montpellier, France.
- Université de Montpellier, Cirad, Inra, Montpellier SupAgro, F-34000, Montpellier, France.
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Fayos I, Mieulet D, Petit J, Meunier AC, Périn C, Nicolas A, Guiderdoni E. Engineering meiotic recombination pathways in rice. Plant Biotechnol J 2019; 17:2062-2077. [PMID: 31199561 PMCID: PMC6790369 DOI: 10.1111/pbi.13189] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Revised: 06/01/2019] [Accepted: 06/05/2019] [Indexed: 05/02/2023]
Abstract
In the last 15 years, outstanding progress has been made in understanding the function of meiotic genes in the model dicot and monocot plants Arabidopsis and rice (Oryza sativa L.), respectively. This knowledge allowed to modulate meiotic recombination in Arabidopsis and, more recently, in rice. For instance, the overall frequency of crossovers (COs) has been stimulated 2.3- and 3.2-fold through the inactivation of the rice FANCM and RECQ4 DNA helicases, respectively, two genes involved in the repair of DNA double-strand breaks (DSBs) as noncrossovers (NCOs) of the Class II crossover pathway. Differently, the programmed induction of DSBs and COs at desired sites is currently explored by guiding the SPO11-1 topoisomerase-like transesterase, initiating meiotic recombination in all eukaryotes, to specific target regions of the rice genome. Furthermore, the inactivation of 3 meiosis-specific genes, namely PAIR1, OsREC8 and OsOSD1, in the Mitosis instead of Meiosis (MiMe) mutant turned rice meiosis into mitosis, thereby abolishing recombination and achieving the first component of apomixis, apomeiosis. The successful translation of Arabidopsis results into a crop further allowed the implementation of two breakthrough strategies that triggered parthenogenesis from the MiMe unreduced clonal egg cell and completed the second component of diplosporous apomixis. Here, we review the most recent advances in and future prospects of the manipulation of meiotic recombination in rice and potentially other major crops, all essential for global food security.
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Affiliation(s)
- Ian Fayos
- CiradUMR AGAPMontpellierFrance
- Université de MontpellierCirad-Inra-Montpellier SupAgroMontpellierFrance
| | - Delphine Mieulet
- CiradUMR AGAPMontpellierFrance
- Université de MontpellierCirad-Inra-Montpellier SupAgroMontpellierFrance
| | - Julie Petit
- CiradUMR AGAPMontpellierFrance
- Université de MontpellierCirad-Inra-Montpellier SupAgroMontpellierFrance
| | - Anne Cécile Meunier
- CiradUMR AGAPMontpellierFrance
- Université de MontpellierCirad-Inra-Montpellier SupAgroMontpellierFrance
| | - Christophe Périn
- CiradUMR AGAPMontpellierFrance
- Université de MontpellierCirad-Inra-Montpellier SupAgroMontpellierFrance
| | - Alain Nicolas
- Institut Curie, CNRS UMR 3244University PSLParisFrance
- MeiogenixParisFrance
| | - Emmanuel Guiderdoni
- CiradUMR AGAPMontpellierFrance
- Université de MontpellierCirad-Inra-Montpellier SupAgroMontpellierFrance
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Bureau C, Lanau N, Ingouff M, Hassan B, Meunier AC, Divol F, Sevilla R, Mieulet D, Dievart A, Périn C. A protocol combining multiphoton microscopy and propidium iodide for deep 3D root meristem imaging in rice: application for the screening and identification of tissue-specific enhancer trap lines. Plant Methods 2018; 14:96. [PMID: 30386414 PMCID: PMC6206838 DOI: 10.1186/s13007-018-0364-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 10/21/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND The clear visualization of 3D organization at the cellular level in plant tissues is needed to fully understand plant development processes. Imaging tools allow the visualization of the main fluorophores and in vivo growth monitoring. Confocal microscopy coupled with the use of propidium iodide (PI) counter-staining is one of the most popular tools used to characterize the structure of root meristems in A. thaliana. However, such an approach is relatively ineffective in species with more complex and thicker root systems. RESULTS We adapted a PI counter-staining protocol to visualize the internal 3D architecture of rice root meristems using multiphoton microscopy. This protocol is simple and compatible with the main fluorophores (CFP, GFP and mCherry). The efficiency and applicability of this protocol were demonstrated by screening a population of 57 enhancer trap lines. We successfully characterized GFP expression in all of the lines and identified 5 lines with tissue-specific expression. CONCLUSIONS All of these resources are now available for the rice community and represent critical tools for future studies of root development.
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Affiliation(s)
- Charlotte Bureau
- CIRAD, UMR-AGAP, Université de Montpellier, Avenue Agropolis, 34398 Montpellier Cedex 5, France
| | - Nadège Lanau
- CIRAD, UMR-AGAP, Université de Montpellier, Avenue Agropolis, 34398 Montpellier Cedex 5, France
| | - Mathieu Ingouff
- UMR DIADE, Université de Montpellier, 911 Avenue Agropolis, 34394 Montpellier Cedex 5, France
| | - Boukhaddaoui Hassan
- INSERM U1051, Institut des Neurosciences de Montpellier, 34095 Montpellier, France
| | - Anne-Cécile Meunier
- CIRAD, UMR-AGAP, Université de Montpellier, Avenue Agropolis, 34398 Montpellier Cedex 5, France
| | - Fanchon Divol
- UMR Biochimie et Physiologie Moléculaire des Plantes, INRA, Campus INRA/SupAgro, 2 Place Viala, 34060 Montpellier Cedex 2, France
| | - Rosie Sevilla
- CIRAD, UMR-AGAP, Université de Montpellier, Avenue Agropolis, 34398 Montpellier Cedex 5, France
| | - Delphine Mieulet
- CIRAD, UMR-AGAP, Université de Montpellier, Avenue Agropolis, 34398 Montpellier Cedex 5, France
| | - Anne Dievart
- CIRAD, UMR-AGAP, Université de Montpellier, Avenue Agropolis, 34398 Montpellier Cedex 5, France
| | - Christophe Périn
- CIRAD, UMR-AGAP, Université de Montpellier, Avenue Agropolis, 34398 Montpellier Cedex 5, France
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Chu TTH, Hoang TG, Trinh DC, Bureau C, Meynard D, Vernet A, Ingouff M, Do NV, Périn C, Guiderdoni E, Gantet P, Maurel C, Luu DT. Sub-cellular markers highlight intracellular dynamics of membrane proteins in response to abiotic treatments in rice. Rice (N Y) 2018; 11:23. [PMID: 29651780 PMCID: PMC5897272 DOI: 10.1186/s12284-018-0209-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Accepted: 03/16/2018] [Indexed: 05/20/2023]
Abstract
BACKGROUND Cell biology approach using membrane protein markers tagged with fluorescent proteins highlights the dynamic behaviour of plant cell membranes, not only in the standard but also in changing environmental conditions. In the past, this strategy has been extensively developed in plant models such as Arabidopsis. RESULTS Here, we generated a set of transgenic lines expressing membrane protein markers to extend this approach to rice, one of the most cultivated crop in the world and an emerging plant model. Lines expressing individually eight membrane protein markers including five aquaporins (OsPIP1;1, OsPIP2;4, OsPIP2;5, OsTIP1;1, OsTIP2;2) and three endosomal trafficking proteins (OsRab5a, OsGAP1, OsSCAMP1) were obtained. Importantly, we challenged in roots the aquaporin-expressing transgenic lines upon salt and osmotic stress and uncovered a highly dynamic behaviour of cell membrane. CONCLUSION We have uncovered the relocalization and dynamics of plasma membrane aquaporins upon salt and osmotic stresses in rice. Importantly, our data support a model where relocalization of OsPIPs is concomitant with their high cycling dynamics.
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Affiliation(s)
- Thi Thu Huyen Chu
- BPMP, Univ Montpellier, CNRS, INRA, SupAgro, Montpellier, France
- University of Science and Technology of Hanoi, LMI RICE, 18 Hoang Quoc Viet, Nghia Do, Cau Giay, Hanoi, Vietnam
| | - Thi Giang Hoang
- National key laboratory for Plant Cell Biotechnology, Agricultural Genetics Institute, Pham Van Dong, Co Nhue, Tuliem, Hanoi, Vietnam
- University of Science and Technology of Hanoi, LMI RICE, 18 Hoang Quoc Viet, Nghia Do, Cau Giay, Hanoi, Vietnam
- IRD, LMI RICE, Agricultural Genetics Institute, Pham Van Dong road, Co Nhue, Tuliem, Hanoï, Vietnam
| | - Duy Chi Trinh
- BPMP, Univ Montpellier, CNRS, INRA, SupAgro, Montpellier, France
- University of Science and Technology of Hanoi, LMI RICE, 18 Hoang Quoc Viet, Nghia Do, Cau Giay, Hanoi, Vietnam
| | - Charlotte Bureau
- CIRAD, UMR AGAP, 34398, Montpellier, France
- Université de Montpellier, CIRAD-INRA-Montpellier SupAgro, 34000, Montpellier, France
| | - Donaldo Meynard
- CIRAD, UMR AGAP, 34398, Montpellier, France
- Université de Montpellier, CIRAD-INRA-Montpellier SupAgro, 34000, Montpellier, France
| | - Aurore Vernet
- CIRAD, UMR AGAP, 34398, Montpellier, France
- Université de Montpellier, CIRAD-INRA-Montpellier SupAgro, 34000, Montpellier, France
| | - Mathieu Ingouff
- Université de Montpellier, UMR DIADE, 911 Avenue Agropolis, 34394, Montpellier Cedex 5, France
| | - Nang Vinh Do
- National key laboratory for Plant Cell Biotechnology, Agricultural Genetics Institute, Pham Van Dong, Co Nhue, Tuliem, Hanoi, Vietnam
- IRD, LMI RICE, Agricultural Genetics Institute, Pham Van Dong road, Co Nhue, Tuliem, Hanoï, Vietnam
| | - Christophe Périn
- CIRAD, UMR AGAP, 34398, Montpellier, France
- Université de Montpellier, CIRAD-INRA-Montpellier SupAgro, 34000, Montpellier, France
| | - Emmanuel Guiderdoni
- CIRAD, UMR AGAP, 34398, Montpellier, France
- Université de Montpellier, CIRAD-INRA-Montpellier SupAgro, 34000, Montpellier, France
| | - Pascal Gantet
- University of Science and Technology of Hanoi, LMI RICE, 18 Hoang Quoc Viet, Nghia Do, Cau Giay, Hanoi, Vietnam
- IRD, LMI RICE, Agricultural Genetics Institute, Pham Van Dong road, Co Nhue, Tuliem, Hanoï, Vietnam
- Université de Montpellier, UMR DIADE, 911 Avenue Agropolis, 34394, Montpellier Cedex 5, France
| | | | - Doan-Trung Luu
- BPMP, Univ Montpellier, CNRS, INRA, SupAgro, Montpellier, France.
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10
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Frouin J, Languillaume A, Mas J, Mieulet D, Boisnard A, Labeyrie A, Bettembourg M, Bureau C, Lorenzini E, Portefaix M, Turquay P, Vernet A, Périn C, Ahmadi N, Courtois B. Tolerance to mild salinity stress in japonica rice: A genome-wide association mapping study highlights calcium signaling and metabolism genes. PLoS One 2018; 13:e0190964. [PMID: 29342194 PMCID: PMC5771603 DOI: 10.1371/journal.pone.0190964] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 12/22/2017] [Indexed: 01/08/2023] Open
Abstract
Salinity tolerance is an important quality for European rice grown in river deltas. We evaluated the salinity tolerance of a panel of 235 temperate japonica rice accessions genotyped with 30,000 SNP markers. The panel was exposed to mild salt stress (50 mM NaCl; conductivity of 6 dS m-1) at the seedling stage. Eight different root and shoot growth parameters were measured for both the control and stressed treatments. The Na+ and K+ mass fractions of the stressed plants were measured using atomic absorption spectroscopy. The salt treatment affected plant growth, particularly the shoot parameters. The panel showed a wide range of Na+/K+ ratio and the temperate accessions were distributed over an increasing axis, from the most resistant to the most susceptible checks. We conducted a genome-wide association study on indices of stress response and ion mass fractions in the leaves using a classical mixed model controlling structure and kinship. A total of 27 QTLs validated by sub-sampling were identified. For indices of stress responses, we also used another model that focused on marker × treatment interactions and detected 50 QTLs, three of which were also identified using the classical method. We compared the positions of the significant QTLs to those of approximately 300 genes that play a role in rice salt tolerance. The positions of several QTLs were close to those of genes involved in calcium signaling and metabolism, while other QTLs were close to those of kinases. These results reveal the salinity tolerance of accessions with a temperate japonica background. Although the detected QTLs must be confirmed by other approaches, the number of associations linked to candidate genes involved in calcium-mediated ion homeostasis highlights pathways to explore in priority to understand the salinity tolerance of temperate rice.
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Affiliation(s)
- Julien Frouin
- Centre de coopération internationale en recherche agronomique pour le développement, Unité mixte de recherche Amélioration génétique et adaptation des plantes méditerranéennes et tropicales, Montpellier, France
| | - Antoine Languillaume
- Centre de coopération internationale en recherche agronomique pour le développement, Unité mixte de recherche Amélioration génétique et adaptation des plantes méditerranéennes et tropicales, Montpellier, France
| | - Justine Mas
- Centre de coopération internationale en recherche agronomique pour le développement, Unité mixte de recherche Amélioration génétique et adaptation des plantes méditerranéennes et tropicales, Montpellier, France
| | - Delphine Mieulet
- Centre de coopération internationale en recherche agronomique pour le développement, Unité mixte de recherche Amélioration génétique et adaptation des plantes méditerranéennes et tropicales, Montpellier, France
| | | | - Axel Labeyrie
- Centre de coopération internationale en recherche agronomique pour le développement, Unité mixte de recherche Amélioration génétique et adaptation des plantes méditerranéennes et tropicales, Montpellier, France
| | - Mathilde Bettembourg
- Centre de coopération internationale en recherche agronomique pour le développement, Unité mixte de recherche Amélioration génétique et adaptation des plantes méditerranéennes et tropicales, Montpellier, France
| | - Charlotte Bureau
- Centre de coopération internationale en recherche agronomique pour le développement, Unité mixte de recherche Amélioration génétique et adaptation des plantes méditerranéennes et tropicales, Montpellier, France
| | - Eve Lorenzini
- Centre de coopération internationale en recherche agronomique pour le développement, Unité mixte de recherche Amélioration génétique et adaptation des plantes méditerranéennes et tropicales, Montpellier, France
| | - Muriel Portefaix
- Institut National de la Recherche Agronomique, Unité mixte de recherche Amélioration génétique et adaptation des plantes méditerranéennes et tropicales, Montpellier, France
| | - Patricia Turquay
- Centre de coopération internationale en recherche agronomique pour le développement, Unité mixte de recherche Amélioration génétique et adaptation des plantes méditerranéennes et tropicales, Montpellier, France
| | - Aurore Vernet
- Centre de coopération internationale en recherche agronomique pour le développement, Unité mixte de recherche Amélioration génétique et adaptation des plantes méditerranéennes et tropicales, Montpellier, France
| | - Christophe Périn
- Centre de coopération internationale en recherche agronomique pour le développement, Unité mixte de recherche Amélioration génétique et adaptation des plantes méditerranéennes et tropicales, Montpellier, France
| | - Nourollah Ahmadi
- Centre de coopération internationale en recherche agronomique pour le développement, Unité mixte de recherche Amélioration génétique et adaptation des plantes méditerranéennes et tropicales, Montpellier, France
| | - Brigitte Courtois
- Centre de coopération internationale en recherche agronomique pour le développement, Unité mixte de recherche Amélioration génétique et adaptation des plantes méditerranéennes et tropicales, Montpellier, France
- * E-mail:
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11
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Nieves-Cordones M, Mohamed S, Tanoi K, Kobayashi NI, Takagi K, Vernet A, Guiderdoni E, Périn C, Sentenac H, Véry AA. Production of low-Cs + rice plants by inactivation of the K + transporter OsHAK1 with the CRISPR-Cas system. Plant J 2017; 92:43-56. [PMID: 28670755 DOI: 10.1111/tpj.13632] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 06/20/2017] [Accepted: 06/29/2017] [Indexed: 05/20/2023]
Abstract
The occurrence of radiocesium in food has raised sharp health concerns after nuclear accidents. Despite being present at low concentrations in contaminated soils (below μm), cesium (Cs+ ) can be taken up by crops and transported to their edible parts. This plant capacity to take up Cs+ from low concentrations has notably affected the production of rice (Oryza sativa L.) in Japan after the nuclear accident at Fukushima in 2011. Several strategies have been put into practice to reduce Cs+ content in this crop species such as contaminated soil removal or adaptation of agricultural practices, including dedicated fertilizer management, with limited impact or pernicious side-effects. Conversely, the development of biotechnological approaches aimed at reducing Cs+ accumulation in rice remain challenging. Here, we show that inactivation of the Cs+ -permeable K+ transporter OsHAK1 with the CRISPR-Cas system dramatically reduced Cs+ uptake by rice plants. Cs+ uptake in rice roots and in transformed yeast cells that expressed OsHAK1 displayed very similar kinetics parameters. In rice, Cs+ uptake is dependent on two functional properties of OsHAK1: (i) a poor capacity of this system to discriminate between Cs+ and K+ ; and (ii) a high capacity to transport Cs+ from very low external concentrations that is likely to involve an active transport mechanism. In an experiment with a Fukushima soil highly contaminated with 137 Cs+ , plants lacking OsHAK1 function displayed strikingly reduced levels of 137 Cs+ in roots and shoots. These results open stimulating perspectives to smartly produce safe food in regions contaminated by nuclear accidents.
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Affiliation(s)
- Manuel Nieves-Cordones
- Biochimie et Physiologie Moléculaire des Plantes, Institut de Biologie Intégrative des Plantes, UMR 5004 CNRS/386 INRA/Montpellier SupAgro/Université Montpellier, Montpellier Cedex 2, 34060, France
| | - Sonia Mohamed
- Biochimie et Physiologie Moléculaire des Plantes, Institut de Biologie Intégrative des Plantes, UMR 5004 CNRS/386 INRA/Montpellier SupAgro/Université Montpellier, Montpellier Cedex 2, 34060, France
- CIRAD, UMR AGAP, Montpellier Cedex 5, 34398, France
| | - Keitaro Tanoi
- Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
- PRESTO, Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan
| | - Natsuko I Kobayashi
- Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Keiko Takagi
- Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | | | | | | | - Hervé Sentenac
- Biochimie et Physiologie Moléculaire des Plantes, Institut de Biologie Intégrative des Plantes, UMR 5004 CNRS/386 INRA/Montpellier SupAgro/Université Montpellier, Montpellier Cedex 2, 34060, France
| | - Anne-Aliénor Véry
- Biochimie et Physiologie Moléculaire des Plantes, Institut de Biologie Intégrative des Plantes, UMR 5004 CNRS/386 INRA/Montpellier SupAgro/Université Montpellier, Montpellier Cedex 2, 34060, France
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12
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Dufayard JF, Bettembourg M, Fischer I, Droc G, Guiderdoni E, Périn C, Chantret N, Diévart A. Corrigendum: New Insights on Leucine-Rich Repeats Receptor-Like Kinase Orthologous Relationships in Angiosperms. Front Plant Sci 2017; 8:916. [PMID: 28553311 PMCID: PMC5443148 DOI: 10.3389/fpls.2017.00916] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 05/15/2017] [Indexed: 05/30/2023]
Abstract
[This corrects the article on p. 381 in vol. 8, PMID: 28424707.].
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13
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Yang J, Yuan Z, Meng Q, Huang G, Périn C, Bureau C, Meunier AC, Ingouff M, Bennett MJ, Liang W, Zhang D. Dynamic Regulation of Auxin Response during Rice Development Revealed by Newly Established Hormone Biosensor Markers. Front Plant Sci 2017; 8:256. [PMID: 28326089 PMCID: PMC5339295 DOI: 10.3389/fpls.2017.00256] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 02/10/2017] [Indexed: 05/18/2023]
Abstract
The hormone auxin is critical for many plant developmental processes. Unlike the model eudicot plant Arabidopsis (Arabidopsis thaliana), auxin distribution and signaling in rice tissues has not been systematically investigated due to the absence of suitable auxin response reporters. In this study we observed the conservation of auxin signaling components between Arabidopsis and model monocot crop rice (Oryza sativa), and generated complementary types of auxin biosensor constructs, one derived from the Aux/IAA-based biosensor DII-VENUS but constitutively driven by maize ubiquitin-1 promoter, and the other termed DR5-VENUS in which a synthetic auxin-responsive promoter (DR5rev ) was used to drive expression of the yellow fluorescent protein (YFP). Using the obtained transgenic lines, we observed that during the vegetative development, accumulation of DR5-VENUS signal was at young and mature leaves, tiller buds and stem base. Notably, abundant DR5-VENUS signals were observed in the cytoplasm of cortex cells surrounding lateral root primordia (LRP) in rice. In addition, auxin maxima and dynamic re-localization were seen at the initiation sites of inflorescence and spikelet primordia including branch meristems (BMs), female and male organs. The comparison of these observations among Arabidopsis, rice and maize suggests the unique role of auxin in regulating rice lateral root emergence and reproduction. Moreover, protein localization of auxin transporters PIN1 homologs and GFP tagged OsAUX1 overlapped with DR5-VENUS during spikelet development, helping validate these auxin response reporters are reliable markers in rice. This work firstly reveals the direct correspondence between auxin distribution and rice reproductive and root development at tissue and cellular level, and provides high-resolution auxin tools to probe fundamental developmental processes in rice and to establish links between auxin, development and agronomical traits like yield or root architecture.
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Affiliation(s)
- Jing Yang
- Key Laboratory of Systems Biomedicine, Ministry of Education, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong UniversityShanghai, China
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University–University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong UniversityShanghai, China
| | - Zheng Yuan
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University–University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong UniversityShanghai, China
| | - Qingcai Meng
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University–University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong UniversityShanghai, China
| | - Guoqiang Huang
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University–University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong UniversityShanghai, China
| | | | | | | | | | - Malcolm J. Bennett
- Centre for Plant Integrative Biology, School of Biosciences, University of NottinghamSutton Bonington, UK
| | - Wanqi Liang
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University–University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong UniversityShanghai, China
| | - Dabing Zhang
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University–University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong UniversityShanghai, China
- School of Agriculture, Food and Wine, University of AdelaideUrrbrae, SA, Australia
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14
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Dufayard JF, Bettembourg M, Fischer I, Droc G, Guiderdoni E, Périn C, Chantret N, Diévart A. New Insights on Leucine-Rich Repeats Receptor-Like Kinase Orthologous Relationships in Angiosperms. Front Plant Sci 2017; 8:381. [PMID: 28424707 PMCID: PMC5380761 DOI: 10.3389/fpls.2017.00381] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 03/06/2017] [Indexed: 05/18/2023]
Abstract
Leucine-Rich Repeats Receptor-Like Kinase (LRR-RLK) genes represent a large and complex gene family in plants, mainly involved in development and stress responses. These receptors are composed of an LRR-containing extracellular domain (ECD), a transmembrane domain (TM) and an intracellular kinase domain (KD). To provide new perspectives on functional analyses of these genes in model and non-model plant species, we performed a phylogenetic analysis on 8,360 LRR-RLK receptors in 31 angiosperm genomes (8 monocots and 23 dicots). We identified 101 orthologous groups (OGs) of genes being conserved among almost all monocot and dicot species analyzed. We observed that more than 10% of these OGs are absent in the Brassicaceae species studied. We show that the ECD structural features are not always conserved among orthologs, suggesting that functions may have diverged in some OG sets. Moreover, we looked at targets of positive selection footprints in 12 pairs of OGs and noticed that depending on the subgroups, positive selection occurred more frequently either in the ECDs or in the KDs.
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Affiliation(s)
| | | | | | | | | | | | - Nathalie Chantret
- INRA, UMR AGAPMontpellier, France
- *Correspondence: Anne Diévart, Nathalie Chantret,
| | - Anne Diévart
- CIRAD, UMR AGAPMontpellier, France
- *Correspondence: Anne Diévart, Nathalie Chantret,
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15
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Henry S, Divol F, Bettembourg M, Bureau C, Guiderdoni E, Périn C, Diévart A. Immunoprofiling of Rice Root Cortex Reveals Two Cortical Subdomains. Front Plant Sci 2015; 6:1139. [PMID: 26779208 PMCID: PMC4703777 DOI: 10.3389/fpls.2015.01139] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 12/01/2015] [Indexed: 05/08/2023]
Abstract
The formation and differentiation of aerenchyma, i.e., air-containing cavities that are critical for flooding tolerance, take place exclusively in the cortex. The understanding of development and differentiation of the cortex is thus an important issue; however, studies on this tissue are limited, partly because of the lack of available molecular tools. We screened a commercially available library of cell wall antibodies to identify markers of cortical tissue in rice roots. Out of the 174 antibodies screened, eight were cortex-specific. Our analysis revealed that two types of cortical tissues are present in rice root seedlings. We named these cell layers "inner" and "outer" based on their location relative to the stele. We then used the antibodies to clarify cell identity in lateral roots. Without these markers, previous studies could not distinguish between the cortex and sclerenchyma in small lateral roots. By immunostaining lateral root sections, we showed that the internal ground tissue in small lateral roots has outer cortical identity.
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16
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Ahmadi N, Audebert A, Bennett MJ, Bishopp A, de Oliveira AC, Courtois B, Diedhiou A, Diévart A, Gantet P, Ghesquière A, Guiderdoni E, Henry A, Inukai Y, Kochian L, Laplaze L, Lucas M, Luu DT, Manneh B, Mo X, Muthurajan R, Périn C, Price A, Robin S, Sentenac H, Sine B, Uga Y, Véry AA, Wissuwa M, Wu P, Xu J. The roots of future rice harvests. Rice (N Y) 2014; 7:29. [PMID: 26224558 PMCID: PMC4884021 DOI: 10.1186/s12284-014-0029-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2014] [Accepted: 10/12/2014] [Indexed: 05/05/2023]
Abstract
Rice production faces the challenge to be enhanced by 50% by year 2030 to meet the growth of the population in rice-eating countries. Whereas yield of cereal crops tend to reach plateaus and a yield is likely to be deeply affected by climate instability and resource scarcity in the coming decades, building rice cultivars harboring root systems that can maintain performance by capturing water and nutrient resources unevenly distributed is a major breeding target. Taking advantage of gathering a community of rice root biologists in a Global Rice Science Partnership workshop held in Montpellier, France, we present here the recent progresses accomplished in this area and focal points where an international network of laboratories should direct their efforts.
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Affiliation(s)
| | | | - Malcolm J Bennett
- />Centre for Plant Integrative Biology, University of Nottingham, Loughborough, LE12 5RD UK
| | - Anthony Bishopp
- />Centre for Plant Integrative Biology, University of Nottingham, Loughborough, LE12 5RD UK
| | | | | | - Abdala Diedhiou
- />Université Cheikh Anta Diop (UCAD), Département de Biologie Végétale, Laboratoire Commun de Microbiologie IRD/ISRA/UCAD, Centre de Recherche de Bel Air - BP 1386, CP 18524 Dakar, Sénégal
- />Laboratoire Mixte International Adaptation des Plantes et microorganismes associés aux Stress Environnementaux (LAPSE), Centre de Recherche de Bel Air - BP 1386, CP 18524 Dakar, Sénégal
| | - Anne Diévart
- />CIRAD, UMR AGAP, Montpellier Cedex 5, 34398 France
| | - Pascal Gantet
- />Université Montpellier 2, UMR DIADE, Montpellier, France
- />IRD, LMI RICE, USTH, Agronomical Genetics Institute, Hanoi, Vietnam
| | | | | | | | - Yoshiaki Inukai
- />International Cooperation Center for Agricultural Education (ICCAE), Nagoya University, Furo-cho, Chikusa 464-8601 Nagoya, Japan
| | - Leon Kochian
- />Robert W. Holley Center for Agriculture and Health, USDA-ARS and Department of Plant Biology, Cornell University, Ithaca, 14853 NY USA
| | - Laurent Laplaze
- />Laboratoire Mixte International Adaptation des Plantes et microorganismes associés aux Stress Environnementaux (LAPSE), Centre de Recherche de Bel Air - BP 1386, CP 18524 Dakar, Sénégal
- />IRD, UMR DIADE, Montpellier, France
| | | | - Doan Trung Luu
- />Biochimie et Physiologie Moléculaire des Plantes, Institut de Biologie Intégrative des Plantes, UMR 5004 CNRS/386 INRA/Montpellier SupAgro/Université Montpellier 2, F-34060 Montpellier Cedex 2, France
| | - Baboucarr Manneh
- />Africa Rice Center, AfricaRice Sahel Regional Station, B.P. 96, St Louis, Senegal
| | - Xiaorong Mo
- />State Key Laboratory of Plant Physiology and Biochemistry, College of Life Science, Zhejiang University, Hangzhou, 310058 China
| | | | | | - Adam Price
- />University of Aberdeen, Aberdeen, AB24 3UU UK
| | | | - Hervé Sentenac
- />Biochimie et Physiologie Moléculaire des Plantes, Institut de Biologie Intégrative des Plantes, UMR 5004 CNRS/386 INRA/Montpellier SupAgro/Université Montpellier 2, F-34060 Montpellier Cedex 2, France
| | - Bassirou Sine
- />Laboratoire Mixte International Adaptation des Plantes et microorganismes associés aux Stress Environnementaux (LAPSE), Centre de Recherche de Bel Air - BP 1386, CP 18524 Dakar, Sénégal
- />ISRA, CERAAS, Thiès, Senegal
| | - Yusaku Uga
- />National Institute of Agrobiological Sciences (NIAS), 2-1-2 Kannondai, Tsukuba, 305-8602 Ibaraki, Japan
| | - Anne Aliénor Véry
- />Biochimie et Physiologie Moléculaire des Plantes, Institut de Biologie Intégrative des Plantes, UMR 5004 CNRS/386 INRA/Montpellier SupAgro/Université Montpellier 2, F-34060 Montpellier Cedex 2, France
| | - Matthias Wissuwa
- />Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, 305-8686 Japan
| | - Ping Wu
- />State Key Laboratory of Plant Physiology and Biochemistry, College of Life Science, Zhejiang University, Hangzhou, 310058 China
| | - Jian Xu
- />Department of Biological Sciences and NUS Centre for BioImaging Sciences, Faculty of Science, National University of Singapore, Singapore 117543 Singapore
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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 Biotechnol J 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] [What about the content of this article? (0)] [Affiliation(s)] [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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18
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Pauluzzi G, Divol F, Puig J, Guiderdoni E, Dievart A, Périn C. Surfing along the root ground tissue gene network. Dev Biol 2012; 365:14-22. [PMID: 22349629 DOI: 10.1016/j.ydbio.2012.02.007] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2011] [Revised: 01/31/2012] [Accepted: 02/06/2012] [Indexed: 11/19/2022]
Abstract
Organization of tissues in Arabidopsis thaliana root is made of, from outside in, epidermis, cortex, middle cortex, endodermis, pericycle and vascular tissues. Cortex, middle cortex and endodermis form the ground tissue (GT) system. Functional and molecular characterization of GT patterning mutants' properties has greatly increased our understanding of fundamental processes of plant root development. These studies have demonstrated GT is an elegant model that can be used to study how different cell types and cell fates are specified. This review analyzes GT mutants to provide a detailed account of the molecular network that regulates GT formation in A. thaliana. The most recent results indicate an unexpectedly complex network of transcription factors, epigenetic and hormonal controls that play crucial roles in GT development. Major differences exist between GT formation in dicots and monocots, particularly in the model plant rice, opening the way for evo-devo of GT formation in angiosperm. In rice, adaptation to submergence relies on a multilayered cortex. Moreover, variation in the number of cortex cell layers is also observed between the five root types. A mechanism of control for cortical cell number should then exist in rice and it remains to be determined if any of the Arabidopsis thaliana identified GT network members are also involved in this process in rice. Alternatively, a totally different network may have been invented. However, first available results suggest functional conservation in rice of at least two transcription factors, SHORT ROOT (SHR) and SCARECROW (SCR), involved in ground tissue formation in Arabidopsis.
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Affiliation(s)
- G Pauluzzi
- CIRAD, UMR AGAP, F-34398 Montpellier, France
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19
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Diévart A, Gilbert N, Droc G, Attard A, Gourgues M, Guiderdoni E, Périn C. Leucine-rich repeat receptor kinases are sporadically distributed in eukaryotic genomes. BMC Evol Biol 2011; 11:367. [PMID: 22185365 PMCID: PMC3268121 DOI: 10.1186/1471-2148-11-367] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2011] [Accepted: 12/20/2011] [Indexed: 11/16/2022] Open
Abstract
Background Plant leucine-rich repeat receptor-like kinases (LRR-RLKs) are receptor kinases that contain LRRs in their extracellular domain. In the last 15 years, many research groups have demonstrated major roles played by LRR-RLKs in plants during almost all developmental processes throughout the life of the plant and in defense/resistance against a large range of pathogens. Recently, a breakthrough has been made in this field that challenges the dogma of the specificity of plant LRR-RLKs. Results We analyzed ~1000 complete genomes and show that LRR-RK genes have now been identified in 8 non-plant genomes. We performed an exhaustive phylogenetic analysis of all of these receptors, revealing that all of the LRR-containing receptor subfamilies form lineage-specific clades. Our results suggest that the association of LRRs with RKs appeared independently at least four times in eukaryotic evolutionary history. Moreover, the molecular evolutionary history of the LRR-RKs found in oomycetes is reminiscent of the pattern observed in plants: expansion with amplification/deletion and evolution of the domain organization leading to the functional diversification of members of the gene family. Finally, the expression data suggest that oomycete LRR-RKs may play a role in several stages of the oomycete life cycle. Conclusions In view of the key roles that LRR-RLKs play throughout the entire lifetime of plants and plant-environment interactions, the emergence and expansion of this type of receptor in several phyla along the evolution of eukaryotes, and particularly in oomycete genomes, questions their intrinsic functions in mimicry and/or in the coevolution of receptors between hosts and pathogens.
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Khong G, Richaud F, Coudert Y, Pati PK, Santi C, Périn C, Breitler JC, Meynard D, Vinh DN, Guiderdoni E, Gantet P. Modulating rice stress tolerance by transcription factors. Biotechnol Genet Eng Rev 2011; 25:381-403. [PMID: 21412363 DOI: 10.5661/bger-25-381] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Plants are non-mobile organisms and have to adapt to environmental stresses mostly by modulating their growth and development in addition to physiological and biochemical changes. Transcription factors (TFs) regulate genome expression in response to environmental and physiological signals, and some of them switch on plant adaptive developmental and physiological pathways. One TF is encoded by a single gene but regulates the expression of several other genes leading to the activation of complex adaptive mechanisms and hence represents major molecular targets to genetically improve the tolerance of crop plants against different stresses. In this review an updated account of the discovery of TFs involved in biotic and abiotic stress tolerance in the model monocotyledonous plant, rice (Oryza sativa L.) is presented. We illustrate how the elucidation of the function of these TFs can be used to set up genetic engineering strategies and to rationalize molecular breeding using molecular assisted selection towards enhancement of rice tolerance to various stresses. Attempts have also been made to provide information on the molecular mechanisms involved in stress resistance or tolerance processes. We discuss how the comparison of the action of TFs isolated from the dicotyledonous model plant Arabidopsis thaliana in rice and vice versa can contribute to determine whether common or divergent mechanisms underlie stress tolerance in the two plant species. Lastly, we discuss the necessity to discover TFs controlling specifically the root adaptive development which constitutes a major way for the plant to escape to several stresses such as water deficit or mineral nutrient deficiency.
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Affiliation(s)
- Giang Khong
- UMR 1098 DAP, Université Montpellier 2, CIRAD, TA A96/03, Avenue Agropolis, 34398, Montpellier Cedex 5, France
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21
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Rouard M, Guignon V, Aluome C, Laporte MA, Droc G, Walde C, Zmasek CM, Périn C, Conte MG. GreenPhylDB v2.0: comparative and functional genomics in plants. Nucleic Acids Res 2011; 39:D1095-102. [PMID: 20864446 PMCID: PMC3013755 DOI: 10.1093/nar/gkq811] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2010] [Revised: 08/19/2010] [Accepted: 08/23/2010] [Indexed: 11/20/2022] Open
Abstract
GreenPhylDB is a database designed for comparative and functional genomics based on complete genomes. Version 2 now contains sixteen full genomes of members of the plantae kingdom, ranging from algae to angiosperms, automatically clustered into gene families. Gene families are manually annotated and then analyzed phylogenetically in order to elucidate orthologous and paralogous relationships. The database offers various lists of gene families including plant, phylum and species specific gene families. For each gene cluster or gene family, easy access to gene composition, protein domains, publications, external links and orthologous gene predictions is provided. Web interfaces have been further developed to improve the navigation through information related to gene families. New analysis tools are also available, such as a gene family ontology browser that facilitates exploration. GreenPhylDB is a component of the South Green Bioinformatics Platform (http://southgreen.cirad.fr/) and is accessible at http://greenphyl.cirad.fr. It enables comparative genomics in a broad taxonomy context to enhance the understanding of evolutionary processes and thus tends to speed up gene discovery.
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Affiliation(s)
- Mathieu Rouard
- Bioversity International - CfL programme Parc Scientifique Agropolis II, 34397 Montpellier, France.
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22
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Lin SI, Santi C, Jobet E, Lacut E, El Kholti N, Karlowski WM, Verdeil JL, Breitler JC, Périn C, Ko SS, Guiderdoni E, Chiou TJ, Echeverria M. Complex regulation of two target genes encoding SPX-MFS proteins by rice miR827 in response to phosphate starvation. Plant Cell Physiol 2010; 51:2119-31. [PMID: 21062869 DOI: 10.1093/pcp/pcq170] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Here we report on the characterization of rice osa-miR827 and its two target genes, OsSPX-MFS1 and OsSPX-MFS2, which encode SPX-MFS proteins predicted to be implicated in phosphate (Pi) sensing or transport. We first show by Northern blot analysis that osa-miR827 is strongly induced by Pi starvation in both shoots and roots. Hybridization of osa-miR827 in situ confirms its strong induction by Pi starvation, with signals concentrated in mesophyll, epidermis and ground tissues of roots. In parallel, we analyzed the responses of the two OsSPX-MFS1 and OsSPX-MFS2 gene targets to Pi starvation. OsSPX-MFS1 mRNA is mainly expressed in shoots under sufficient Pi supply while its expression is reduced on Pi starvation, revealing a direct relationship between induction of osa-miR827 and down-regulation of OsSPX-MFS1. In contrast, OsSPX-MFS2 responds in a diametrically opposed manner to Pi starvation. The accumulation of OsSPX-MFS2 mRNA is dramatically enhanced under Pi starvation, suggesting the involvement of complex regulation of osa-miR827 and its two target genes. We further produced transgenic rice lines overexpressing osa-miR827 and T-DNA knockout mutant lines in which the expression of osa-miR827 is abolished. Compared with wild-type controls, both target mRNAs exhibit similar changes, their expression being reduced and increased in overexpressing and knockout lines, respectively. This suggests that OsSPX-MFS1 and OsSPX-MFS2 are both negatively regulated by osa-miR827 abundance although they respond differently to external Pi conditions. We propose that this is a complex mechanism comprising fine tuning of spatial or temporal regulation of both targets by osa-miR827.
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MESH Headings
- Adaptation, Physiological
- DNA, Bacterial
- Gene Expression Regulation, Plant
- Genes, Plant
- MicroRNAs/physiology
- Oryza/cytology
- Oryza/genetics
- Oryza/metabolism
- Phosphates/deficiency
- Phosphates/metabolism
- Plant Roots/genetics
- Plant Shoots/genetics
- Plants, Genetically Modified/cytology
- Plants, Genetically Modified/genetics
- Plants, Genetically Modified/metabolism
- RNA Transport
- RNA, Messenger/genetics
- RNA, Plant/genetics
- Sequence Deletion
- Stress, Physiological
- Transcription, Genetic
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Affiliation(s)
- Shu-I Lin
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115, Taiwan
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23
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Coudert Y, Périn C, Courtois B, Khong NG, Gantet P. Genetic control of root development in rice, the model cereal. Trends Plant Sci 2010; 15:219-26. [PMID: 20153971 DOI: 10.1016/j.tplants.2010.01.008] [Citation(s) in RCA: 184] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2009] [Revised: 01/14/2010] [Accepted: 01/18/2010] [Indexed: 05/19/2023]
Abstract
Cereals possess a fibrous root system that is mainly composed of crown roots that emerge postembryonically from the nodes of the stem. Because the root system is not directly accessible and consequently difficult to study, it remains a target for breeders to improve the ability of plants to exploit the mineral and water resources of the soil. Breeding for root architecture necessitates identifying the genetic determinants of root development. This research is now underway in cereals, particularly in rice, the monocot model species. In this review, we examine recent data identifying genes that govern root development in cereals, such as ARL1/CRL1 in rice and RTCS in maize which encodes a conserved lateral organ boundary domain transcription factor involved in crown root initiation and development in response to auxin. Finally, we discuss the detection and validation of root development quantitative trait loci.
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Affiliation(s)
- Yoan Coudert
- Université Montpellier 2, UMR 1098 Développement et Adaptation des Plantes, Bat 15, CC 002, Place Eugène Bataillon, 34095 Montpellier Cedex 5, France
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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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25
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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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26
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Larmande P, Gay C, Lorieux M, Périn C, Bouniol M, Droc G, Sallaud C, Perez P, Barnola I, Biderre-Petit C, Martin J, Morel JB, Johnson AAT, Bourgis F, Ghesquière A, Ruiz M, Courtois B, Guiderdoni E. Oryza Tag Line, a phenotypic mutant database for the Genoplante rice insertion line library. Nucleic Acids Res 2007; 36:D1022-7. [PMID: 17947330 PMCID: PMC2238859 DOI: 10.1093/nar/gkm762] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
To organize data resulting from the phenotypic characterization of a library of 30,000 T-DNA enhancer trap (ET) insertion lines of rice (Oryza sativa L cv. Nipponbare), we developed the Oryza Tag Line (OTL) database (http://urgi.versailles.inra.fr/OryzaTagLine/). OTL structure facilitates forward genetic search for specific phenotypes, putatively resulting from gene disruption, and/or for GUSA or GFP reporter gene expression patterns, reflecting ET-mediated endogenous gene detection. In the latest version, OTL gathers the detailed morpho-physiological alterations observed during field evaluation and specific screens in a first set of 13,928 lines. Detection of GUS or GFP activity in specific organ/tissues in a subset of the library is also provided. Search in OTL can be achieved through trait ontology category, organ and/or developmental stage, keywords, expression of reporter gene in specific organ/tissue as well as line identification number. OTL now contains the description of 9721 mutant phenotypic traits observed in 2636 lines and 1234 GUS or GFP expression patterns. Each insertion line is documented through a generic passport data including production records, seed stocks and FST information. 8004 and 6101 of the 13,928 lines are characterized by at least one T-DNA and one Tos17 FST, respectively that OTL links to the rice genome browser OryGenesDB.
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Affiliation(s)
- Pierre Larmande
- CIRAD-INRA-SUPAGRO-UMII, UMR 1098 DAP, Biological Systems Department, 2477 Avenue Agropolis, F-34398 Montpellier Cedex 5, France
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27
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Luquet D, Song YH, Elbelt S, This D, Clément-Vidal A, Périn C, Fabre D, Dingkuhn M. Model-assisted physiological analysis of Phyllo, a rice architectural mutant. Funct Plant Biol 2007; 34:11-23. [PMID: 32689327 DOI: 10.1071/fp06180] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2006] [Accepted: 10/11/2006] [Indexed: 06/11/2023]
Abstract
Studies of phenotype of knockout mutants can provide new insights into physiological, phenological and architectural feedbacks in the plant system. Phyllo, a mutant of Nippon Bare rice (Oryza sativa L.) producing small leaves in rapid succession, was isolated during multiplication of a T-DNA insertion library. Phyllo phenotype was compared with the wild type (WT) during vegetative development in hydroponics culture using a wide range of physiological and biometric measurements. These were integrated with the help of the functional-structural model EcoMeristem, explicitly designed to study interactions between morphogenesis and carbon assimilation. Although the phenotype of the mutant was caused by a single recessive gene, it differed in many ways from the WT, suggesting a pleiotropic effect of this mutation. Phyllochron was 25 (1-4 leaf stage) to 38% (>>4 leaf stage) shorter but showed normal transition from juvenile to adult phase after leaf 4. Leaf size also increased steadily with leaf position as in WT. The mutant had reduced leaf blade length : width and blade : sheath length ratios, particularly during the transition from heterotrophic to autotrophic growth. During the same period, root : shoot dry weight ratio was significantly diminished. Specific leaf area (SLA) was strongly increased in the mutant but showed normal descending patterns with leaf position. Probably related to high SLA, the mutant had much lower light-saturated leaf photosynthetic rates and lower radiation use efficiency (RUE) than the WT. Leaf extension rates were strongly reduced in absolute terms but were high in relative terms (normalised by final leaf length). The application of the EcoMeristem model to these data indicated that the mutant was severely deficient in assimilate, resulting from low RUE and high organ initiation rate causing high assimilate demand. This was particularly pronounced during the heterotrophic-autotrophic transition, probably causing shorter leaf blades relative to sheaths, as well as a temporary reduction of assimilate partitioning to roots. The model accurately simulated the mutant's high leaf mortality and absence of tillering. The simulated assimilate shortage was supported by observed reductions in starch storage in sheaths. Soluble sugar concentrations differed between mutant and WT in roots but not in shoots. Specifically, the hexose : sucrose ratio was 50% lower in the roots of the mutant, possibly indicating low invertase activity. Furthermore, two OsCIN genes coding for cell wall invertases were not expressed in roots, and others were expressed weakly. This was interpreted as natural silencing via sugar signalling. In summary, the authors attributed the majority of observed allometric and metabolic modifications in the mutant to an extreme assimilate shortage caused by hastened shoot organogenesis and inefficient leaf morphology.
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Affiliation(s)
- Delphine Luquet
- CIRAD, Amis Dpt, TA40/01 Avenue Agropolis, 34398 Montpellier Cedex 5, France
| | - You Hong Song
- Institute of Botany, the Chinese Academy of sciences, 100093, Beijing, China
| | - Sonia Elbelt
- CIRAD, Amis Dpt, TA40/01 Avenue Agropolis, 34398 Montpellier Cedex 5, France
| | - Dominique This
- Ecole Nationale Supérieure Agronomique de Montpellier, UMR 1096, 2, place P. Viala, 34060 Montpellier Cedex, France
| | - Anne Clément-Vidal
- CIRAD, Amis Dpt, TA40/01 Avenue Agropolis, 34398 Montpellier Cedex 5, France
| | - Christophe Périn
- CIRAD, Amis Dpt, TA40/01 Avenue Agropolis, 34398 Montpellier Cedex 5, France
| | - Denis Fabre
- CIRAD, Amis Dpt, TA40/01 Avenue Agropolis, 34398 Montpellier Cedex 5, France
| | - Michael Dingkuhn
- CIRAD, Amis Dpt, TA40/01 Avenue Agropolis, 34398 Montpellier Cedex 5, France
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Droc G, Ruiz M, Larmande P, Pereira A, Piffanelli P, Morel JB, Dievart A, Courtois B, Guiderdoni E, Périn C. OryGenesDB: a database for rice reverse genetics. Nucleic Acids Res 2006; 34:D736-40. [PMID: 16381969 PMCID: PMC1347375 DOI: 10.1093/nar/gkj012] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Insertional mutant databases containing Flanking Sequence Tags (FSTs) are becoming key resources for plant functional genomics. We have developed OryGenesDB (), a database dedicated to rice reverse genetics. Insertion mutants of rice genes are catalogued by Flanking Sequence Tag (FST) information that can be readily accessed by this database. Our database presently contains 44166 FSTs generated by most of the rice insertional mutagenesis projects. The OryGenesDB genome browser is based on the powerful Generic Genome Browser (GGB) developed in the framework of the Generic Model Organism Project (GMOD). The main interface of our web site displays search and analysis interfaces to look for insertions in any candidate gene of interest. Several starting points can be used to exhaustively retrieve the insertions positions and associated genomic information using blast, keywords or gene name search. The toolbox integrated in our database also includes an ‘anchoring’ option that allows immediate mapping and visualization of up to 50 nucleic acid sequences in the rice Genome Browser of OryGenesDB. As a first step toward plant comparative genomics, we have linked the rice and Arabidopsis whole genome using all the predicted pairs of orthologs by best BLAST mutual hit (BBMH) connectors.
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Affiliation(s)
| | | | | | - A. Pereira
- Wageningen UR, Plant Research InternationalPO Box 16, 6700 AA, Wageningen, The Netherlands
| | | | - J. B. Morel
- CIRAD/INRAUMR BGPI TA 41/K Campus International de Baillarguet 34398 Montpellier Cedex 05, France
| | | | | | | | - C. Périn
- To whom correspondence should be addressed at TA40/03 Avenue Agropolis, 34398 Montpellier Cedex 5, France. Tel: +33 4 67 61 71 85;
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29
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Sallaud C, Gay C, Larmande P, Bès M, Piffanelli P, Piégu B, Droc G, Regad F, Bourgeois E, Meynard D, Périn C, Sabau X, Ghesquière A, Glaszmann JC, Delseny M, Guiderdoni E. High throughput T-DNA insertion mutagenesis in rice: a first step towards in silico reverse genetics. Plant J 2004; 39:450-64. [PMID: 15255873 DOI: 10.1111/j.1365-313x.2004.02145.x] [Citation(s) in RCA: 109] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
A library of 29,482 T-DNA enhancer trap lines has been generated in rice cv. Nipponbare. The regions flanking the T-DNA left border from the first 12,707 primary transformants were systematically isolated by adapter anchor PCR and sequenced. A survey of the 7480 genomic sequences larger than 30 bp (average length 250 bp), representing 56.4% of the total readable sequences and matching the rice bacterial artificial chromosome/phage artificial chromosome (BAC/PAC) sequences assembled in pseudomolecules allowed the assigning of 6645 (88.8%) T-DNA insertion sites to at least one position in the rice genome of cv. Nipponbare. T-DNA insertions appear to be rather randomly distributed over the 12 rice chromosomes, with a slightly higher insertion frequency in chromosomes 1, 2, 3 and 6. The distribution of 723 independent T-DNA insertions along the chromosome 1 pseudomolecule did not differ significantly from that of the predicted coding sequences in exhibiting a lower insertion density around the centromere region and a higher density in the subtelomeric regions where the gene density is higher. Further establishment of density graphs of T-DNA inserts along the recently released 12 rice pseudomolecules confirmed this non-uniform chromosome distribution. T-DNA appeared less prone to hot spots and cold spots of integration when compared with those revealed by a concurrent assignment of the Tos17 retrotransposon flanking sequences deposited in the National Center for Biotechnology Information (NCBI). T-DNA inserts rarely integrated into repetitive sequences. Based on the predicted gene annotation of chromosome 1, preferential insertion within the first 250 bp from the putative ATG start codon has been observed. Using 4 kb of sequences surrounding the insertion points, 62% of the sequences showed significant similarity to gene encoding known proteins (E-value < 1.00 e(-05)). To illustrate the in silico reverse genetic approach, identification of 83 T-DNA insertions within genes coding for transcription factors (TF) is presented. Based both on the estimated number of members of several large TF gene families (e.g. Myb, WRKY, HD-ZIP, Zinc-finger) and on the frequency of insertions in chromosome 1 predicted genes, we could extrapolate that 7-10% of the rice gene complement is already tagged by T-DNA insertion in the 6116 independent transformant population. This large resource is of high significance while assisting studies unravelling gene function in rice and cereals, notably through in silico reverse genetics.
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Périn C, Gomez-Jimenez M, Hagen L, Dogimont C, Pech JC, Latché A, Pitrat M, Lelièvre JM. Molecular and genetic characterization of a non-climacteric phenotype in melon reveals two loci conferring altered ethylene response in fruit. Plant Physiol 2002; 129:300-9. [PMID: 12011360 PMCID: PMC155893 DOI: 10.1104/pp.010613] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2001] [Revised: 11/01/2001] [Accepted: 02/04/2002] [Indexed: 05/19/2023]
Abstract
Fruit ripening and abscission are associated with an ethylene burst in several melon (Cucumis melo) genotypes. In cantaloupe as in other climacteric fruit, exogenous ethylene can prematurely induce abscission, ethylene production, and ripening. Melon genotypes without fruit abscission or without ethylene burst also exist and are, therefore, non-climacteric. In the nonabscising melon fruit PI 161375, exogenous ethylene failed to stimulate abscission, loss of firmness, ethylene production, and expression of all target genes tested. However, the PI 161375 etiolated seedlings displayed the usual ethylene-induced triple response. Genetic analysis on a population of recombinant cantaloupe Charentais x PI 161375 inbred lines in segregation for fruit abscission and ethylene production indicated that both characters are controlled by two independent loci, abscission layer (Al)-3 and Al-4. The non-climacteric phenotype in fruit tissues is attributable to ethylene insensitivity conferred by the recessive allelic forms from PI 161375. Five candidate genes (two ACO, two ACS, and ERS) that were localized on the melon genetic map did not exhibit colocalization with Al-3 or Al-4.
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Affiliation(s)
- Christophe Périn
- Institut National de la Recherche Agronomique, Station de Génétique et d'Amélioration des Fruits et Légumes, Domaine St. Maurice, Boîte Postale 94, 84143 Montfavet cedex, France
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Périn C, Hagen S, De Conto V, Katzir N, Danin-Poleg Y, Portnoy V, Baudracco-Arnas S, Chadoeuf J, Dogimont C, Pitrat M. A reference map of Cucumis melo based on two recombinant inbred line populations. Theor Appl Genet 2002; 104:1017-1034. [PMID: 12582608 DOI: 10.1007/s00122-002-0864-x] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2001] [Accepted: 10/25/2001] [Indexed: 05/22/2023]
Abstract
A composite genetic melon map was generated based on two recombinant inbred line (RI) populations. By analyzing the segregation of 346 AFLPs, 113 IMAs and phenotypic characters on a RI population of 163 individuals derived from the cross Védrantais x PI 161375, a first map was constructed. About 20% of the molecular markers were skewed, and the residual heterozygosity was estimated at 4.43% which was not significantly different from the theoretical value of 4.2%. The genome distribution of molecular markers among the 12 linkage groups was not different from a random distribution with the exception of linkage group XII which was found significantly less populated. The genome distributions of IMAs and AFLPs were complementary. AFLPs were found mainly in the middle of each linkage group and sometimes clustered, whereas IMAs were found mainly at the end. A total of 318 molecular markers, mainly AFLP and IMA markers, were mapped on 63 RIs of the second population, Védrantais x PI 414723. Comparison of the maps enables one to conclude that AFLPs and IMAs of like molecular size, amplified with the same primer combination, correspond to the same genetic locus. Both maps were joined through 116 common markers comprising 106 comigrating AFLPs/IMAs, plus five SSRs and five phenotypic markers. The integrated melon map contained 668 loci issuing from the segregation of 1,093 molecular markers in the two RI populations. The composite map spanned 1,654 cM on 12 linkage groups which is the haploid number of chromosomes in melon. Thirty two known-function probes, i.e. known-function genes (9) and morphological traits (23), were included in this map. In addition, the composite map was anchored to previously published maps through SSRs, RFLPs and phenotypic characters.
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Affiliation(s)
- C. Périn
- INRA, Station de Génétique et d'Amélioration des fruits et légumes, BP 94, 84143 Montfavet Cedex, France
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Périn C, Hagen LS, Giovinazzo N, Besombes D, Dogimont C, Pitrat M. Genetic control of fruit shape acts prior to anthesis in melon ( Cucumis melo L.). Mol Genet Genomics 2002; 266:933-41. [PMID: 11862487 DOI: 10.1007/s00438-001-0612-y] [Citation(s) in RCA: 80] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2001] [Accepted: 10/22/2001] [Indexed: 11/26/2022]
Abstract
Genetic control of fruit shape in Cucumis melo was studied using QTL analysis in two Recombinant Inbred (RI) populations consisting of 163 and 63 individuals, respectively, obtained by crossing the same round-fruited parent with two different elongated-fruit lines. Fruit shape is mainly explained by fruit length in these two populations. Most QTLs for fruit shape and ovary shape detected were found to co-segregate, thus demonstrating early control of fruit shape during ovary development. A high level of correlation between fruit shape and ovary shape was also found in 14 unrelated genetic lines, a finding which suggests that control of fruit shape by gene(s) active early in the ovary is a general feature in C. melo. Two major flower genes, a ( monoecious) and p ( pentamerous), were shown to have major effects on fruit shape. Major tightly linked QTLs for fruit and ovary shape were found close to the a and p genes, probably reflecting their pleiotropic effect on fruit shape. Moreover, one of the two QTLs detected in the Védrantais x PI 414723 population was also found in the Védrantais x PI 161375 population. Variation of fruit shape in melon could be due to variations having quantitative effects on a large set of genes that are probably involved in ovary development.
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Affiliation(s)
- C Périn
- INRA, Station de Génétique et d'Amélioration des Fruits et Légumes, Domaine St Maurice, B.P. 94, 84143 Montfavet Cedex, France
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Lelièvre J, Amor M, Flores B, Gomez M, El-Yahyaoui F, Chatenet C, Périn C, Hernandez JA, Romojaro F, Latché A, Bouzayen M, Pitrat M, Dogimont C, Pech J. ETHYLENE-REGULATED GENES AND CLARIFICATION OF THE ROLE OF ETHYLENE IN THE REGULATION OF RIPENING AND QUALITY IN CANTALOUPE MELON FRUIT. ACTA ACUST UNITED AC 2000. [DOI: 10.17660/actahortic.2000.510.77] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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