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4 results on '"LMI RICE, Agronomical Genetics Institute"'

1. Genome-wide Association Study of a Panel of Vietnamese Rice Landraces Reveals New QTLs for Tolerance to Water Deficit During the Vegetative Phase

Author

Hoang, Giang Thi, Van Dinh, Lam, Nguyen, Thom Thi, Ta, Nhung Kim, Gathignol, Floran, Mai, Chung Duc, Jouannic, Stefan, Tran, Khanh Dang, Khuat, Trung Huu, Do, Vinh Nang, Lebrun, Michel, Courtois, Brigitte, Gantet, Pascal, Hanoi University of Science and Technology (HUST), LMI RICE, Agronomical Genetics Institute, National Key Laboratory for Plant Cell Biotechnology, Université de Montpellier (UM), Diversité, adaptation, développement des plantes (UMR DIADE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Agricultural Genetics Institute, Laboratoire des symbioses tropicales et méditerranéennes (UMR LSTM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université Montpellier 1 (UM1)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), French Ministry of Foreign Affairs and International Development, Ministry of Science and Technology of Vietnam, Global Rice Science Partnership (2011-2016), CGIAR Research Program (CRP) on rice agri-food systems (RICE, 2017-2022), and Agricultural Genetics Institute (AGI)

Subjects
Locus des caractères quantitatifs, Quantitative trait loci, Tolérance à la sécheresse, F62 - Physiologie végétale - Croissance et développement, Oryza sativa, lcsh:Plant culture, F30 - Génétique et amélioration des plantes, Association mapping, Drought tolerance, Genotyping by sequencing, Rice, Vietnamese landraces, Variété indigène, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, lcsh:SB1-1110, Vegetal Biology, fungi, food and beverages, Taux de croissance, Carte génétique, Original Article, Biologie végétale
Abstract

Background Drought tolerance is a major challenge in breeding rice for unfavorable environments. In this study, we used a panel of 180 Vietnamese rice landraces genotyped with 21,623 single-nucleotide polymorphism markers to perform a genome-wide association study (GWAS) for different drought response and recovery traits during the vegetative stage. These landraces originate from different geographical locations and are adapted to different agrosystems characterized by contrasted water regimes. Vietnamese landraces are often underrepresented in international panels used for GWAS, but they can contain original genetic determinants related to drought resistance. Results The panel of 180 rice varieties was phenotyped under greenhouse conditions for several drought-related traits in an experimental design with 3 replicates. Plants were grown in pots for 4 weeks and drought-stressed by stopping irrigation for an additional 4 weeks. Drought sensitivity scores and leaf relative water content were measured throughout the drought stress. The recovery capacity was measured 2 weeks after plant rewatering. Several QTLs associated with these drought tolerance traits were identified by GWAS using a mixed model with control of structure and kinship. The number of detected QTLs consisted of 14 for leaf relative water content, 9 for slope of relative water content, 12 for drought sensitivity score, 3 for recovery ability and 1 for relative crop growth rate. This set of 39 QTLs actually corresponded to a total of 17 different QTLs because 9 were simultaneously associated with two or more traits, which indicates that these common loci may have pleiotropic effects on drought-related traits. No QTL was found in association with the same traits in both the indica and japonica subpanels. The possible candidate genes underlying the quantitative trait loci are reviewed. Conclusions Some of the identified QTLs contain promising candidate genes with a function related to drought tolerance by osmotic stress adjustment. Electronic supplementary material The online version of this article (10.1186/s12284-018-0258-6) contains supplementary material, which is available to authorized users.

Published
2019
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2. Apparition of the NAC Transcription Factors Predates the Emergence of Land Plants

Author

Patrick Laufs, Aude Maugarny-Calès, Beatriz Gonçalves, Michael Melkonian, Gane Ka-Shu Wong, Stefan Jouannic, Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Université Paris Saclay (COmUE), Diversité, adaptation, développement des plantes (UMR DIADE), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), University of sciences and technologies of hanoi (USTH), LMI RICE, Agronomical Genetics Institute, National Key Laboratory for Plant Cell Biotechnology, University of Cologne, Beijing Genomics Institute [Shenzhen] (BGI), University of Alberta, This work was supported by the Agence National de la Recherche grantsMorphoLeaf (ANR-10-BLAN-1614) and LeafNet (ANR-12-PDOC-0003).The IJPB benefits from the support of the Labex Saclay Plant Sciences-SPS (ANR-10-LABX-0040-SPS), ANR-10-BLAN-1614,MorphoLeaf,Du réseau de gènes à la forme des organes : une étude interdisciplinaire du développement foliaire.(2010), ANR-12-PDOC-0003,LEAFNET,Etude des cibles et de la spécificité des facteurs de transcription CUCs au cours du dévelopment folliaire: Vers la construction d'un réseau de gènes à haute résolution(2012), and ANR-10-LABX-0040,SPS,Saclay Plant Sciences(2010)

Subjects
0106 biological sciences, 0301 basic medicine, Regulation of gene expression, Thesaurus (information retrieval), [SDV]Life Sciences [q-bio], Plant Science, Computational biology, Biology, 01 natural sciences, 03 medical and health sciences, Origin, 030104 developmental biology, Gene Expression Regulation, Plant, [SDV.IDA]Life Sciences [q-bio]/Food engineering, Embryophyta, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SPI.GPROC]Engineering Sciences [physics]/Chemical and Process Engineering, Adaptation, Molecular Biology, Transcription factor, Gene, Plant Proteins, Transcription Factors, 010606 plant biology & botany
Abstract

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Published
2016
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3. miR2118-triggered phased siRNAs are differentially expressed during the panicle development of wild and domesticated African rice species

Author

François Sabot, Pascal Gantet, Kim Nhung Ta, Yves Vigouroux, Stefan Jouannic, S. De Mita, N. V. Do, Alain Ghesquière, Hélène Adam, LMI RICE, Agronomical Genetics Institute, National Key Laboratory for Plant Cell Biotechnology, Diversité, adaptation, développement des plantes (UMR DIADE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Interactions Arbres-Microorganismes (IAM), Université de Lorraine (UL)-Institut National de la Recherche Agronomique (INRA), Agropolis Fondation (through the 'Investissements d'avenir' programme) [ANR-10-LABX-0001-01], Fondazione Cariplo [EVOREPRICE 1201-004], Institut de Recherche pour le Developpement (IRD), Agropolis foundation (ARCAD project), Vietnamese government [322], Global Rice Science Partnership (GRiSP) scholarship program, Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), and Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)

Subjects
0106 biological sciences, 0301 basic medicine, Panicle, Meristem, Small RNAs, phasiRNAs, miR2118, Domestication, Oryza barthii, Oryza glaberrima, Small RNA, [SDV]Life Sciences [q-bio], Population, Soil Science, Plant Science, Biology, 01 natural sciences, 03 medical and health sciences, Botany, education, Gene, 2. Zero hunger, education.field_of_study, food and beverages, biology.organism_classification, Gene expression profiling, 030104 developmental biology, Original Article, Agronomy and Crop Science, 010606 plant biology & botany
Abstract

Background Rice exhibits a wide range of panicle structures. To explain these variations, much emphasis has been placed on changes in transcriptional regulation, but no large-scale study has yet reported on changes in small RNA regulation in the various rice species. To evaluate this aspect, we performed deep sequencing and expression profiling of small RNAs from two closely related species with contrasting panicle development: the cultivated African rice Oryza glaberrima and its wild relative Oryza barthii. Results Our RNA-seq analysis revealed a dramatic difference between the two species in the 21 nucleotide small RNA population, corresponding mainly to miR2118-triggered phased siRNAs. A detailed expression profiling during the panicle development of O. glaberrima and O. barthii using qRT-PCRs and in situ hybridization, confirmed a delayed expression of the phased siRNAs as well as their lncRNA precursors and regulators (miR2118 and MEL1 gene) in O. glaberrima compared to O. barthii. We provide evidence that the 21-nt phasiRNA pathway in rice is associated with male-gametogenesis but is initiated in spikelet meristems. Conclusion Differential expression of the miR2118-triggered 21-nt phasiRNA pathway between the two African rice species reflects differential rates of determinate fate acquisition of panicle meristems between the two species. Electronic supplementary material The online version of this article (doi:10.1186/s12284-016-0082-9) contains supplementary material, which is available to authorized users.

Published
2016
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4. Identification of CROWN ROOTLESS1-regulated genes in rice reveals specific and conserved elements of postembryonic root formation

Author

Yoan Coudert, Martine Bes, Hélène Adam, Florence Vignols, Van Anh Thi Le, Stefan Jouannic, Emmanuel Guiderdoni, Pascal Gantet, Université de Montpellier (UM), Diversité, adaptation, développement des plantes (UMR DIADE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), LMI RICE, Agronomical Genetics Institute, National Key Laboratory for Plant Cell Biotechnology, University of sciences and technologies of hanoi (USTH), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Résistance des plantes aux bio-agresseurs (UMR RPB), Université Montpellier 2 - Sciences et Techniques (UM2)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), This work was financially supported by a Fellowship from the French Ministere de la Recherche et l’Enseignement Supérieur (Y.C.), a Fellowship of the VietnameseMinistry of Education and Formation (V.A.T.L.) and by the University of Montpellier 2, IRD and CIRAD, LMI RICE, UMR - Interactions Plantes Microorganismes Environnement (UMR IPME), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud]), Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université Montpellier 2 - Sciences et Techniques (UM2)

Subjects
Physiology, crown root, [SDV]Life Sciences [q-bio], Arabidopsis, F62 - Physiologie végétale - Croissance et développement, gene regulatory, Plant Science, F50 - Anatomie et morphologie des plantes, Plant Roots, F30 - Génétique et amélioration des plantes, Système racinaire, Transcriptome, Plant Growth Regulators, Gene Expression Regulation, Plant, Expression des gènes, Lateral root formation, ComputingMilieux_MISCELLANEOUS, Plant Proteins, 2. Zero hunger, chemistry.chemical_classification, Genetics, biology, food and beverages, Plants, Genetically Modified, postembryonic root, CROWN ROOTLESS1 (CRL1), Meristem, Oryza sativa, rice (Oryza sativa), Gene regulatory Network, Auxin, Crown root, Postembryonic root, Gene, Transcription factor, adventitious root, Morphologie végétale, Indoleacetic Acids, Gene Expression Profiling, LOB-domain transcription factor (LBD), Oryza, biology.organism_classification, Adventitious roots, LOB-DOMAIN PROTEIN, chemistry, Rhizosphère, network, Homeobox, Rice, Transcription Factors
Abstract

International audience; In monocotyledons, the root system is mostly composed of postembryonic shoot-borne roots called crown roots. In rice (Oryza sativa), auxin promotes crown root initiation via the LOB-domain transcription factor (LBD) transcription factor CROWN ROOTLESS1 (CRL1); however, the gene regulatory network downstream of CRL1 remains largely unknown. We tested CRL1 transcriptional activity in yeast and in planta, identified CRL1-regulated genes using an inducible gene expression system and a transcriptome analysis, and used in situ hybridization to demonstrate coexpression of a sample of CRL1-regulated genes with CRL1 in crown root primordia. We show that CRL1 positively regulates 277 genes, including key genes involved in meristem patterning (such as QUIESCENT-CENTER SPECIFIC HOMEOBOX; QHB), cell proliferation and hormone homeostasis. Many genes are homologous to Arabidopsis genes involved in lateral root formation, but about a quarter are rice-specific. Our study reveals that several genes acting downstream of LBD transcription factors controlling postembryonic root formation are conserved between monocots and dicots. It also provides evidence that specific genes are involved in the formation of shoot-derived roots in rice.

Published
2014
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