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Kirolinko C, Hobecker K, Cueva M, Botto F, Christ A, Niebel A, Ariel F, Blanco FA, Crespi M, Zanetti ME. A lateral organ boundaries domain transcription factor acts downstream of the auxin response factor 2 to control nodulation and root architecture in Medicago truncatula. THE NEW PHYTOLOGIST 2024; 242:2746-2762. [PMID: 38666352 DOI: 10.1111/nph.19766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 03/21/2024] [Indexed: 05/24/2024]
Abstract
Legume plants develop two types of root postembryonic organs, lateral roots and symbiotic nodules, using shared regulatory components. The module composed by the microRNA390, the Trans-Acting SIRNA3 (TAS3) RNA and the Auxin Response Factors (ARF)2, ARF3, and ARF4 (miR390/TAS3/ARFs) mediates the control of both lateral roots and symbiotic nodules in legumes. Here, a transcriptomic approach identified a member of the Lateral Organ Boundaries Domain (LBD) family of transcription factors in Medicago truncatula, designated MtLBD17/29a, which is regulated by the miR390/TAS3/ARFs module. ChIP-PCR experiments evidenced that MtARF2 binds to an Auxin Response Element present in the MtLBD17/29a promoter. MtLBD17/29a is expressed in root meristems, lateral root primordia, and noninfected cells of symbiotic nodules. Knockdown of MtLBD17/29a reduced the length of primary and lateral roots and enhanced lateral root formation, whereas overexpression of MtLBD17/29a produced the opposite phenotype. Interestingly, both knockdown and overexpression of MtLBD17/29a reduced nodule number and infection events and impaired the induction of the symbiotic genes Nodulation Signaling Pathway (NSP) 1 and 2. Our results demonstrate that MtLBD17/29a is regulated by the miR390/TAS3/ARFs module and a direct target of MtARF2, revealing a new lateral root regulatory hub recruited by legumes to act in the root nodule symbiotic program.
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Affiliation(s)
- Cristina Kirolinko
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Centro Científico y Tecnológico-La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, 1900, La Plata, Argentina
| | - Karen Hobecker
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Centro Científico y Tecnológico-La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, 1900, La Plata, Argentina
| | - Marianela Cueva
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Centro Científico y Tecnológico-La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, 1900, La Plata, Argentina
| | - Florencia Botto
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Centro Científico y Tecnológico-La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, 1900, La Plata, Argentina
| | - Aurélie Christ
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Universities Paris-Sud, Evry and Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment 630, 91405, Orsay, France
| | - Andreas Niebel
- Laboratoire des Interactions Plantes-Microorganismes, Université de Toulouse, INRAE, CNRS, 31326, Castanet-Tolosan, France
| | - Federico Ariel
- Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, 3000, Santa Fe, Argentina
| | - Flavio Antonio Blanco
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Centro Científico y Tecnológico-La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, 1900, La Plata, Argentina
| | - Martín Crespi
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Universities Paris-Sud, Evry and Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment 630, 91405, Orsay, France
| | - María Eugenia Zanetti
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Centro Científico y Tecnológico-La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, 1900, La Plata, Argentina
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Zhao X, Yu J, Chanda B, Zhao J, Wu S, Zheng Y, Sun H, Levi A, Ling KS, Fei Z. Genomic and pangenomic analyses provide insights into the population history and genomic diversification of bottle gourd. THE NEW PHYTOLOGIST 2024. [PMID: 38503725 DOI: 10.1111/nph.19673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Accepted: 02/27/2024] [Indexed: 03/21/2024]
Abstract
Bottle gourd (Lagenaria siceraria (Mol.) Strandl.) is an economically important vegetable crop and one of the earliest domesticated crops. However, the population history and genomic diversification of bottle gourd have not been extensively studied. We generated a comprehensive bottle gourd genome variation map from genome sequences of 197 world-wide representative accessions, which enables a genome-wide association study for identifying genomic loci associated with resistance to zucchini yellow mosaic virus, and constructed a bottle gourd pangenome that harbors 1534 protein-coding genes absent in the reference genome. Demographic analyses uncover that domesticated bottle gourd originated in Southern Africa c. 12 000 yr ago, and subsequently radiated to the New World via the Atlantic drift and to Eurasia through the efforts of early farmers in the initial Holocene. The identified highly differentiated genomic regions among different bottle gourd populations harbor many genes contributing to their local adaptations such as those related to disease resistance and stress tolerance. Presence/absence variation analysis of genes in the pangenome reveals numerous genes including those involved in abiotic/biotic stress responses that have been under selection during the world-wide expansion of bottle gourds. The bottle gourd variation map and pangenome provide valuable resources for future functional studies and genomics-assisted breeding.
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Affiliation(s)
- Xuebo Zhao
- Boyce Thompson Institute, Ithaca, NY, 14853, USA
| | - Jingyin Yu
- Boyce Thompson Institute, Ithaca, NY, 14853, USA
| | - Bidisha Chanda
- USDA-ARS, US Vegetable Laboratory, Charleston, SC, 29414, USA
| | - Jiantao Zhao
- Boyce Thompson Institute, Ithaca, NY, 14853, USA
| | - Shan Wu
- Boyce Thompson Institute, Ithaca, NY, 14853, USA
| | - Yi Zheng
- Boyce Thompson Institute, Ithaca, NY, 14853, USA
| | - Honghe Sun
- Boyce Thompson Institute, Ithaca, NY, 14853, USA
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Amnon Levi
- USDA-ARS, US Vegetable Laboratory, Charleston, SC, 29414, USA
| | - Kai-Shu Ling
- USDA-ARS, US Vegetable Laboratory, Charleston, SC, 29414, USA
| | - Zhangjun Fei
- Boyce Thompson Institute, Ithaca, NY, 14853, USA
- USDA-ARS Robert W. Holley Center for Agriculture and Health, Ithaca, NY, 14853, USA
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Cao H, Zhang X, Li F, Han Z, Guo X, Zhang Y. Glucosinolate O-methyltransferase mediated callus formation and affected ROS homeostasis in Arabidopsis thaliana. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2024; 30:109-121. [PMID: 38435856 PMCID: PMC10902236 DOI: 10.1007/s12298-023-01409-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 12/08/2023] [Accepted: 12/21/2023] [Indexed: 03/05/2024]
Abstract
Auxin-induced callus formation was largely dependent on the function of Lateral Organ Boundaries Domain (LBD) family transcription factors. We previously revealed that two IGMT (Indole glucosinolate oxy-methyl transferase) genes, IGMT2 and IGMT3, may be involved in the callus formation process as potential target genes of LBD29. Overexpression of the IGMT genes induces spontaneous callus formation. However, the details of the IGMT involvement in callus formation process were not well studied. IGMT1-4, but not IGMT5, are targeted and induced by LBD29 during the early stage of callus formation. Cell membrane and nucleus localized IGMT3 was mainly expressed in the elongation and maturation zones tissues of the primary root and lateral root, which could be further accumulated after CIM treatment. The igmts quadruple mutant, which obtained by CRISPR/Cas9 technology, exhibits a phenotype of attenuated callus formation. Enhanced indole glucosinolate anabolic pathway caused by IGMT1-4 overexpression promotes callus formation. In addition, the IGMT genes were involved in the reactive oxygen species homeostasis, which could be responsible for its role on callus formation. This study provides novel insights into the role of IGMTs gene-mediated callus formation. Activation of the Indole glucosinolate anabolic pathway is an inducing factor for plant callus initiation. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-023-01409-2.
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Affiliation(s)
- Huifen Cao
- College of Agriculture and Life Science, Shanxi Datong University, Datong, 037009 Shanxi Province China
- Key Laboratory of Organic Dry Farming for Special Crops in Datong City, Datong, 037009 Shanxi Province China
| | - Xiao Zhang
- Key Laboratory of National Forest and Grass Administration for the Application of Graphene in Forestry, Engineering Research Center of Coal-based Ecological Carbon Sequestration Technology of the Ministry of Education, Shanxi Datong University, Datong, 037009 Shanxi Province China
| | - Feng Li
- College of Agriculture and Life Science, Shanxi Datong University, Datong, 037009 Shanxi Province China
- Key Laboratory of Organic Dry Farming for Special Crops in Datong City, Datong, 037009 Shanxi Province China
| | - Zhiping Han
- College of Agriculture and Life Science, Shanxi Datong University, Datong, 037009 Shanxi Province China
- Key Laboratory of Organic Dry Farming for Special Crops in Datong City, Datong, 037009 Shanxi Province China
| | - Xuhu Guo
- College of Agriculture and Life Science, Shanxi Datong University, Datong, 037009 Shanxi Province China
| | - Yongfang Zhang
- College of Agriculture and Life Science, Shanxi Datong University, Datong, 037009 Shanxi Province China
- Key Laboratory of Organic Dry Farming for Special Crops in Datong City, Datong, 037009 Shanxi Province China
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Nakagami S, Aoyama T, Sato Y, Kajiwara T, Ishida T, Sawa S. CLE3 and its homologs share overlapping functions in the modulation of lateral root formation through CLV1 and BAM1 in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 113:1176-1191. [PMID: 36628476 DOI: 10.1111/tpj.16103] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 12/23/2022] [Accepted: 01/04/2023] [Indexed: 06/17/2023]
Abstract
Lateral roots are important for a wide range of processes, including uptake of water and nutrients. The CLAVATA3 (CLV3)/EMBRYO SURROUNDING REGION-RELATED (CLE) 1 ~ 7 peptide family and their cognate receptor CLV1 have been shown to negatively regulate lateral root formation under low-nitrate conditions. However, little is known about how CLE signaling regulates lateral root formation. A persistent obstacle in CLE peptide research is their functional redundancies, which makes functional analyses difficult. To address this problem, we generate the cle1 ~ 7 septuple mutant (cle1 ~ 7-cr1, cr stands for mutant allele generated with CRISPR/Cas9). cle1 ~ 7-cr1 exhibits longer lateral roots under normal conditions. Specifically, in cle1 ~ 7-cr1, the lateral root density is increased, and lateral root primordia initiation is found to be accelerated. Further analysis shows that cle3 single mutant exhibits slightly longer lateral roots. On the other hand, plants that overexpress CLE2 and CLE3 exhibit decreased lateral root lengths. To explore cognate receptor(s) of CLE2 and CLE3, we analyze lateral root lengths in clv1 barely any meristem 1(bam1) double mutant. Mutating both the CLV1 and BAM1 causes longer lateral roots, but not in each single mutant. In addition, genetic analysis reveals that CLV1 and BAM1 are epistatic to CLE2 and CLE3. Furthermore, gene expression analysis shows that the LATERAL ORGAN BOUNDARIES DOMAIN/ASYMMETRIC LEAVES2-LIKE (LBD/ASL) genes, which promote lateral root formation, are upregulated in cle1 ~ 7-cr1 and clv1 bam1. We therefore propose that CLE2 and CLE3 peptides are perceived by CLV1 and BAM1 to mediate lateral root formation through LBDs regulation.
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Affiliation(s)
- Satoru Nakagami
- Graduate School of Science and Technology, Kumamoto University, Kumamoto, 860-8555, Japan
| | - Tsuyoshi Aoyama
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya, 464-8601, Japan
| | - Yoshikatsu Sato
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya, 464-8601, Japan
| | - Taiki Kajiwara
- Graduate School of Science and Technology, Kumamoto University, Kumamoto, 860-8555, Japan
| | - Takashi Ishida
- Graduate School of Science and Technology, Kumamoto University, Kumamoto, 860-8555, Japan
- International Research Organization for Advanced Science and Technology (IROAST), Kumamoto University, Kumamoto, 860-8555, Japan
| | - Shinichiro Sawa
- Graduate School of Science and Technology, Kumamoto University, Kumamoto, 860-8555, Japan
- International Research Organization for Advanced Science and Technology (IROAST), Kumamoto University, Kumamoto, 860-8555, Japan
- International Research Center for Agriculture and Environmental Biology, Kumamoto University, Kumamoto, 860-8555, Japan
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Jobert F, Soriano A, Brottier L, Casset C, Divol F, Safran J, Lefebvre V, Pelloux J, Robert S, Péret B. Auxin triggers pectin modification during rootlet emergence in white lupin. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 112:1127-1140. [PMID: 36178138 DOI: 10.1111/tpj.15993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 09/23/2022] [Accepted: 09/25/2022] [Indexed: 06/16/2023]
Abstract
Emergence of secondary roots through parental tissue is a highly controlled developmental process. Although the model plant Arabidopsis has been useful to uncover the predominant role of auxin in this process, its simple root structure is not representative of how emergence takes place in most plants, which display more complex root anatomy. White lupin is a legume crop producing structures called cluster roots, where closely spaced rootlets emerge synchronously. Rootlet primordia push their way through several cortical cell layers while maintaining the parent root integrity, reflecting more generally the lateral root emergence process in most multilayered species. In this study, we showed that lupin rootlet emergence is associated with an upregulation of cell wall pectin modifying and degrading genes under the active control of auxin. Among them, we identified LaPG3, a polygalacturonase gene typically expressed in cells surrounding the rootlet primordium and we showed that its downregulation delays emergence. Immunolabeling of pectin epitopes and their quantification uncovered a gradual pectin demethylesterification in the emergence zone, which was further enhanced by auxin treatment, revealing a direct hormonal control of cell wall properties. We also report rhamnogalacturonan-I modifications affecting cortical cells that undergo separation as a consequence of primordium outgrowth. In conclusion, we describe a model of how external tissues in front of rootlet primordia display cell wall modifications to allow for the passage of newly formed rootlets.
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Affiliation(s)
- François Jobert
- IPSiM, Univ Montpellier, CNRS, INRAE, Supagro, 34060, Montpellier, France
- Umeå Plant Science Centre (UPSC), Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 901 83, Umeå, Sweden
| | - Alexandre Soriano
- IPSiM, Univ Montpellier, CNRS, INRAE, Supagro, 34060, Montpellier, France
| | - Laurent Brottier
- IPSiM, Univ Montpellier, CNRS, INRAE, Supagro, 34060, Montpellier, France
| | - Célia Casset
- IPSiM, Univ Montpellier, CNRS, INRAE, Supagro, 34060, Montpellier, France
| | - Fanchon Divol
- IPSiM, Univ Montpellier, CNRS, INRAE, Supagro, 34060, Montpellier, France
| | - Josip Safran
- UMR INRAE 1158 BioEcoAgro, BIOPI Biologie des Plantes et Innovation, SFR Condorcet FR CNRS 3417, Université de Picardie, 80039, Amiens, France
| | - Valérie Lefebvre
- UMR INRAE 1158 BioEcoAgro, BIOPI Biologie des Plantes et Innovation, SFR Condorcet FR CNRS 3417, Université de Picardie, 80039, Amiens, France
| | - Jérôme Pelloux
- UMR INRAE 1158 BioEcoAgro, BIOPI Biologie des Plantes et Innovation, SFR Condorcet FR CNRS 3417, Université de Picardie, 80039, Amiens, France
| | - Stéphanie Robert
- Umeå Plant Science Centre (UPSC), Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 901 83, Umeå, Sweden
| | - Benjamin Péret
- IPSiM, Univ Montpellier, CNRS, INRAE, Supagro, 34060, Montpellier, France
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Li L, Hong D, An C, Chen Y, Zhao P, Li X, Xiong F, Ren M, Xu R. Overexpression of TaLAX3-1B alters the stomatal aperture and improves the salt stress resistance of tobacco. Mol Biol Rep 2022; 49:7455-7464. [PMID: 35624389 DOI: 10.1007/s11033-022-07548-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Accepted: 04/29/2022] [Indexed: 10/18/2022]
Abstract
BACKGROUND Stomata, which play important roles in both optimizing photosynthesis efficiency and adapting to stress, are closely related to IAA and ABA. In plants, the auxin influx carrier LAX3 has been found to play roles in development and stress tolerance. However, the function of LAX3 in stomata and in response to salt stress remains largely unknown. METHODS AND RESULTS Here, we show that overexpression of wheat TaLAX3-1B in tobacco results in a decrease in stomatal aperture and a relatively closed state of the stomata. In addition, the stomatal movement of the OxTaLAX3-1B lines was less sensitive to ABA than that of the WT. Consistently, compared with the WT, the OxTaLAX3-1B lines showed significantly higher expression of stomate-, IAA- and ABA-related genes and endogenous IAA and ABA contents. Furthermore, compared with the WT, the OxTaLAX3-1B lines exhibited higher proline content, salt stress-related gene expression and ROS antioxidant enzyme activity but lower MDA content and ROS accumulation after salt treatment. CONCLUSIONS The present results suggest that TaLAX3-1B plays a positive role in regulating stomatal closure and enhancing salt stress tolerance.
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Affiliation(s)
- Luhua Li
- College of Agriculture, Guizhou University, Guiyang, 550025, China
- Guizhou Sub-Center of National Wheat Improvement Center, Guiyang, 550025, China
| | - Dingli Hong
- College of Agriculture, Guizhou University, Guiyang, 550025, China
- Guizhou Sub-Center of National Wheat Improvement Center, Guiyang, 550025, China
| | - Chang An
- College of Agriculture, Guizhou University, Guiyang, 550025, China
- Guizhou Sub-Center of National Wheat Improvement Center, Guiyang, 550025, China
| | - Yuxuan Chen
- College of Agriculture, Guizhou University, Guiyang, 550025, China
- Guizhou Sub-Center of National Wheat Improvement Center, Guiyang, 550025, China
| | - Pengpeng Zhao
- College of Agriculture, Guizhou University, Guiyang, 550025, China
- Guizhou Sub-Center of National Wheat Improvement Center, Guiyang, 550025, China
| | - Xin Li
- College of Agriculture, Guizhou University, Guiyang, 550025, China
- Guizhou Sub-Center of National Wheat Improvement Center, Guiyang, 550025, China
| | - Fumin Xiong
- College of Agriculture, Guizhou University, Guiyang, 550025, China
- Guizhou Sub-Center of National Wheat Improvement Center, Guiyang, 550025, China
| | - Mingjian Ren
- College of Agriculture, Guizhou University, Guiyang, 550025, China
- Guizhou Sub-Center of National Wheat Improvement Center, Guiyang, 550025, China
| | - Ruhong Xu
- College of Agriculture, Guizhou University, Guiyang, 550025, China.
- Guizhou Sub-Center of National Wheat Improvement Center, Guiyang, 550025, China.
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Genome-Wide Association Studies of Root-Related Traits in Brassica napus L. under Low-Potassium Conditions. PLANTS 2022; 11:plants11141826. [PMID: 35890461 PMCID: PMC9318150 DOI: 10.3390/plants11141826] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 06/20/2022] [Accepted: 07/06/2022] [Indexed: 11/17/2022]
Abstract
Roots are essential organs for a plant’s ability to absorb water and obtain mineral nutrients, hence they are critical to its development. Plants use root architectural alterations to improve their chances of absorbing nutrients when their supply is low. Nine root traits of a Brassica napus association panel were explored in hydroponic-system studies under low potassium (K) stress to unravel the genetic basis of root growth in rapeseed. The quantitative trait loci (QTL) and candidate genes for root development were discovered using a multilocus genome-wide association study (ML-GWAS). For the nine traits, a total of 453 significant associated single-nucleotide polymorphism (SNP) loci were discovered, which were then integrated into 206 QTL clusters. There were 45 pleiotropic clusters, and qRTA04-4 and qRTC04-7 were linked to TRL, TSA, and TRV at the same time, contributing 5.25–11.48% of the phenotypic variance explained (PVE) to the root traits. Additionally, 1360 annotated genes were discovered by examining genomic regions within 100 kb upstream and downstream of lead SNPs within the 45 loci. Thirty-five genes were identified as possibly regulating root-system development. As per protein–protein interaction analyses, homologs of three genes (BnaC08g29120D, BnaA07g10150D, and BnaC04g45700D) have been shown to influence root growth in earlier investigations. The QTL clusters and candidate genes identified in this work will help us better understand the genetics of root growth traits and could be employed in marker-assisted breeding for rapeseed adaptable to various conditions with low K levels.
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Omary M, Gil-Yarom N, Yahav C, Steiner E, Hendelman A, Efroni I. A conserved superlocus regulates above- and belowground root initiation. Science 2022; 375:eabf4368. [PMID: 35239373 DOI: 10.1101/2020.11.11.377937] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Plants continuously form new organs in different developmental contexts in response to environmental cues. Underground lateral roots initiate from prepatterned cells in the main root, but cells can also bypass the root-shoot trajectory separation and generate shoot-borne roots through an unknown mechanism. We mapped tomato (Solanum lycopersicum) shoot-borne root development at single-cell resolution and showed that these roots initiate from phloem-associated cells through a unique transition state. This state requires the activity of a transcription factor that we named SHOOTBORNE ROOTLESS (SBRL). Evolutionary analysis reveals that SBRL's function and cis regulation are conserved in angiosperms and that it arose as an ancient duplication, with paralogs controlling wound-induced and lateral root initiation. We propose that the activation of a common transition state by context-specific regulators underlies the plasticity of plant root systems.
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Affiliation(s)
- Moutasem Omary
- The Institute of Plant Science and Genetics in Agriculture, Faculty of Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Naama Gil-Yarom
- The Institute of Plant Science and Genetics in Agriculture, Faculty of Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Chen Yahav
- The Institute of Plant Science and Genetics in Agriculture, Faculty of Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Evyatar Steiner
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Anat Hendelman
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Idan Efroni
- The Institute of Plant Science and Genetics in Agriculture, Faculty of Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
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9
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Li H, Chen H, Chen L, Wang C. The Role of Hydrogen Sulfide in Plant Roots during Development and in Response to Abiotic Stress. Int J Mol Sci 2022; 23:ijms23031024. [PMID: 35162947 PMCID: PMC8835357 DOI: 10.3390/ijms23031024] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 01/16/2022] [Accepted: 01/17/2022] [Indexed: 12/31/2022] Open
Abstract
Hydrogen sulfide (H2S) is regarded as a “New Warrior” for managing plant stress. It also plays an important role in plant growth and development. The regulation of root system architecture (RSA) by H2S has been widely recognized. Plants are dependent on the RSA to meet their water and nutritional requirements. They are also partially dependent on the RSA for adapting to environment change. Therefore, a good understanding of how H2S affects the RSA could lead to improvements in both crop function and resistance to environmental change. In this review, we summarized the regulating effects of H2S on the RSA in terms of primary root growth, lateral and adventitious root formation, root hair development, and the formation of nodules. We also discussed the genes involved in the regulation of the RSA by H2S, and the relationships with other signal pathways. In addition, we discussed how H2S regulates root growth in response to abiotic stress. This review could provide a comprehensive understanding of the role of H2S in roots during development and under abiotic stress.
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Affiliation(s)
- Hua Li
- College of Life Science, Henan Agricultural University, Zhengzhou 450002, China; (H.C.); (L.C.)
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Taian 271018, China
- Correspondence: (H.L.); (C.W.)
| | - Hongyu Chen
- College of Life Science, Henan Agricultural University, Zhengzhou 450002, China; (H.C.); (L.C.)
| | - Lulu Chen
- College of Life Science, Henan Agricultural University, Zhengzhou 450002, China; (H.C.); (L.C.)
| | - Chenyang Wang
- College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
- State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University,
Zhengzhou 450002, China
- Correspondence: (H.L.); (C.W.)
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10
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Ishfaq M, Zhong Y, Wang Y, Li X. Magnesium Limitation Leads to Transcriptional Down-Tuning of Auxin Synthesis, Transport, and Signaling in the Tomato Root. FRONTIERS IN PLANT SCIENCE 2021; 12:802399. [PMID: 35003191 PMCID: PMC8733655 DOI: 10.3389/fpls.2021.802399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 12/06/2021] [Indexed: 05/08/2023]
Abstract
Magnesium (Mg) deficiency is becoming a widespread limiting factor for crop production. How crops adapt to Mg limitation remains largely unclear at the molecular level. Using hydroponic-cultured tomato seedlings, we found that total Mg2+ content significantly decreased by ∼80% under Mg limitation while K+ and Ca2+ concentrations increased. Phylogenetic analysis suggested that Mg transporters (MRS2/MGTs) constitute a previously uncharacterized 3-clade tree in planta with two rounds of asymmetric duplications, providing evolutionary evidence for further molecular investigation. In adaptation to internal Mg deficiency, the expression of six representative MGTs (two in the shoot and four in the root) was up-regulated in Mg-deficient plants. Contradictory to the transcriptional elevation of most of MGTs, Mg limitation resulted in the ∼50% smaller root system. Auxin concentrations particularly decreased by ∼23% in the Mg-deficient root, despite the enhanced accumulation of gibberellin, cytokinin, and ABA. In accordance with such auxin reduction was overall transcriptional down-regulation of thirteen genes controlling auxin biosynthesis (TAR/YUCs), transport (LAXs, PINs), and signaling (IAAs, ARFs). Together, systemic down-tuning of gene expression in the auxin signaling pathway under Mg limitation preconditions a smaller tomato root system, expectedly stimulating MGT transcription for Mg uptake or translocation.
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Affiliation(s)
- Muhammad Ishfaq
- Key Laboratory of Plant-Soil Interactions, College of Resources and Environmental Sciences, Ministry of Education, National Academy of Agriculture Green Development, China Agricultural University, Beijing, China
| | - Yanting Zhong
- Key Laboratory of Plant-Soil Interactions, College of Resources and Environmental Sciences, Ministry of Education, National Academy of Agriculture Green Development, China Agricultural University, Beijing, China
- Department of Vegetable Sciences, China Agricultural University, Beijing, China
| | - Yongqi Wang
- Key Laboratory of Plant-Soil Interactions, College of Resources and Environmental Sciences, Ministry of Education, National Academy of Agriculture Green Development, China Agricultural University, Beijing, China
| | - Xuexian Li
- Key Laboratory of Plant-Soil Interactions, College of Resources and Environmental Sciences, Ministry of Education, National Academy of Agriculture Green Development, China Agricultural University, Beijing, China
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11
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DeMott L, Oblessuc PR, Pierce A, Student J, Melotto M. Spatiotemporal regulation of JAZ4 expression and splicing contribute to ethylene- and auxin-mediated responses in Arabidopsis roots. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:1266-1282. [PMID: 34562337 DOI: 10.1111/tpj.15508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 08/26/2021] [Accepted: 09/02/2021] [Indexed: 06/13/2023]
Abstract
Jasmonic acid (JA) signaling controls several processes related to plant growth, development, and defense, which are modulated by the transcription regulator and receptor JASMONATE-ZIM DOMAIN (JAZ) proteins. We recently discovered that a member of the JAZ family, JAZ4, has a prominent function in canonical JA signaling as well as other mechanisms. Here, we discovered the existence of two naturally occurring splice variants (SVs) of JAZ4 in planta, JAZ4.1 and JAZ4.2, and employed biochemical and pharmacological approaches to determine protein stability and repression capability of these SVs within JA signaling. We then utilized quantitative and qualitative transcriptional studies to determine spatiotemporal expression and splicing patterns in vivo, which revealed developmental-, tissue-, and organ-specific regulation. Detailed phenotypic and expression analyses suggest a role of JAZ4 in ethylene (ET) and auxin signaling pathways differentially within the zones of root development in seedlings. These results support a model in which JAZ4 functions as a negative regulator of ET signaling and auxin signaling in root tissues above the apex. However, in the root apex JAZ4 functions as a positive regulator of auxin signaling possibly independently of ET. Collectively, our data provide insight into the complexity of spatiotemporal regulation of JAZ4 and how this impacts hormone signaling specificity and diversity in Arabidopsis roots.
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Affiliation(s)
- Logan DeMott
- Department of Plant Sciences, University of California, Davis, CA, USA
- Plant Pathology Graduate Group, University of California, Davis, CA, USA
| | - Paula R Oblessuc
- Department of Plant Sciences, University of California, Davis, CA, USA
| | - Alice Pierce
- Department of Plant Sciences, University of California, Davis, CA, USA
| | - Joseph Student
- Department of Plant Sciences, University of California, Davis, CA, USA
| | - Maeli Melotto
- Department of Plant Sciences, University of California, Davis, CA, USA
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12
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Cantó-Pastor A, Mason GA, Brady SM, Provart NJ. Arabidopsis bioinformatics: tools and strategies. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:1585-1596. [PMID: 34695270 DOI: 10.1111/tpj.15547] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 10/01/2021] [Accepted: 10/19/2021] [Indexed: 06/13/2023]
Abstract
The sequencing of the Arabidopsis thaliana genome 21 years ago ushered in the genomics era for plant research. Since then, an incredible variety of bioinformatic tools permit easy access to large repositories of genomic, transcriptomic, proteomic, epigenomic and other '-omic' data. In this review, we cover some more recent tools (and highlight the 'classics') for exploring such data in order to help formulate quality, testable hypotheses, often without having to generate new experimental data. We cover tools for examining gene expression and co-expression patterns, undertaking promoter analyses and gene set enrichment analyses, and exploring protein-protein and protein-DNA interactions. We will touch on tools that integrate different data sets at the end of the article.
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Affiliation(s)
- Alex Cantó-Pastor
- Department of Plant Biology and Genome Center, University of California Davis, 1 Shields Avenue, Davis, CA, 95616, USA
| | - G Alex Mason
- Department of Plant Biology and Genome Center, University of California Davis, 1 Shields Avenue, Davis, CA, 95616, USA
| | - Siobhan M Brady
- Department of Plant Biology and Genome Center, University of California Davis, 1 Shields Avenue, Davis, CA, 95616, USA
| | - Nicholas J Provart
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks Street, Toronto, ON, M5S 3B2, Canada
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13
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Hu QQ, Shu JQ, Li WM, Wang GZ. Role of Auxin and Nitrate Signaling in the Development of Root System Architecture. FRONTIERS IN PLANT SCIENCE 2021; 12:690363. [PMID: 34858444 PMCID: PMC8631788 DOI: 10.3389/fpls.2021.690363] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 10/25/2021] [Indexed: 06/12/2023]
Abstract
The plant root is an important storage organ that stores indole-3-acetic acid (IAA) from the apical meristem, as well as nitrogen, which is obtained from the external environment. IAA and nitrogen act as signaling molecules that promote root growth to obtain further resources. Fluctuations in the distribution of nitrogen in the soil environment induce plants to develop a set of strategies that effectively improve nitrogen use efficiency. Auxin integrates the information regarding the nitrate status inside and outside the plant body to reasonably distribute resources and sustainably construct the plant root system. In this review, we focus on the main factors involved in the process of nitrate- and auxin-mediated regulation of root structure to better understand how the root system integrates the internal and external information and how this information is utilized to modify the root system architecture.
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Depuydt T, Vandepoele K. Multi-omics network-based functional annotation of unknown Arabidopsis genes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:1193-1212. [PMID: 34562334 DOI: 10.1111/tpj.15507] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 09/20/2021] [Indexed: 06/13/2023]
Abstract
Unraveling gene function is pivotal to understanding the signaling cascades that control plant development and stress responses. As experimental profiling is costly and labor intensive, there is a clear need for high-confidence computational annotation. In contrast to detailed gene-specific functional information, transcriptomics data are widely available for both model and crop species. Here, we describe a novel automated function prediction method, which leverages complementary information from multiple expression datasets by analyzing study-specific gene co-expression networks. First, we benchmarked the prediction performance on recently characterized Arabidopsis thaliana genes, and showed that our method outperforms state-of-the-art expression-based approaches. Next, we predicted biological process annotations for known (n = 15 790) and unknown (n = 11 865) genes in A. thaliana and validated our predictions using experimental protein-DNA and protein-protein interaction data (covering >220 000 interactions in total), obtaining a set of high-confidence functional annotations. Our method assigned at least one validated annotation to 5054 (42.6%) unknown genes, and at least one novel validated function to 3408 (53.0%) genes with computational annotations only. These omics-supported functional annotations shed light on a variety of developmental processes and molecular responses, such as flower and root development, defense responses to fungi and bacteria, and phytohormone signaling, and help fill the information gap on biological process annotations in Arabidopsis. An in-depth analysis of two context-specific networks, modeling seed development and response to water deprivation, shows how previously uncharacterized genes function within the respective networks. Moreover, our automated function prediction approach can be applied in future studies to facilitate gene discovery for crop improvement.
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Affiliation(s)
- Thomas Depuydt
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, Vlaams Instituut voor Biotechnologie, Ghent, Belgium
| | - Klaas Vandepoele
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, Vlaams Instituut voor Biotechnologie, Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium
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15
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Ma Y, Wolf S, Lohmann JU. Casting the Net-Connecting Auxin Signaling to the Plant Genome. Cold Spring Harb Perspect Biol 2021; 13:a040006. [PMID: 33903151 PMCID: PMC8559546 DOI: 10.1101/cshperspect.a040006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Auxin represents one of the most potent and most versatile hormonal signals in the plant kingdom. Built on a simple core of only a few dedicated components, the auxin signaling system plays important roles for diverse aspects of plant development, physiology, and defense. Key to the diversity of context-dependent functional outputs generated by cells in response to this small molecule are gene duplication events and sub-functionalization of signaling components on the one hand, and a deep embedding of the auxin signaling system into complex regulatory networks on the other hand. Together, these evolutionary innovations provide the mechanisms to allow each cell to display a highly specific auxin response that suits its individual requirements. In this review, we discuss the regulatory networks connecting auxin with a large number of diverse pathways at all relevant levels of the signaling system ranging from biosynthesis to transcriptional response.
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Affiliation(s)
- Yanfei Ma
- Department of Stem Cell Biology, Centre for Organismal Studies, Heidelberg University, D-69120 Heidelberg, Germany
| | - Sebastian Wolf
- Cell Wall Signalling Group, Centre for Organismal Studies, Heidelberg University, D-69120 Heidelberg, Germany
| | - Jan U Lohmann
- Department of Stem Cell Biology, Centre for Organismal Studies, Heidelberg University, D-69120 Heidelberg, Germany
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16
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Genome-Wide Identification of LATERAL ORGAN BOUNDARIES DOMAIN (LBD) Transcription Factors and Screening of Salt Stress Candidates of Rosa rugosa Thunb. BIOLOGY 2021; 10:biology10100992. [PMID: 34681091 PMCID: PMC8533445 DOI: 10.3390/biology10100992] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/26/2021] [Accepted: 09/30/2021] [Indexed: 01/04/2023]
Abstract
LATERAL ORGAN BOUNDARIES DOMAIN (LBD) transcription factors are regulators of lateral organ morphogenesis, boundary establishment, and secondary metabolism in plants. The responsive role of LBD gene family in plant abiotic stress is emerging, whereas its salt stress responsive mechanism in Rosa spp. is still unclear. The wild plant of Rosa rugosa Thunb., which exhibits strong salt tolerance to stress, is an ideal material to explore the salt-responsive LBD genes. In our study, we identified 41 RrLBD genes based on the R. rugosa genome. According to phylogenetic analysis, all RrLBD genes were categorized into Classes I and II with conserved domains and motifs. The cis-acting element prediction revealed that the promoter regions of most RrLBD genes contain defense and stress responsiveness and plant hormone response elements. Gene expression patterns under salt stress indicated that RrLBD12c, RrLBD25, RrLBD39, and RrLBD40 may be potential regulators of salt stress signaling. Our analysis provides useful information on the evolution and development of RrLBD gene family and indicates that the candidate RrLBD genes are involved in salt stress signaling, laying a foundation for the exploration of the mechanism of LBD genes in regulating abiotic stress.
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17
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Wu B, Li N, Deng Z, Luo F, Duan Y. Selection and Evaluation of a Thornless and HLB-Tolerant Bud-Sport of Pummelo Citrus With an Emphasis on Molecular Mechanisms. FRONTIERS IN PLANT SCIENCE 2021; 12:739108. [PMID: 34531892 PMCID: PMC8438139 DOI: 10.3389/fpls.2021.739108] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Accepted: 08/04/2021] [Indexed: 06/01/2023]
Abstract
The selection of elite bud-sports is an important breeding approach in horticulture. We discovered and evaluated a thornless pummelo bud-sport (TL) that grew more vigorously and was more tolerant to Huanglongbing (HLB) than the thorny wild type (W). To reveal the underlying molecular mechanisms, we carried out whole-genome sequencing of W, and transcriptome comparisons of W, TL, and partially recovered thorny "mutants" (T). The results showed W, TL, and T varied in gene expression, allelic expression, and alternative splicing. Most genes/pathways with significantly altered expression in TL compared to W remained similarly altered in T. Pathway and gene ontology enrichment analysis revealed that the expression of multiple pathways, including photosynthesis and cell wall biosynthesis, was altered among the three genotypes. Remarkably, two polar auxin transporter genes, PIN7 and LAX3, were expressed at a significantly lower level in TL than in both W and T, implying alternation of polar auxin transport in TL may be responsible for the vigorous growth and thornless phenotype. Furthermore, 131 and 68 plant defense-related genes were significantly upregulated and downregulated, respectively, in TL and T compared with W. These genes may be involved in enhanced salicylic acid (SA) dependent defense and repression of defense inducing callose deposition and programmed cell death. Overall, these results indicated that the phenotype changes of the TL bud-sport were associated with tremendous transcriptome alterations, providing new clues and targets for breeding and gene editing for citrus improvement.
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Affiliation(s)
- Bo Wu
- School of Computing, Clemson University, Clemson, SC, United States
| | - Na Li
- United States Department of Agriculture-Agriculture Research Service-United States Horticultural Research Laboratory, Fort Pierce, FL, United States
- College of Horticulture, Hunan Agricultural University, Changsha, China
| | - Zhanao Deng
- Department of Environmental Horticulture, Gulf Coast Research and Education Center, IFAS, University of Florida, Wimauma, FL, United States
| | - Feng Luo
- School of Computing, Clemson University, Clemson, SC, United States
| | - Yongping Duan
- United States Department of Agriculture-Agriculture Research Service-United States Horticultural Research Laboratory, Fort Pierce, FL, United States
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18
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Wu X, Du A, Zhang S, Wang W, Liang J, Peng F, Xiao Y. Regulation of growth in peach roots by exogenous hydrogen sulfide based on RNA-Seq. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 159:179-192. [PMID: 33383385 DOI: 10.1016/j.plaphy.2020.12.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 12/17/2020] [Indexed: 06/12/2023]
Abstract
Hydrogen sulfide (H2S) has been shown to regulate many physiological processes of plants. In this study, we observed that 0.2 mM sodium hydrosulfide (NaHS), a donor of H2S, can regulate the root architecture of peach seedlings, increasing the number of lateral roots by 40.63%. To investigate the specific mechanisms by which H2S regulates root growth in peach, we used RNA sequencing and heterologous expression technology. Our results showed that exogenous H2S led to a 44.50% increase in the concentration of endogenous auxin. Analyses of differentially expressed genes (DEGs) revealed that 963 and 1113 genes responded to H2S on days one and five of treatment, respectively. Among the DEGs, 26 genes were involved in auxin biosynthesis, transport, and signal transduction. Using weighted correlation network analysis, we found that the auxin-related genes in the H2S-specific gene module were disproportionately involved in polar transport, which may play an important role in H2S-induced root growth. In addition, we observed that the expression of LATERAL ORGAN BOUNDARIES DOMAIN 16 (PpLBD16) was significantly up-regulated by exogenous application of H2S in peach. Overexpression of PpLBD16 in an Arabidopsis system yielded a 66.83% increase in the number of lateral roots. Under exposure to exogenous H2S, there was also increased expression of genes related to cell proliferation, indicating that H2S regulates the growth of peach roots. Our work represents the first comprehensive transcriptomic analysis of the effects of exogenous application of H2S on the roots of peach, and provides new insights into the mechanisms underlying H2S-induced root growth.
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Affiliation(s)
- Xuelian Wu
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, 271018, China
| | - Anqi Du
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, 271018, China
| | - Shuhui Zhang
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, 271018, China
| | - Wenru Wang
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, 271018, China
| | - Jiahui Liang
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, 271018, China
| | - Futian Peng
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, 271018, China.
| | - Yuansong Xiao
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, 271018, China.
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19
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Tessi TM, Brumm S, Winklbauer E, Schumacher B, Pettinari G, Lescano I, González CA, Wanke D, Maurino VG, Harter K, Desimone M. Arabidopsis AZG2 transports cytokinins in vivo and regulates lateral root emergence. THE NEW PHYTOLOGIST 2021; 229:979-993. [PMID: 33070379 DOI: 10.1111/nph.16943] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 08/23/2020] [Indexed: 05/06/2023]
Abstract
Cytokinin and auxin are key regulators of plant growth and development. During the last decade transport mechanisms have turned out to be the key for the control of local and long-distance hormone distributions. In contrast with auxin, cytokinin transport is poorly understood. Here, we show that Arabidopsis thaliana AZG2, a member of the AZG purine transporter family, acts as cytokinin transporter involved in root system architecture determination. Even though purines are substrates for both AZG1 and AZG2, we found distinct transport mechanisms. The expression of AZG2 is restricted to a small group of cells surrounding the lateral root (LR) primordia and induced by auxins. Compared to the wild-type (WT), mutants carrying loss-of-function alleles of AZG2 have higher LR density, suggesting that AZG2 is part of a regulatory pathway in LR emergence. Moreover, azg2 is partially insensitive to exogenous cytokinin, which is consistent with the observation that the cytokinin reporter TCSnpro :GFP showed lower fluorescence signal in the roots of azg2 compared to the WT. These results indicate a defective cytokinin signalling pathway in the region of LR primordia. The integration of AZG2 subcellular localization and cytokinin transport capacity data allowed us to propose a local cytokinin : auxin signalling model for the regulation of LR emergence.
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Affiliation(s)
- Tomás M Tessi
- Instituto Multidisciplinario de Biología Vegetal (IMBIV), CONICET, Av. Vélez Sarsfield 299, Córdoba, 5000, Argentina
| | - Sabine Brumm
- Zentrum für Molekularbiologie der Pflanzen, Universität Tübingen, Auf der Morgenstelle 1, Tübingen, 72076, Germany
| | - Eva Winklbauer
- Zentrum für Molekularbiologie der Pflanzen, Universität Tübingen, Auf der Morgenstelle 1, Tübingen, 72076, Germany
| | - Benjamin Schumacher
- Zentrum für Molekularbiologie der Pflanzen, Universität Tübingen, Auf der Morgenstelle 1, Tübingen, 72076, Germany
| | - Georgina Pettinari
- Facultad de Ciencias Exactas Físicas y Naturales, Universidad Nacional de Córdoba, Av. Vélez Sarsfield 299, Córdoba, 5000, Argentina
| | - Ignacio Lescano
- Instituto Multidisciplinario de Biología Vegetal (IMBIV), CONICET, Av. Vélez Sarsfield 299, Córdoba, 5000, Argentina
| | - Claudio A González
- Facultad de Ciencias Exactas Físicas y Naturales, Universidad Nacional de Córdoba, Av. Vélez Sarsfield 299, Córdoba, 5000, Argentina
| | - Dierk Wanke
- Zentrum für Molekularbiologie der Pflanzen, Universität Tübingen, Auf der Morgenstelle 1, Tübingen, 72076, Germany
| | - Verónica G Maurino
- Institut für Molekulare Physiologie und Biotechnologie der Pflanzen, Abteilung Molekulare Pflanzenphysiologie, Universität Bonn, Kirschallee 1, Bonn, 53115, Germany
| | - Klaus Harter
- Zentrum für Molekularbiologie der Pflanzen, Universität Tübingen, Auf der Morgenstelle 1, Tübingen, 72076, Germany
| | - Marcelo Desimone
- Instituto Multidisciplinario de Biología Vegetal (IMBIV), CONICET, Av. Vélez Sarsfield 299, Córdoba, 5000, Argentina
- Facultad de Ciencias Exactas Físicas y Naturales, Universidad Nacional de Córdoba, Av. Vélez Sarsfield 299, Córdoba, 5000, Argentina
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20
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Abstract
Bioinformatic tools are now an everyday part of a plant researcher's collection of protocols. They allow almost instantaneous access to large data sets encompassing genomes, transcriptomes, proteomes, epigenomes, and other "-omes," which are now being generated with increasing speed and decreasing cost. With the appropriate queries, such tools can generate quality hypotheses, sometimes without the need for new experimental data. In this chapter, we will investigate some of the tools used for examining gene expression and coexpression patterns, performing promoter analyses and functional classification enrichment for sets of genes, and exploring protein-protein and protein-DNA interactions in Arabidopsis. We will also cover additional tools that allow integration of data from several sources for improved hypothesis generation.
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Affiliation(s)
- G Alex Mason
- Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA, USA
| | - Alex Cantó-Pastor
- Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA, USA
| | - Siobhan M Brady
- Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA, USA
| | - Nicholas J Provart
- Department of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, Canada.
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21
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Chapman JM, Muday GK. Flavonols modulate lateral root emergence by scavenging reactive oxygen species in Arabidopsis thaliana. J Biol Chem 2021; 296:100222. [PMID: 33839683 PMCID: PMC7948594 DOI: 10.1074/jbc.ra120.014543] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 12/19/2020] [Accepted: 12/21/2020] [Indexed: 11/20/2022] Open
Abstract
Flavonoids are a class of specialized metabolites with subclasses including flavonols and anthocyanins, which have unique properties as antioxidants. Flavonoids modulate plant development, but whether and how they impact lateral root development is unclear. We examined potential roles for flavonols in this process using Arabidopsis thaliana mutants with defects in genes encoding key enzymes in flavonoid biosynthesis. We observed the tt4 and fls1 mutants, which produce no flavonols, have increased lateral root emergence. The tt4 root phenotype was reversed by genetic and chemical complementation. To more specifically define the flavonoids involved, we tested an array of flavonoid biosynthetic mutants, eliminating roles for anthocyanins and the flavonols quercetin and isorhamnetin in modulating lateral root development. Instead, two tt7 mutant alleles, with defects in a branchpoint enzyme blocking quercetin biosynthesis, formed reduced numbers of lateral roots and tt7-2 had elevated levels of kaempferol. Using a flavonol-specific dye, we observed that in the tt7-2 mutant, kaempferol accumulated within lateral root primordia at higher levels than wild-type. These data are consistent with kaempferol, or downstream derivatives, acting as a negative regulator of lateral root emergence. We examined ROS accumulation using ROS-responsive probes and found reduced fluorescence of a superoxide-selective probe within the primordia of tt7-2 compared with wild-type, but not in the tt4 mutant, consistent with opposite effects of these mutants on lateral root emergence. These results support a model in which increased level of kaempferol in the lateral root primordia of tt7-2 reduces superoxide concentration and ROS-stimulated lateral root emergence.
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Affiliation(s)
- Jordan M Chapman
- Biology Department, Wake Forest University, Winston Salem, North Carolina, USA
| | - Gloria K Muday
- Biology Department, Wake Forest University, Winston Salem, North Carolina, USA.
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22
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Yue J, Yang H, Yang S, Wang J. TDIF regulates auxin accumulation and modulates auxin sensitivity to enhance both adventitious root and lateral root formation in poplar trees. TREE PHYSIOLOGY 2020; 40:1534-1547. [PMID: 32598454 DOI: 10.1093/treephys/tpaa077] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 05/11/2020] [Accepted: 06/16/2020] [Indexed: 05/25/2023]
Abstract
Of six TRACHEARY ELEMENT DIFFERENTIATION INHIBITORY FACTOR (TDIF)-encoding genes in poplar, PtTDIF1 is predominantly expressed in adventitious roots (ARs), and the other five PtTDIFs are preferentially expressed in lateral roots (LRs). Upon auxin application, expression of all PtTDIFs declined in ARs but transiently increased in LRs. Both exogenous TDIF peptides and overexpression of PtTDIFs in poplar positively regulated the initiation and elongation of LRs, and overexpression of PtTDIFs also increased the number of ARs. As visualized by the auxin-responsive marker DR5:GUS, TDIF had differential impacts on the auxin signaling activity in ARs and LRs, which was corroborated by the free indole-3-acetic acid (IAA) measurements in them. Shoot tips of PtTDIF2- and PtTDIFL2-overexpressing (together as PtTDIFsOE) trees revealed an enhanced IAA biosynthetic capacity, and removal of the aerial tissues dramatically diminished the root phenotypes of micro-propagated PtTDIFsOE trees. Furthermore, PtTDIFsOE poplars displayed an increased sensitivity for exogenous IAA, and N-1-naphthylphthalamic acid (NPA) completely blocked the TDIF-induced AR and LR formation. In PtTDIFsOE roots, several auxin-related LR initiation markers such as GATA23, LBD16 and LBD29 were transcriptionally upregulated, further supporting that TDIF regulates LR organogenesis by strengthening the spatiotemporal auxin cues and that dynamic interplays between hormones govern root branching and developmental plasticity in tree species.
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Affiliation(s)
- Jing Yue
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300072, China
| | - Heyu Yang
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300072, China
| | - Shaohui Yang
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300072, China
| | - Jiehua Wang
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300072, China
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Lay-Pruitt KS, Takahashi H. Integrating N signals and root growth: the role of nitrate transceptor NRT1.1 in auxin-mediated lateral root development. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:4365-4368. [PMID: 32710785 PMCID: PMC7382374 DOI: 10.1093/jxb/eraa243] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
This article comments on: Maghiaoui A, Bouguyon E, Cuesta C, Perrine-Walker F, Alcon C, Krouk G, Benková E, Nacry P, Gojon A and Bach L. 2020. The Arabidopsis NRT1.1 transceptor coordinately controls auxin biosynthesis and transport to regulate root branching in response to nitrate. Journal of Experimental Botany 71, 4480–4494.
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Affiliation(s)
- Katerina S Lay-Pruitt
- Genetics and Genome Sciences Program, Michigan State University, East Lansing, MI, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Hideki Takahashi
- Genetics and Genome Sciences Program, Michigan State University, East Lansing, MI, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
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24
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Maghiaoui A, Bouguyon E, Cuesta C, Perrine-Walker F, Alcon C, Krouk G, Benková E, Nacry P, Gojon A, Bach L. The Arabidopsis NRT1.1 transceptor coordinately controls auxin biosynthesis and transport to regulate root branching in response to nitrate. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:4480-4494. [PMID: 32428238 DOI: 10.1093/jxb/eraa242] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Accepted: 05/13/2020] [Indexed: 05/21/2023]
Abstract
In agricultural systems, nitrate is the main source of nitrogen available for plants. Besides its role as a nutrient, nitrate has been shown to act as a signal molecule in plant growth, development, and stress responses. In Arabidopsis, the NRT1.1 nitrate transceptor represses lateral root (LR) development at low nitrate availability by promoting auxin basipetal transport out of the LR primordia (LRPs). Here we show that NRT1.1 acts as a negative regulator of the TAR2 auxin biosynthetic gene in the root stele. This is expected to repress local auxin biosynthesis and thus to reduce acropetal auxin supply to the LRPs. Moreover, NRT1.1 also negatively affects expression of the LAX3 auxin influx carrier, thus preventing the cell wall remodeling required for overlying tissue separation during LRP emergence. NRT1.1-mediated repression of both TAR2 and LAX3 is suppressed at high nitrate availability, resulting in nitrate induction of the TAR2 and LAX3 expression that is required for optimal stimulation of LR development by nitrate. Altogether, our results indicate that the NRT1.1 transceptor coordinately controls several crucial auxin-associated processes required for LRP development, and as a consequence that NRT1.1 plays a much more integrated role than previously expected in regulating the nitrate response of root system architecture.
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Affiliation(s)
- Amel Maghiaoui
- BPMP, Univ Montpellier, CNRS, INRAE, Institut Agro, Montpellier, France
| | - Eléonore Bouguyon
- BPMP, Univ Montpellier, CNRS, INRAE, Institut Agro, Montpellier, France
| | - Candela Cuesta
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | | | - Carine Alcon
- BPMP, Univ Montpellier, CNRS, INRAE, Institut Agro, Montpellier, France
| | - Gabriel Krouk
- BPMP, Univ Montpellier, CNRS, INRAE, Institut Agro, Montpellier, France
| | - Eva Benková
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Philippe Nacry
- BPMP, Univ Montpellier, CNRS, INRAE, Institut Agro, Montpellier, France
| | - Alain Gojon
- BPMP, Univ Montpellier, CNRS, INRAE, Institut Agro, Montpellier, France
| | - Liên Bach
- BPMP, Univ Montpellier, CNRS, INRAE, Institut Agro, Montpellier, France
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25
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Chapman K, Ivanovici A, Taleski M, Sturrock CJ, Ng JLP, Mohd-Radzman NA, Frugier F, Bennett MJ, Mathesius U, Djordjevic MA. CEP receptor signalling controls root system architecture in Arabidopsis and Medicago. THE NEW PHYTOLOGIST 2020; 226:1809-1821. [PMID: 32048296 DOI: 10.1111/nph.16483] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 02/04/2020] [Indexed: 06/10/2023]
Abstract
Root system architecture (RSA) influences the effectiveness of resources acquisition from soils but the genetic networks that control RSA remain largely unclear. We used rhizoboxes, X-ray computed tomography, grafting, auxin transport measurements and hormone quantification to demonstrate that Arabidopsis and Medicago CEP (C-TERMINALLY ENCODED PEPTIDE)-CEP RECEPTOR signalling controls RSA, the gravitropic set-point angle (GSA) of lateral roots (LRs), auxin levels and auxin transport. We showed that soil-grown Arabidopsis and Medicago CEP receptor mutants have a narrower RSA, which results from a steeper LR GSA. Grafting showed that CEPR1 in the shoot controls GSA. CEP receptor mutants exhibited an increase in rootward auxin transport and elevated shoot auxin levels. Consistently, the application of auxin to wild-type shoots induced a steeper GSA and auxin transport inhibitors counteracted the CEP receptor mutant's steep GSA phenotype. Concordantly, CEP peptides increased GSA and inhibited rootward auxin transport in wild-type but not in CEP receptor mutants. The results indicated that CEP-CEP receptor-dependent signalling outputs in Arabidopsis and Medicago control overall RSA, LR GSA, shoot auxin levels and rootward auxin transport. We propose that manipulating CEP signalling strength or CEP receptor downstream targets may provide means to alter RSA.
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Affiliation(s)
- Kelly Chapman
- Division of Plant Sciences, Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Ariel Ivanovici
- Division of Plant Sciences, Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Michael Taleski
- Division of Plant Sciences, Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Craig J Sturrock
- The Hounsfield Facility, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK
| | - Jason L P Ng
- Division of Plant Sciences, Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Nadiatul A Mohd-Radzman
- Division of Plant Sciences, Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Florian Frugier
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, Université, Paris Sud, Université, Paris Diderot, INRA, Univ d'Evry, Université Paris-Saclay, 91190, Gif-sur-Yvette, France
| | - Malcolm J Bennett
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK
| | - Ulrike Mathesius
- Division of Plant Sciences, Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Michael A Djordjevic
- Division of Plant Sciences, Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
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Dai X, Liu N, Wang L, Li J, Zheng X, Xiang F, Liu Z. MYB94 and MYB96 additively inhibit callus formation via directly repressing LBD29 expression in Arabidopsis thaliana. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 293:110323. [PMID: 32081254 DOI: 10.1016/j.plantsci.2019.110323] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 10/01/2019] [Accepted: 10/23/2019] [Indexed: 06/10/2023]
Abstract
Plant somatic cells can be reprogrammed during in vitro culture. Callus induction is the initial step of a typical plant regeneration system. Recent studies showed that auxin-induced callus formation in multiple organs occurs from the pericycle or pericycle-like cells via a root developmental pathway. However, the molecular control of callus formation is largely unknown. Here, two MYB transcription factors, MYB94 and MYB96, were shown to play negative roles in auxin-induced callus formation in Arabidopsis. MYB94 and MYB96 were expressed in the newly formed callus. myb96, myb94, and myb94 myb96 generated more calli than the WT, with myb94 myb96 producing the most. MYB94 and MYB96 repressed expression of LATERAL ORGAN BOUNDARIES-DOMAIN 29 (LBD29) via directly binding to the gene's promoter. The loss of function of LBD29 partly rescued the callus formation defect of myb94 myb96. Our findings found MYB94 and MYB96 to be important repressors of callus formation and MYB94/96-LBD29 as a new regulatory pathway acting in parallel with ARF7/19-LBDs' pathway to modulate in vitro callus formation.
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Affiliation(s)
- Xuehuan Dai
- The Key Laboratory of the Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, Shandong, China
| | - Na Liu
- The Key Laboratory of the Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, Shandong, China
| | - Lijuan Wang
- The Key Laboratory of the Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, Shandong, China
| | - Juan Li
- The Key Laboratory of the Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, Shandong, China
| | - Xiaojian Zheng
- The Key Laboratory of the Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, Shandong, China
| | - Fengning Xiang
- The Key Laboratory of the Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, Shandong, China.
| | - Zhenhua Liu
- The Key Laboratory of the Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, Shandong, China.
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Zhang Y, Li Z, Ma B, Hou Q, Wan X. Phylogeny and Functions of LOB Domain Proteins in Plants. Int J Mol Sci 2020; 21:ijms21072278. [PMID: 32224847 PMCID: PMC7178066 DOI: 10.3390/ijms21072278] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 03/22/2020] [Accepted: 03/23/2020] [Indexed: 02/07/2023] Open
Abstract
Lateral organ boundaries (LOB) domain (LBD) genes, a gene family encoding plant-specific transcription factors, play important roles in plant growth and development. At present, though there have been a number of genome-wide analyses on LBD gene families and functional studies on individual LBD proteins, the diverse functions of LBD family members still confuse researchers and an effective strategy is required to summarize their functional diversity. To further integrate and improve our understanding of the phylogenetic classification, functional characteristics and regulatory mechanisms of LBD proteins, we review and discuss the functional characteristics of LBD proteins according to their classifications under a phylogenetic framework. It is proved that this strategy is effective in the anatomy of diverse functions of LBD family members. Additionally, by phylogenetic analysis, one monocot-specific and one eudicot-specific subclade of LBD proteins were found and their biological significance in monocot and eudicot development were also discussed separately. The review will help us better understand the functional diversity of LBD proteins and facilitate further studies on this plant-specific transcription factor family.
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Affiliation(s)
- Yuwen Zhang
- Zhongzhi International Institute of Agricultural Biosciences, Biology and Agriculture Research Center, University of Science and Technology Beijing, Beijing 100024, China; (Y.Z.); (Z.L.); (B.M.); (Q.H.)
- Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Beijing Solidwill Sci-Tech Co., Ltd., Beijing 100192, China
| | - Ziwen Li
- Zhongzhi International Institute of Agricultural Biosciences, Biology and Agriculture Research Center, University of Science and Technology Beijing, Beijing 100024, China; (Y.Z.); (Z.L.); (B.M.); (Q.H.)
- Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Beijing Solidwill Sci-Tech Co., Ltd., Beijing 100192, China
| | - Biao Ma
- Zhongzhi International Institute of Agricultural Biosciences, Biology and Agriculture Research Center, University of Science and Technology Beijing, Beijing 100024, China; (Y.Z.); (Z.L.); (B.M.); (Q.H.)
- Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Beijing Solidwill Sci-Tech Co., Ltd., Beijing 100192, China
| | - Quancan Hou
- Zhongzhi International Institute of Agricultural Biosciences, Biology and Agriculture Research Center, University of Science and Technology Beijing, Beijing 100024, China; (Y.Z.); (Z.L.); (B.M.); (Q.H.)
- Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Beijing Solidwill Sci-Tech Co., Ltd., Beijing 100192, China
| | - Xiangyuan Wan
- Zhongzhi International Institute of Agricultural Biosciences, Biology and Agriculture Research Center, University of Science and Technology Beijing, Beijing 100024, China; (Y.Z.); (Z.L.); (B.M.); (Q.H.)
- Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Beijing Solidwill Sci-Tech Co., Ltd., Beijing 100192, China
- Correspondence: or ; Tel.: +86-10-6299-5866
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28
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Zhang F, Tao W, Sun R, Wang J, Li C, Kong X, Tian H, Ding Z. PRH1 mediates ARF7-LBD dependent auxin signaling to regulate lateral root development in Arabidopsis thaliana. PLoS Genet 2020; 16:e1008044. [PMID: 32032352 PMCID: PMC7006904 DOI: 10.1371/journal.pgen.1008044] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 12/22/2019] [Indexed: 11/19/2022] Open
Abstract
The development of lateral roots in Arabidopsis thaliana is strongly dependent on signaling directed by the AUXIN RESPONSE FACTOR7 (ARF7), which in turn activates LATERAL ORGAN BOUNDARIES DOMAIN (LBD) transcription factors (LBD16, LBD18 and LBD29). Here, the product of PRH1, a PR-1 homolog annotated previously as encoding a pathogen-responsive protein, was identified as a target of ARF7-mediated auxin signaling and also as participating in the development of lateral roots. PRH1 was shown to be strongly induced by auxin treatment, and plants lacking a functional copy of PRH1 formed fewer lateral roots. The transcription of PRH1 was controlled by the binding of both ARF7 and LBDs to its promoter region. In Arabidopsis thaliana AUXIN RESPONSE FACTOR7 (ARF7)-mediated auxin signaling plays a key role in lateral roots (LRs) development. The LATERAL ORGAN BOUNDARIES DOMAIN (LBD) transcription factors (LBD16, LBD18 and LBD29) act downstream of ARF7-mediated auxin signaling to control LRs formation. Here, the PR-1 homolog PRH1 was identified as a novel target of both ARF7 and LBDs (especially the LBD29) during auxin induced LRs formation, as both ARF7 and LBDs were able to bind to the PRH1 promoter. This study provides new insights about how auxin regulates lateral root development.
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Affiliation(s)
- Feng Zhang
- The Key Laboratory of the Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, Shandong, China
| | - Wenqing Tao
- The Key Laboratory of the Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, Shandong, China
| | - Ruiqi Sun
- The Key Laboratory of the Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, Shandong, China
| | - Junxia Wang
- The Key Laboratory of the Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, Shandong, China
| | - Cuiling Li
- The Key Laboratory of the Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, Shandong, China
| | - Xiangpei Kong
- The Key Laboratory of the Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, Shandong, China
| | - Huiyu Tian
- The Key Laboratory of the Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, Shandong, China
| | - Zhaojun Ding
- The Key Laboratory of the Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, Shandong, China
- * E-mail:
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29
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Pegg T, Edelmann RR, Gladish DK. Immunoprofiling of Cell Wall Carbohydrate Modifications During Flooding-Induced Aerenchyma Formation in Fabaceae Roots. FRONTIERS IN PLANT SCIENCE 2020; 10:1805. [PMID: 32117353 PMCID: PMC7008352 DOI: 10.3389/fpls.2019.01805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 12/24/2019] [Indexed: 05/12/2023]
Abstract
Understanding plant adaptation mechanisms to prolonged water immersion provides options for genetic modification of existing crops to create cultivars more tolerant of periodic flooding. An important advancement in understanding flooding adaptation would be to elucidate mechanisms, such as aerenchyma air-space formation induced by hypoxic conditions, consistent with prolonged immersion. Lysigenous aerenchyma formation occurs through programmed cell death (PCD), which may entail the chemical modification of polysaccharides in root tissue cell walls. We investigated if a relationship exists between modification of pectic polysaccharides through de-methyl esterification (DME) and the formation of root aerenchyma in select Fabaceae species. To test this hypothesis, we first characterized the progression of aerenchyma formation within the vascular stele of three different legumes-Pisum sativum, Cicer arietinum, and Phaseolus coccineus-through traditional light microscopy histological staining and scanning electron microscopy. We assessed alterations in stele morphology, cavity dimensions, and cell wall chemistry. Then we conducted an immunolabeling protocol to detect specific degrees of DME among species during a 48-hour flooding time series. Additionally, we performed an enzymatic pretreatment to remove select cell wall polymers prior to immunolabeling for DME pectins. We were able to determine that all species possessed similar aerenchyma formation mechanisms that begin with degradation of root vascular stele metaxylem cells. Immunolabeling results demonstrated DME occurs prior to aerenchyma formation and prepares vascular tissues for the beginning of cavity formation in flooded roots. Furthermore, enzymatic pretreatment demonstrated that removal of cellulose and select hemicellulosic carbohydrates unmasks additional antigen binding sites for DME pectin antibodies. These results suggest that additional carbohydrate modification may be required to permit DME and subsequent enzyme activity to form aerenchyma. By providing a greater understanding of cell wall pectin remodeling among legume species, we encourage further investigation into the mechanism of carbohydrate modifications during aerenchyma formation and possible avenues for flood-tolerance improvement of legume crops.
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Affiliation(s)
- Timothy Pegg
- Department of Biology, Miami University, Oxford, OH, United States
| | - Richard R. Edelmann
- Department of Biology, Miami University, Oxford, OH, United States
- Center for Advance Microscopy & Imaging, Miami University, Oxford, OH, United States
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30
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Ye H, Ren F, Guo H, Guo L, Bai J, Wang Y. Identification of key genes and transcription factors in ageing Arabidopsis papilla cells by transcriptome analysis. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 147:1-9. [PMID: 31837555 DOI: 10.1016/j.plaphy.2019.12.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 12/04/2019] [Accepted: 12/06/2019] [Indexed: 06/10/2023]
Abstract
Programmed cell death (PCD) play essential roles in plant growth and development. Stigmatic papilla cells form an indispensable organ for plant reproduction. The lifetime of papilla cells is tightly controlled, and the developmental PCD (dPCD) process is involved in papilla cell death. Hence, papilla cell death is a good model for studying on PCD process. In this study, the dPCD signal was visualized in dying papilla cells by detecting the GUS signal of the PCD-related reporter gene BIFUNCTIONAL NUCLEASE 1 (BFN1). We found that the GUS was not expressed at young stage, but strongly expressed in papilla cells at the ageing stage, indicating the PCD process was triggered to terminate the papilla cell fate. Given this, the RNA-Seq data set, which covered the information of the whole lifespan of papilla cells, was analyzed aiming to understand which genes and pathways were involved in papilla cell death. 37 differential expressed genes (DEGs) were isolated. Moreover, the pathways related to energy production and transportation, autophagy, and plant hormone signal transduction were considered as the key pathways involved in the papilla cell death. 9 types, total of 104 transcriptional factors (TFs) were identified as well. Finally, a putative working model of papilla cell death was integrated. The findings herein will enrich the knowledge of the dPCD-mediated pathway in regulating plant organ/tissue growth, development, senescence, and death. Our study will provide some referential gene resources for studying on the dPCD in other plant organs or tissues.
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Affiliation(s)
- Hong Ye
- Division of Biological Science, Nara Institute of Science and Technology, Ikoma, 6300192, Japan
| | - Fei Ren
- School of Agricultural Science and Engineering, Shaoguan University, 288 Daxue Road, Zhenjiang District, Shaoguan, 512000, PR China
| | - Haoyu Guo
- College of Life Science, Capital Normal University, Beijing, 100048, PR China
| | - Liping Guo
- School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, PR China
| | - Jianfang Bai
- Beijing Engineering Research Center for Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, PR China.
| | - Yukun Wang
- Division of Biological Science, Nara Institute of Science and Technology, Ikoma, 6300192, Japan.
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31
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Lee H, Ganguly A, Lee RD, Park M, Cho HT. Intracellularly Localized PIN-FORMED8 Promotes Lateral Root Emergence in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2020; 10:1808. [PMID: 32082353 PMCID: PMC7005106 DOI: 10.3389/fpls.2019.01808] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Accepted: 12/24/2019] [Indexed: 05/28/2023]
Abstract
PIN-FORMED (PIN) auxin efflux carriers with a long central hydrophilic loop (long PINs) have been implicated in organogenesis. However, the role of short hydrophilic loop PINs (short PINs) in organogenesis is largely unknown. In this study, we investigated the role of a short PIN, PIN8, in lateral root (LR) development in Arabidopsis thaliana. The loss-of-function mutation in PIN8 significantly decreased LR density, mostly by affecting the emergence stage. PIN8 showed a sporadic expression pattern along the root vascular cells in the phloem, where the PIN8 protein predominantly localized to intracellular compartments. During LR primordium development, PIN8 was expressed at the late stage. Plasma membrane (PM)-localized long PINs suppressed LR formation when expressed in the PIN8 domain. Conversely, an auxin influx carrier, AUX1, restored the wild-type (WT) LR density when expressed in the PIN8 domain of the pin8 mutant root. Moreover, LR emergence was considerably inhibited when AXR2-1, the dominant negative form of Aux/IAA7, compromised auxin signaling in the PIN8 domain. Consistent with these observations, the expression of many genes implicated in late LR development was suppressed in the pin8 mutant compared with the WT. Our results suggest that the intracellularly localized PIN8 affects LR development most likely by modulating intracellular auxin translocation. Thus, the function of PIN8 is distinctive from that of PM-localized long PINs, where they generate local auxin gradients for organogenesis by conducting cell-to-cell auxin reflux.
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32
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Escamez S, André D, Sztojka B, Bollhöner B, Hall H, Berthet B, Voß U, Lers A, Maizel A, Andersson M, Bennett M, Tuominen H. Cell Death in Cells Overlying Lateral Root Primordia Facilitates Organ Growth in Arabidopsis. Curr Biol 2020; 30:455-464.e7. [PMID: 31956028 DOI: 10.1016/j.cub.2019.11.078] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 11/22/2019] [Accepted: 11/26/2019] [Indexed: 02/06/2023]
Abstract
Plant organ growth is widely accepted to be determined by cell division and cell expansion, but, unlike that in animals, the contribution of cell elimination has rarely been recognized. We investigated this paradigm during Arabidopsis lateral root formation, when the lateral root primordia (LRP) must traverse three overlying cell layers within the parent root. A subset of LRP-overlying cells displayed the induction of marker genes for cell types undergoing developmental cell death, and their cell death was detected by electron, confocal, and light sheet microscopy techniques. LRP growth was delayed in cell-death-deficient mutants lacking the positive cell death regulator ORESARA1/ANAC092 (ORE1). LRP growth was restored in ore1-2 knockout plants by genetically inducing cell elimination in cells overlying the LRP or by physically killing LRP-overlying cells by ablation with optical tweezers. Our results support that, in addition to previously discovered mechanisms, cell elimination contributes to regulating lateral root emergence.
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Affiliation(s)
- Sacha Escamez
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 901 87 Umeå, Sweden
| | - Domenique André
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 901 87 Umeå, Sweden
| | - Bernadette Sztojka
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 901 87 Umeå, Sweden
| | - Benjamin Bollhöner
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 901 87 Umeå, Sweden
| | - Hardy Hall
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 901 87 Umeå, Sweden
| | - Béatrice Berthet
- Center for Organismal Studies (COS), University of Heidelberg, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany
| | - Ute Voß
- Centre for Plant Integrative Biology, University of Nottingham, Nottingham LE12 SRD, UK
| | - Amnon Lers
- Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, Volcani Center, Rishon LeZion, 7528809, Israel
| | - Alexis Maizel
- Center for Organismal Studies (COS), University of Heidelberg, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany
| | | | - Malcolm Bennett
- Centre for Plant Integrative Biology, University of Nottingham, Nottingham LE12 SRD, UK
| | - Hannele Tuominen
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 901 87 Umeå, Sweden.
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33
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Yuan TT, Xu HH, Li J, Lu YT. Auxin abolishes SHI-RELATED SEQUENCE5-mediated inhibition of lateral root development in Arabidopsis. THE NEW PHYTOLOGIST 2020; 225:297-309. [PMID: 31403703 DOI: 10.1111/nph.16115] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 08/03/2019] [Indexed: 06/10/2023]
Abstract
Lateral roots (LRs), which form in the plant postembryonically, determine the architecture of the root system. While negative regulatory factors that inhibit LR formation and are counteracted by auxin exist in the pericycle, these factors have not been characterised. Here, we report that SHI-RELATED SEQUENCE5 (SRS5) is an intrinsic negative regulator of LR formation and that auxin signalling abolishes this inhibitory effect of SRS5. Whereas LR primordia (LRPs) and LRs were fewer and less dense in SRS5ox and Pro35S:SRS5-GFP plants than in the wild-type, they were more abundant and denser in the srs5-2 loss-of-function mutant. SRS5 inhibited LR formation by directly downregulating the expression of LATERAL ORGAN BOUNDARIES-DOMAIN 16 (LBD16) and LBD29. Auxin repressed SRS5 expression. Auxin-mediated repression of SRS5 expression was not observed in the arf7-1 arf19-1 double mutant, likely because ARF7 and ARF19 bind to the promoter of SRS5 and inhibit its expression in response to auxin. Taken together, our data reveal that SRS5 negatively regulates LR formation by repressing the expression of LBD16 and LBD29 and that auxin releases this inhibitory effect through ARF7 and ARF19.
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Affiliation(s)
- Ting-Ting Yuan
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Heng-Hao Xu
- Laboratory of Marine Pharmaceutical Compound Screening, Co-Innovation Center of Jiangsu Marine Bio-Industry Technology, Huaihai Institute of Technology, Lianyungang, 222005, China
| | - Juan Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Ying-Tang Lu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
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Singh S, Yadav S, Singh A, Mahima M, Singh A, Gautam V, Sarkar AK. Auxin signaling modulates LATERAL ROOT PRIMORDIUM1 (LRP1) expression during lateral root development in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 101:87-100. [PMID: 31483536 DOI: 10.1111/tpj.14520] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 08/17/2019] [Accepted: 08/21/2019] [Indexed: 05/18/2023]
Abstract
Auxin signaling mediated by various auxin/indole-3-acetic acid (Aux/IAAs) and AUXIN RESPONSE FACTORs (ARFs) regulate lateral root (LR) development by controlling the expression of downstream genes. LATERAL ROOT PRIMORDIUM1 (LRP1), a member of the SHORT INTERNODES/STYLISH (SHI/STY) family, was identified as an auxin-inducible gene. The precise developmental role and molecular regulation of LRP1 in root development remain to be understood. Here we show that LRP1 is expressed in all stages of LR development, besides the primary root. The expression of LRP1 is regulated by histone deacetylation in an auxin-dependent manner. Our genetic interaction studies showed that LRP1 acts downstream of auxin responsive Aux/IAAs-ARFs modules during LR development. We showed that auxin-mediated induction of LRP1 is lost in emerging LRs of slr-1 and arf7arf19 mutants roots. NPA treatment studies showed that LRP1 acts after LR founder cell specification and asymmetric division during LR development. Overexpression of LRP1 (LRP1 OE) showed an increased number of LR primordia (LRP) at stages I, IV and V, resulting in reduced emerged LR density, which suggests that it is involved in LRP development. Interestingly, LRP1-induced expression of YUC4, which is involved in auxin biosynthesis, contributes to the increased accumulation of endogenous auxin in LRP1 OE roots. LRP1 interacts with SHI, STY1, SRS3, SRS6 and SRS7 proteins of the SHI/STY family, indicating their possible redundant role during root development. Our results suggested that auxin and histone deacetylation affect LRP1 expression and it acts downstream of LR forming auxin response modules to negatively regulate LRP development by modulating auxin homeostasis in Arabidopsis thaliana.
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Affiliation(s)
- Sharmila Singh
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Sandeep Yadav
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Alka Singh
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Mahima Mahima
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Archita Singh
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Vibhav Gautam
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
- Centre of Experimental Medicine and Surgery, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Ananda K Sarkar
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
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Li R, Jiang H, Zhang Z, Zhao Y, Xie J, Wang Q, Zheng H, Hou L, Xiong X, Xin D, Hu Z, Liu C, Wu X, Chen Q. Combined Linkage Mapping and BSA to Identify QTL and Candidate Genes for Plant Height and the Number of Nodes on the Main Stem in Soybean. Int J Mol Sci 2019; 21:E42. [PMID: 31861685 PMCID: PMC6981803 DOI: 10.3390/ijms21010042] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 12/12/2019] [Accepted: 12/17/2019] [Indexed: 11/16/2022] Open
Abstract
Soybean is one of the most important food and oil crops in the world. Plant height (PH) and the number of nodes on the main stem (NNMS) are quantitative traits closely related to soybean yield. In this study, we used 208 chromosome segment substitution lines (CSSL) populations constructed using "SN14" and "ZYD00006" for quantitative trait locus (QTL) mapping of PH and NNMS. Combined with bulked segregant analysis (BSA) by extreme materials, 8 consistent QTLs were identified. According to the gene annotation of the QTL interval, a total of 335 genes were obtained. Five of which were associated with PH and NNMS, potentially representing candidate genes. RT-qPCR of these 5 candidate genes revealed two genes with differential relative expression levels in the stems of different materials. Haplotype analysis showed that different single nucleotide polymorphisms (SNPs) between the excellent haplotypes in Glyma.04G251900 and Glyma.16G156700 may be the cause of changes in these traits. These results provide the basis for research on candidate genes and marker-assisted selection (MAS) in soybean breeding.
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Affiliation(s)
- Ruichao Li
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (R.L.); (Z.Z.); (Y.Z.); (J.X.); (Q.W.); (H.Z.); (L.H.); (X.X.); (D.X.); (Z.H.); (C.L.)
| | - Hongwei Jiang
- Jilin Academy of Agricultural Sciences, Soybean Research Institute, Changchun 130033, China;
| | - Zhanguo Zhang
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (R.L.); (Z.Z.); (Y.Z.); (J.X.); (Q.W.); (H.Z.); (L.H.); (X.X.); (D.X.); (Z.H.); (C.L.)
| | - Yuanyuan Zhao
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (R.L.); (Z.Z.); (Y.Z.); (J.X.); (Q.W.); (H.Z.); (L.H.); (X.X.); (D.X.); (Z.H.); (C.L.)
| | - Jianguo Xie
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (R.L.); (Z.Z.); (Y.Z.); (J.X.); (Q.W.); (H.Z.); (L.H.); (X.X.); (D.X.); (Z.H.); (C.L.)
| | - Qiao Wang
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (R.L.); (Z.Z.); (Y.Z.); (J.X.); (Q.W.); (H.Z.); (L.H.); (X.X.); (D.X.); (Z.H.); (C.L.)
| | - Haiyang Zheng
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (R.L.); (Z.Z.); (Y.Z.); (J.X.); (Q.W.); (H.Z.); (L.H.); (X.X.); (D.X.); (Z.H.); (C.L.)
| | - Lilong Hou
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (R.L.); (Z.Z.); (Y.Z.); (J.X.); (Q.W.); (H.Z.); (L.H.); (X.X.); (D.X.); (Z.H.); (C.L.)
| | - Xin Xiong
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (R.L.); (Z.Z.); (Y.Z.); (J.X.); (Q.W.); (H.Z.); (L.H.); (X.X.); (D.X.); (Z.H.); (C.L.)
| | - Dawei Xin
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (R.L.); (Z.Z.); (Y.Z.); (J.X.); (Q.W.); (H.Z.); (L.H.); (X.X.); (D.X.); (Z.H.); (C.L.)
| | - Zhenbang Hu
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (R.L.); (Z.Z.); (Y.Z.); (J.X.); (Q.W.); (H.Z.); (L.H.); (X.X.); (D.X.); (Z.H.); (C.L.)
| | - Chunyan Liu
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (R.L.); (Z.Z.); (Y.Z.); (J.X.); (Q.W.); (H.Z.); (L.H.); (X.X.); (D.X.); (Z.H.); (C.L.)
| | - Xiaoxia Wu
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (R.L.); (Z.Z.); (Y.Z.); (J.X.); (Q.W.); (H.Z.); (L.H.); (X.X.); (D.X.); (Z.H.); (C.L.)
| | - Qingshan Chen
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (R.L.); (Z.Z.); (Y.Z.); (J.X.); (Q.W.); (H.Z.); (L.H.); (X.X.); (D.X.); (Z.H.); (C.L.)
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Perotti MF, Ribone PA, Cabello JV, Ariel FD, Chan RL. AtHB23 participates in the gene regulatory network controlling root branching, and reveals differences between secondary and tertiary roots. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 100:1224-1236. [PMID: 31444832 DOI: 10.1111/tpj.14511] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 08/02/2019] [Accepted: 08/19/2019] [Indexed: 06/10/2023]
Abstract
In Arabidopsis, lateral root (LR) development is mainly controlled by several known auxin-regulated transcription factors (TFs). Here, we show that AtHB23 (a homeodomain-leucine zipper I TF) participates in this intricate network. Our study of the expression pattern of AtHB23 revealed that it is transcriptionally activated in the early stages of secondary LR primordium (LRP). We found that AtHB23 directly limits the expression of LBD16, a key factor in LR initiation, and also directly induces the auxin transporter gene LAX3. We propose that this HD-Zip I mediates the regulation of LAX3 by ARF7/19. Furthermore, AtHB23 plays distinct roles during the formation of secondary and tertiary roots, exhibiting differential expression patterns. ATHB23 is expressed throughout the tertiary root primordium, whereas it is restricted to early stages in secondary primordia, likely later repressing LBD16 in tertiary LR development and further inhibiting root emergence. Our results suggest that different genetic programs govern the formation of LRP from the main or secondary roots, thereby shaping the global dynamic architecture of the root system.
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Affiliation(s)
- María F Perotti
- Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, CONICET, FBCB, Centro Científico Tecnológico CONICET Santa Fe, Colectora Ruta Nacional No 168 km. 0, Paraje El Pozo, 3000, Santa Fe, Argentina
| | - Pamela A Ribone
- Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, CONICET, FBCB, Centro Científico Tecnológico CONICET Santa Fe, Colectora Ruta Nacional No 168 km. 0, Paraje El Pozo, 3000, Santa Fe, Argentina
| | - Julieta V Cabello
- Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, CONICET, FBCB, Centro Científico Tecnológico CONICET Santa Fe, Colectora Ruta Nacional No 168 km. 0, Paraje El Pozo, 3000, Santa Fe, Argentina
| | - Federico D Ariel
- Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, CONICET, FBCB, Centro Científico Tecnológico CONICET Santa Fe, Colectora Ruta Nacional No 168 km. 0, Paraje El Pozo, 3000, Santa Fe, Argentina
| | - Raquel L Chan
- Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, CONICET, FBCB, Centro Científico Tecnológico CONICET Santa Fe, Colectora Ruta Nacional No 168 km. 0, Paraje El Pozo, 3000, Santa Fe, Argentina
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Müller K, Hošek P, Laňková M, Vosolsobě S, Malínská K, Čarná M, Fílová M, Dobrev PI, Helusová M, Hoyerová K, Petrášek J. Transcription of specific auxin efflux and influx carriers drives auxin homeostasis in tobacco cells. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 100:627-640. [PMID: 31349380 DOI: 10.1111/tpj.14474] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 07/08/2019] [Accepted: 07/12/2019] [Indexed: 06/10/2023]
Abstract
Auxin concentration gradients are informative for the transduction of many developmental cues, triggering downstream gene expression and other responses. The generation of auxin gradients depends significantly on cell-to-cell auxin transport, which is supported by the activities of auxin efflux and influx carriers. However, at the level of individual plant cell, the co-ordination of auxin efflux and influx largely remains uncharacterized. We addressed this issue by analyzing the contribution of canonical PIN-FORMED (PIN) proteins to the carrier-mediated auxin efflux in Nicotiana tabacum L., cv. Bright Yellow (BY-2) tobacco cells. We show here that a majority of canonical NtPINs are transcribed in cultured cells and in planta. Cloning of NtPIN genes and their inducible overexpression in tobacco cells uncovered high auxin efflux activity of NtPIN11, accompanied by auxin starvation symptoms. Auxin transport parameters after NtPIN11 overexpression were further assessed using radiolabelled auxin accumulation and mathematical modelling. Unexpectedly, these experiments showed notable stimulation of auxin influx, which was accompanied by enhanced transcript levels of genes for a specific auxin influx carrier and by decreased transcript levels of other genes for auxin efflux carriers. A similar transcriptional response was observed upon removal of auxin from the culture medium, which resulted in decreased auxin efflux. Overall, our results revealed an auxin transport-based homeostatic mechanism for the maintenance of endogenous auxin levels. OPEN RESEARCH BADGES: This article has earned an Open Data Badge for making publicly available the digitally-shareable data necessary to reproduce the reported results. The data is available at http://osf.io/ka97b/.
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Affiliation(s)
- Karel Müller
- The Czech Academy of Sciences, Institute of Experimental Botany, Rozvojová 263, 165 02 Prague 6, Czech Republic
| | - Petr Hošek
- The Czech Academy of Sciences, Institute of Experimental Botany, Rozvojová 263, 165 02 Prague 6, Czech Republic
| | - Martina Laňková
- The Czech Academy of Sciences, Institute of Experimental Botany, Rozvojová 263, 165 02 Prague 6, Czech Republic
| | - Stanislav Vosolsobě
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Viničná 5, 128 44 Prague 2, Czech Republic
| | - Kateřina Malínská
- The Czech Academy of Sciences, Institute of Experimental Botany, Rozvojová 263, 165 02 Prague 6, Czech Republic
| | - Mária Čarná
- The Czech Academy of Sciences, Institute of Experimental Botany, Rozvojová 263, 165 02 Prague 6, Czech Republic
| | - Markéta Fílová
- The Czech Academy of Sciences, Institute of Experimental Botany, Rozvojová 263, 165 02 Prague 6, Czech Republic
| | - Petre I Dobrev
- The Czech Academy of Sciences, Institute of Experimental Botany, Rozvojová 263, 165 02 Prague 6, Czech Republic
| | - Michaela Helusová
- The Czech Academy of Sciences, Institute of Experimental Botany, Rozvojová 263, 165 02 Prague 6, Czech Republic
| | - Klára Hoyerová
- The Czech Academy of Sciences, Institute of Experimental Botany, Rozvojová 263, 165 02 Prague 6, Czech Republic
| | - Jan Petrášek
- The Czech Academy of Sciences, Institute of Experimental Botany, Rozvojová 263, 165 02 Prague 6, Czech Republic
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Viničná 5, 128 44 Prague 2, Czech Republic
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38
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Xu P, Cai W. Nitrate-responsive OBP4-XTH9 regulatory module controls lateral root development in Arabidopsis thaliana. PLoS Genet 2019; 15:e1008465. [PMID: 31626627 PMCID: PMC6821136 DOI: 10.1371/journal.pgen.1008465] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 10/30/2019] [Accepted: 10/07/2019] [Indexed: 11/19/2022] Open
Abstract
Plant root system architecture in response to nitrate availability represents a notable example to study developmental plasticity, but the underlying mechanism remains largely unknown. Xyloglucan endotransglucosylases (XTHs) play a critical role in cell wall biosynthesis. Here we assessed the gene expression of XTH1-11 belonging to group I of XTHs in lateral root (LR) primordia and found that XTH9 was highly expressed. Correspondingly, an xth9 mutant displayed less LR, while overexpressing XTH9 presented more LR, suggesting the potential function of XTH9 in controlling LR development. XTH9 gene mutation obviously alters the properties of the cell wall. Furthermore, nitrogen signals stimulated the expression of XTH9 to promote LRs. Genetic analysis revealed that the function of XTH9 was dependent on auxin-mediated ARF7/19 and downstream AFB3 in response to nitrogen signals. In addition, we identified another transcription factor, OBP4, that was also induced by nitrogen treatment, but the induction was much slower than that of XTH9. In contrast to XTH9, overexpressing OBP4 caused fewer LRs while OBP4 knockdown with OBP4-RNAi or an artificial miRNA silenced amiOBP4 line produced more LR. We further found OBP4 bound to the promoter of XTH9 to suppress XTH9 expression. In agreement with this, both OBP4-RNAi and crossed OBP4-RNAi & 35S::XTH9 lines led to more LR, but OBP4-RNAi & xth9 produced less LR, similar to xth9. Based on these findings we propose a novel mechanism by which OBP4 antagonistically controls XTH9 expression and the OBP4-XTH9 module elaborately sustains LR development in response to nitrate treatment. Nitrate is not only a nutrient, but also a signal that controls downstream signaling genes at the whole-plant level. In plants, changes in root system architecture in response to nitrate availability represent a notable example of developmental plasticity in response to environmental stimuli. However, the molecular mechanisms underlying nitrate-associated modulation are largely unknown. Here, we identified a nitrogen-responsive signaling module that comprises both xyloglucan endotransglucosylase 9 (XTH9) and the Dof transcription factor OBP4 and controls lateral root (LR) development. We used root gravitropic bending assays to observe the gene expression of group 1 xyloglucan endotransglucosylases (XTHs) involved in LR primordia. The results showed that XTH9 expression patterns were changed and that xth9 knockout mutants displayed altered LR growth. XTH9 was expressed in the LRs and in response to nitrate treatment, and the xth9 mutants were defective in nitrate-promoted LR growth. Moreover, XTH9 overexpression increased LR length and increased tolerance to low-nitrate stress. We found that OBP4 could negatively regulate XTH9 and inhibited root growth. OBP4 and XTH9 worked downstream of ARF7/9. We conclude that OBP4 and XTH9 constitute a regulatory module which contributes to LR growth in response to different environmental nitrate concentration signals.
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Affiliation(s)
- Peipei Xu
- Laboratory of Photosynthesis and Environment, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Weiming Cai
- Laboratory of Photosynthesis and Environment, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- * E-mail:
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Goh T, Toyokura K, Yamaguchi N, Okamoto Y, Uehara T, Kaneko S, Takebayashi Y, Kasahara H, Ikeyama Y, Okushima Y, Nakajima K, Mimura T, Tasaka M, Fukaki H. Lateral root initiation requires the sequential induction of transcription factors LBD16 and PUCHI in Arabidopsis thaliana. THE NEW PHYTOLOGIST 2019; 224:749-760. [PMID: 31310684 DOI: 10.1111/nph.16065] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 06/26/2019] [Indexed: 05/11/2023]
Abstract
Lateral root (LR) formation in Arabidopsis thaliana is initiated by asymmetric division of founder cells, followed by coordinated cell proliferation and differentiation for patterning new primordia. The sequential developmental processes of LR formation are triggered by a localized auxin response. LATERAL ORGAN BOUNDARIES-DOMAIN 16 (LBD16), an auxin-inducible transcription factor, is one of the key regulators linking auxin response in LR founder cells to LR initiation. We identified key genes for LR formation that are activated by LBD16 in an auxin-dependent manner. LBD16 targets identified include the transcription factor gene PUCHI, which is required for LR primordium patterning. We demonstrate that LBD16 activity is required for the auxin-inducible expression of PUCHI. We show that PUCHI expression is initiated after the first round of asymmetric cell division of LR founder cells and that premature induction of PUCHI during the preinitiation phase disrupts LR primordium formation. Our results indicate that LR initiation requires the sequential induction of transcription factors LBD16 and PUCHI.
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Affiliation(s)
- Tatsuaki Goh
- Department of Biology, Graduate School of Science, Kobe University, 1-1 Rokkodai, Kobe, 657-8501, Japan
- Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, 630-0192, Japan
| | - Koichi Toyokura
- Department of Biology, Graduate School of Science, Kobe University, 1-1 Rokkodai, Kobe, 657-8501, Japan
- Department of Biological Sciences, Graduate School of Science, Osaka University, 13 Toyonaka, Osaka, 560-0043, Japan
- Faculty of Science and Engineering, Konan University, Kobe, 658-5801, Japan
| | - Nobutoshi Yamaguchi
- Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, 630-0192, Japan
| | - Yoshie Okamoto
- Department of Biology, Graduate School of Science, Kobe University, 1-1 Rokkodai, Kobe, 657-8501, Japan
| | - Takeo Uehara
- Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, 630-0192, Japan
- Graduate School of Science and Technology, Kobe University, 1-1 Rokkodai, Kobe, 657-8501, Japan
| | - Shutaro Kaneko
- Department of Bioregulation and Biointeraction, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai, Fuchu, 183-8509, Japan
| | - Yumiko Takebayashi
- Center for Sustainable Resource Science, Riken, Yokohama, Kanagawa, 230-0045, Japan
| | - Hiroyuki Kasahara
- Center for Sustainable Resource Science, Riken, Yokohama, Kanagawa, 230-0045, Japan
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai, Fuchu, 183-8509, Japan
| | - Yoshifumi Ikeyama
- Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, 630-0192, Japan
| | - Yoko Okushima
- Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, 630-0192, Japan
| | - Keiji Nakajima
- Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, 630-0192, Japan
| | - Tetsuro Mimura
- Department of Biology, Graduate School of Science, Kobe University, 1-1 Rokkodai, Kobe, 657-8501, Japan
| | - Masao Tasaka
- Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, 630-0192, Japan
| | - Hidehiro Fukaki
- Department of Biology, Graduate School of Science, Kobe University, 1-1 Rokkodai, Kobe, 657-8501, Japan
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Denyer T, Ma X, Klesen S, Scacchi E, Nieselt K, Timmermans MCP. Spatiotemporal Developmental Trajectories in the Arabidopsis Root Revealed Using High-Throughput Single-Cell RNA Sequencing. Dev Cell 2019; 48:840-852.e5. [PMID: 30913408 DOI: 10.1016/j.devcel.2019.02.022] [Citation(s) in RCA: 262] [Impact Index Per Article: 52.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 01/30/2019] [Accepted: 02/22/2019] [Indexed: 12/11/2022]
Abstract
High-throughput single-cell RNA sequencing (scRNA-seq) is becoming a cornerstone of developmental research, providing unprecedented power in understanding dynamic processes. Here, we present a high-resolution scRNA-seq expression atlas of the Arabidopsis root composed of thousands of independently profiled cells. This atlas provides detailed spatiotemporal information, identifying defining expression features for all major cell types, including the scarce cells of the quiescent center. These reveal key developmental regulators and downstream genes that translate cell fate into distinctive cell shapes and functions. Developmental trajectories derived from pseudotime analysis depict a finely resolved cascade of cell progressions from the niche through differentiation that are supported by mirroring expression waves of highly interconnected transcription factors. This study demonstrates the power of applying scRNA-seq to plants and provides an unparalleled spatiotemporal perspective of root cell differentiation.
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Affiliation(s)
- Tom Denyer
- Center for Plant Molecular Biology, University of Tübingen, Auf der Morgenstelle 32, Tübingen 72076, Germany
| | - Xiaoli Ma
- Center for Plant Molecular Biology, University of Tübingen, Auf der Morgenstelle 32, Tübingen 72076, Germany
| | - Simon Klesen
- Center for Plant Molecular Biology, University of Tübingen, Auf der Morgenstelle 32, Tübingen 72076, Germany
| | - Emanuele Scacchi
- Center for Plant Molecular Biology, University of Tübingen, Auf der Morgenstelle 32, Tübingen 72076, Germany
| | - Kay Nieselt
- Center for Bioinformatics, University of Tübingen, Sand 14, Tübingen 72076, Germany
| | - Marja C P Timmermans
- Center for Plant Molecular Biology, University of Tübingen, Auf der Morgenstelle 32, Tübingen 72076, Germany.
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41
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Goh T. Long-term live-cell imaging approaches to study lateral root formation in Arabidopsis thaliana. Microscopy (Oxf) 2019; 68:4-12. [PMID: 30476201 DOI: 10.1093/jmicro/dfy135] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 10/23/2018] [Accepted: 10/31/2018] [Indexed: 11/12/2022] Open
Abstract
Lateral roots comprise the majority of the branching root system and are important for acquiring nutrients and water from soil in addition to providing anchorage. Lateral roots develop post-embryonically from existing root parts and originate from a subset of specified pericycle cells (lateral root founder cells) located deep inside roots. Small numbers of these specified pericycle cells undergo several rounds of cell division to create a dome-shaped primordium, which eventually organizes a meristem, an essential region for plant growth with active cell division, and emerges from its parental root as a lateral root. Observing cellular and molecular processes for an extended time at various scales are crucial for understanding biological processes during organogenesis. Lateral root formation is an example of the successful application of live-cell imaging approaches to understand various aspects of developmental events in plants, including cell fate determination, cell proliferation, cell-to-cell interaction and cell wall modification. Here I review the recent progress in understanding the molecular mechanisms of lateral root formation and the contribution of live-cell imaging approaches.
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Affiliation(s)
- Tatsuaki Goh
- Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Japan
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Fromm H. Root Plasticity in the Pursuit of Water. PLANTS (BASEL, SWITZERLAND) 2019; 8:E236. [PMID: 31336579 PMCID: PMC6681320 DOI: 10.3390/plants8070236] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 07/19/2019] [Accepted: 07/19/2019] [Indexed: 01/22/2023]
Abstract
One of the greatest challenges of terrestrial vegetation is to acquire water through soil-grown roots. Owing to the scarcity of high-quality water in the soil and the environment's spatial heterogeneity and temporal variability, ranging from extreme flooding to drought, roots have evolutionarily acquired tremendous plasticity regarding their geometric arrangement of individual roots and their three-dimensional organization within the soil. Water deficiency has also become an increasing threat to agriculture and dryland ecosystems due to climate change. As a result, roots have become important targets for genetic selection and modification in an effort to improve crop resilience under water-limiting conditions. This review addresses root plasticity from different angles: Their structures and geometry in response to the environment, potential genetic control of root traits suitable for water-limiting conditions, and contemporary and future studies of the principles underlying root plasticity post-Darwin's 'root-brain' hypothesis. Our increasing knowledge of different disciplines of plant sciences and agriculture should contribute to a sustainable management of natural and agricultural ecosystems for the future of mankind.
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Affiliation(s)
- Hillel Fromm
- School of Plant Sciences and Food Security, Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel.
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Santos Teixeira JA, Ten Tusscher KH. The Systems Biology of Lateral Root Formation: Connecting the Dots. MOLECULAR PLANT 2019; 12:784-803. [PMID: 30953788 DOI: 10.1016/j.molp.2019.03.015] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 03/20/2019] [Accepted: 03/26/2019] [Indexed: 05/29/2023]
Abstract
The root system is a major determinant of a plant's access to water and nutrients. The architecture of the root system to a large extent depends on the repeated formation of new lateral roots. In this review, we discuss lateral root development from a systems biology perspective. We focus on studies combining experiments with computational modeling that have advanced our understanding of how the auxin-centered regulatory modules involved in different stages of lateral root development exert their specific functions. Moreover, we discuss how these regulatory networks may enable robust transitions from one developmental stage to the next, a subject that thus far has received limited attention. In addition, we analyze how environmental factors impinge on these modules, and the different manners in which these environmental signals are being integrated to enable coordinated developmental decision making. Finally, we provide some suggestions for extending current models of lateral root development to incorporate multiple processes and stages. Only through more comprehensive models we can fully elucidate the cooperative effects of multiple processes on later root formation, and how one stage drives the transition to the next.
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Affiliation(s)
- J A Santos Teixeira
- Computational Developmental Biology Group, Department of Biology, Utrecht University, Utrecht, the Netherlands
| | - K H Ten Tusscher
- Computational Developmental Biology Group, Department of Biology, Utrecht University, Utrecht, the Netherlands.
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Cho C, Jeon E, Pandey SK, Ha SH, Kim J. LBD13 positively regulates lateral root formation in Arabidopsis. PLANTA 2019; 249:1251-1258. [PMID: 30627888 DOI: 10.1007/s00425-018-03087-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 12/29/2018] [Indexed: 05/26/2023]
Abstract
Lateral Organ Boundaries Domain 13 (LBD13), which is expressed in emerged lateral roots and encodes a transcriptional activator, plays an important role in lateral root formation in Arabidopsis. Lateral roots (LRs) are major determinants of root system architecture, contributing to the survival strategies of plants. Members of the LBD gene family encode plant-specific transcription factors that play key roles in plant organ development. Several LBD genes, such as LBD14, 16, 18, 29, and 33, have been shown to play important roles in regulating LR development in Arabidopsis. In the present study, we show that LBD13 is expressed in emerged LRs and LR meristems of elongated LRs and regulates LR formation in Arabidopsis. Transient gene expression assays with Arabidopsis protoplasts showed that LBD13 is localized to the nucleus and harbors transcription-activating potential. Knock-down of LBD13 expression by RNA interference resulted in reduced LR formation, whereas overexpression of LBD13 enhanced LR formation in transgenic Arabidopsis. Analysis of β-glucuronidase (GUS) expression under the control of the LBD13 promoter showed that GUS staining was detected in LRs emerged from the primary root, but not in LR primordia. Moreover, both the distribution of LR primordium number and developmental kinetics of LR primordia were not affected either by knock-down or by overexpression of LBD13. Taken together, these results suggest that LBD13 is a nuclear-localized transcriptional activator and controls LR formation during or after LR emergence.
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Affiliation(s)
- Chuloh Cho
- Department of Bioenergy Science and Technology, Chonnam National University, Gwangju, 500-757, South Korea
| | - Eunkyeong Jeon
- Department of Bioenergy Science and Technology, Chonnam National University, Gwangju, 500-757, South Korea
| | - Shashank K Pandey
- Department of Bioenergy Science and Technology, Chonnam National University, Gwangju, 500-757, South Korea
| | - Se Hoon Ha
- Department of Bioenergy Science and Technology, Chonnam National University, Gwangju, 500-757, South Korea
| | - Jungmook Kim
- Department of Bioenergy Science and Technology, Chonnam National University, Gwangju, 500-757, South Korea.
- Kumho Life Science Laboratory, Chonnam National University, Gwangju, 500-757, South Korea.
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Torres-Martínez HH, Rodríguez-Alonso G, Shishkova S, Dubrovsky JG. Lateral Root Primordium Morphogenesis in Angiosperms. FRONTIERS IN PLANT SCIENCE 2019; 10:206. [PMID: 30941149 PMCID: PMC6433717 DOI: 10.3389/fpls.2019.00206] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 02/07/2019] [Indexed: 05/14/2023]
Abstract
Morphogenetic processes are the basis of new organ formation. Lateral roots (LRs) are the building blocks of the root system. After LR initiation and before LR emergence, a new lateral root primordium (LRP) forms. During this period, the organization and functionality of the prospective LR is defined. Thus, proper LRP morphogenesis is a decisive process during root system formation. Most current studies on LRP morphogenesis have been performed in the model species Arabidopsis thaliana; little is known about this process in other angiosperms. To understand LRP morphogenesis from a wider perspective, we review both contemporary and earlier studies. The latter are largely forgotten, and we attempted to integrate them into present-day research. In particular, we consider in detail the participation of parent root tissue in LRP formation, cell proliferation and timing during LRP morphogenesis, and the hormonal and genetic regulation of LRP morphogenesis. Cell type identity acquisition and new stem cell establishement during LRP morphogenesis are also considered. Within each of these facets, unanswered or poorly understood questions are identified to help define future research in the field. Finally, we discuss emerging research avenues and new technologies that could be used to answer the remaining questions in studies of LRP morphogenesis.
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Affiliation(s)
| | | | | | - Joseph G. Dubrovsky
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
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Lee HW, Cho C, Pandey SK, Park Y, Kim MJ, Kim J. LBD16 and LBD18 acting downstream of ARF7 and ARF19 are involved in adventitious root formation in Arabidopsis. BMC PLANT BIOLOGY 2019; 19:46. [PMID: 30704405 PMCID: PMC6357364 DOI: 10.1186/s12870-019-1659-4] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 01/24/2019] [Indexed: 05/06/2023]
Abstract
BACKGROUND Adventitious root (AR) formation is a complex genetic trait, which is controlled by various endogenous and environmental cues. Auxin is known to play a central role in AR formation; however, the mechanisms underlying this role are not well understood. RESULTS In this study, we showed that a previously identified auxin signaling module, AUXIN RESPONSE FACTOR(ARF)7/ARF19-LATERAL ORGAN BOUNDARIES DOMAIN(LBD)16/LBD18 via AUXIN1(AUX1)/LIKE-AUXIN3 (LAX3) auxin influx carriers, which plays important roles in lateral root formation, is involved in AR formation in Arabidopsis. In aux1, lax3, arf7, arf19, lbd16 and lbd18 single mutants, we observed reduced numbers of ARs than in the wild type. Double and triple mutants exhibited an additional decrease in AR numbers compared with the corresponding single or double mutants, respectively, and the aux1 lax3 lbd16 lbd18 quadruple mutant was devoid of ARs. Expression of LBD16 or LBD18 under their own promoters in lbd16 or lbd18 mutants rescued the reduced number of ARs to wild-type levels. LBD16 or LBD18 fused to a dominant SRDX repressor suppressed promoter activity of the cell cycle gene, Cyclin-Dependent Kinase(CDK)A1;1, to some extent. Expression of LBD16 or LBD18 was significantly reduced in arf7 and arf19 mutants during AR formation in a light-dependent manner, but not in arf6 and arf8. GUS expression analysis of promoter-GUS reporter transgenic lines revealed overlapping expression patterns for LBD16, LBD18, ARF7, ARF19 and LAX3 in AR primordia. CONCLUSION These results suggest that the ARF7/ARF19-LBD16/LBD18 transcriptional module via the AUX1/LAX3 auxin influx carriers plays an important role in AR formation in Arabidopsis.
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Affiliation(s)
- Han Woo Lee
- Department of Bioenergy Science and Technology, Chonnam National University, Yongbongro 77, Buk-gu, Gwangju, 61186 South Korea
| | - Chuloh Cho
- Department of Bioenergy Science and Technology, Chonnam National University, Yongbongro 77, Buk-gu, Gwangju, 61186 South Korea
| | - Shashank K. Pandey
- Department of Bioenergy Science and Technology, Chonnam National University, Yongbongro 77, Buk-gu, Gwangju, 61186 South Korea
| | - Yoona Park
- Department of Bioenergy Science and Technology, Chonnam National University, Yongbongro 77, Buk-gu, Gwangju, 61186 South Korea
| | - Min-Jung Kim
- Department of Bioenergy Science and Technology, Chonnam National University, Yongbongro 77, Buk-gu, Gwangju, 61186 South Korea
| | - Jungmook Kim
- Department of Bioenergy Science and Technology, Chonnam National University, Yongbongro 77, Buk-gu, Gwangju, 61186 South Korea
- Kumho Life Science Laboratory, Chonnam National University, Gwangju, 61186 South Korea
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Jing H, Strader LC. Interplay of Auxin and Cytokinin in Lateral Root Development. Int J Mol Sci 2019; 20:ijms20030486. [PMID: 30678102 PMCID: PMC6387363 DOI: 10.3390/ijms20030486] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 01/16/2019] [Accepted: 01/18/2019] [Indexed: 01/19/2023] Open
Abstract
The spacing and distribution of lateral roots are critical determinants of plant root system architecture. In addition to providing anchorage, lateral roots explore the soil to acquire water and nutrients. Over the past several decades, we have deepened our understanding of the regulatory mechanisms governing lateral root formation and development. In this review, we summarize these recent advances and provide an overview of how auxin and cytokinin coordinate the regulation of lateral root formation and development.
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Affiliation(s)
- Hongwei Jing
- Department of Biology, Washington University, St. Louis, MO 63130, USA.
| | - Lucia C Strader
- Department of Biology, Washington University, St. Louis, MO 63130, USA.
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Swarup R, Bhosale R. Developmental Roles of AUX1/LAX Auxin Influx Carriers in Plants. FRONTIERS IN PLANT SCIENCE 2019; 10:1306. [PMID: 31719828 PMCID: PMC6827439 DOI: 10.3389/fpls.2019.01306] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 09/19/2019] [Indexed: 05/06/2023]
Abstract
Plant hormone auxin regulates several aspects of plant growth and development. Auxin is predominantly synthesized in the shoot apex and developing leaf primordia and from there it is transported to the target tissues e.g. roots. Auxin transport is polar in nature and is carrier-mediated. AUXIN1/LIKE-AUX1 (AUX1/LAX) family members are the major auxin influx carriers whereas PIN-FORMED (PIN) family and some members of the P-GLYCOPROTEIN/ATP-BINDING CASSETTE B4 (PGP/ABCB) family are major auxin efflux carriers. AUX1/LAX auxin influx carriers are multi-membrane spanning transmembrane proteins sharing similarity to amino acid permeases. Mutations in AUX1/LAX genes result in auxin related developmental defects and have been implicated in regulating key plant processes including root and lateral root development, root gravitropism, root hair development, vascular patterning, seed germination, apical hook formation, leaf morphogenesis, phyllotactic patterning, female gametophyte development and embryo development. Recently AUX1 has also been implicated in regulating plant responses to abiotic stresses. This review summarizes our current understanding of the developmental roles of AUX1/LAX gene family and will also briefly discuss the modelling approaches that are providing new insight into the role of auxin transport in plant development.
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Affiliation(s)
- Ranjan Swarup
- Plant and Crop Sciences, School of Biosciences, University of Nottingham, Nottingham, United Kingdom
- Center for Plant Integrative Biology (CPIB), University of Nottingham, Nottingham, United Kingdom
- *Correspondence: Ranjan Swarup,
| | - Rahul Bhosale
- Plant and Crop Sciences, School of Biosciences, University of Nottingham, Nottingham, United Kingdom
- Center for Plant Integrative Biology (CPIB), University of Nottingham, Nottingham, United Kingdom
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Olas JJ, Wahl V. Tissue-specific NIA1 and NIA2 expression in Arabidopsis thaliana. PLANT SIGNALING & BEHAVIOR 2019; 14:1656035. [PMID: 31438763 PMCID: PMC6804707 DOI: 10.1080/15592324.2019.1656035] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Nitrogen (N) is an essential macronutrient for optimal plant growth and ultimately for crop productivity Nitrate serves as the main N source for most plants. Although it seems a well-established fact that nitrate concentration affects flowering, its molecular mode of action in flowering time regulation was poorly understood. We recently found how nitrate, present at the shoot apical meristem (SAM), controls flowering time In this short communication, we present data on the tissue-specific expression patterns of NITRATE REDUCTASE 1 (NIA1) and NIA2 in planta. We show that transcripts of both genes are present throughout the life cycle of Arabidopsis thaliana plants with NIA1 being predominantly active in leaves and NIA2 in meristematic tissues.
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Affiliation(s)
- Justyna J. Olas
- Department of Metabolic Networks, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
- Department of Molecular Biology, University of Potsdam, Institute of Biochemistry and Biology, Potsdam-Golm, Germany
| | - Vanessa Wahl
- Department of Metabolic Networks, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
- CONTACT Vanessa Wahl Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
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Chen X, Zhang M, Wang M, Tan G, Zhang M, Hou YX, Wang B, Li Z. The effects of mepiquat chloride on the lateral root initiation of cotton seedlings are associated with auxin and auxin-conjugate homeostasis. BMC PLANT BIOLOGY 2018; 18:361. [PMID: 30563457 PMCID: PMC6299555 DOI: 10.1186/s12870-018-1599-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 12/10/2018] [Indexed: 05/25/2023]
Abstract
BACKGROUND Mepiquat chloride (MC) is a plant growth regulator widely used in cotton (Gossypium hirsutum L.) production to suppress excessive vegetative growth, increase root growth and avoid yield losses. To increase root growth, cotton seeds were treated with MC to increase the number of lateral root (LRs) and improve drought resistance. An increased indole-3-acetic acid (IAA) pool appeared to correlate with LR growth, and the principal source of IAA in germinating seeds is IAA conjugates. Here, the role of IAA homeostasis and signaling was investigated in cotton seedlings treated with MC. RESULTS In the present research, MC significantly increased endogenous IAA levels in the roots, which promoted lateral root initiation (LRI) by upregulating GhARF7/19 and GhLBD18s and subsequently increasing LR quantity and elongation. The levels of IAA-amide conjugates significantly decreased in MC-treated seedlings compared with untreated control seedlings. Sixteen members of the cotton IAA amidohydrolase (IAH) gene family were identified, of which GhIAR3a, GhIAR3b, GhILR1, GhILL3 and GhILL6 were expressed during cotton seed germination. Compared with those in untreated control seedlings, the expression levels of GhIAR3a, GhIAR3b, GhILR1 and GhILL6 in the MC-treated seedlings were markedly elevated. The GhIAR3a/b and GhILR1 genes were cloned and expressed in Escherichia coli; these recombinant proteins exhibited hydrolytic activity that could cleave IAA-phenyalanine (Phe), IAA-methionine (Met), IAA-glycine (Gly) and IAA-leucine (Leu) in vitro, while only GhIAR3a hydrolyzed IAA-alanine (Ala) efficiently. The content of GhIAR3a, as detected via an established sandwich enzyme-linked immunosorbent assay (ELISA), increased in the MC-treated seedlings compared with the untreated control seedlings. In addition, the Arabidopsis iar3 mutant was less responsive to MC-induced LR growth than was wild type. CONCLUSIONS These findings suggested that MC application could mediate IAA homeostasis via increased IAA levels from IAA-amide conjugate hydrolysis by accelerating IAH gene expression, which might promote LRI and increase the LR quantity and elongation.
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Affiliation(s)
- Xiaojiao Chen
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193 China
| | - Man Zhang
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193 China
| | - Mian Wang
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193 China
| | - Guiyu Tan
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193 China
| | - Mingcai Zhang
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193 China
| | - Yu Xia Hou
- College of Science, China Agricultural University, Beijing, 100193 China
| | - Baomin Wang
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193 China
| | - Zhaohu Li
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193 China
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