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Eysholdt-Derzsó E, Hause B, Sauter M, Schmidt-Schippers RR. Hypoxia reshapes Arabidopsis root architecture by integrating ERF-VII factor response and abscisic acid homoeostasis. PLANT, CELL & ENVIRONMENT 2024; 47:2879-2894. [PMID: 38616485 DOI: 10.1111/pce.14914] [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: 11/27/2023] [Revised: 04/02/2024] [Accepted: 04/04/2024] [Indexed: 04/16/2024]
Abstract
Oxygen limitation (hypoxia), arising as a key stress factor due to flooding, negatively affects plant development. Consequently, maintaining root growth under such stress is crucial for plant survival, yet we know little about the root system's adaptions to low-oxygen conditions and its regulation by phytohormones. In this study, we examine the impact of hypoxia and, herein, the regulatory role of group VII ETHYLENE-RESPONSE FACTOR (ERFVII) transcription factors on root growth in Arabidopsis. We found lateral root (LR) elongation to be actively maintained by hypoxia via ERFVII factors, as erfVII seedlings possess hypersensitivity towards hypoxia regarding their LR growth. Pharmacological inhibition of abscisic acid (ABA) biosynthesis revealed ERFVII-driven counteraction of hypoxia-induced inhibition of LR formation in an ABA-dependent manner. However, postemergence LR growth under hypoxia mediated by ERFVIIs was independent of ABA. In roots, ERFVIIs mediate, among others, the induction of ABA-degrading ABA 8'-hydroxylases CYP707A1 expression. RAP2.12 could activate the pCYC707A1:LUC reporter gene, indicating, combined with single mutant analyses, that this transcription factor regulates ABA levels through corresponding transcript upregulation. Collectively, hypoxia-induced adaptation of the Arabidopsis root system is shaped by developmental reprogramming, whereby ERFVII-dependent promotion of LR emergence, but not elongation, is partly executed through regulation of ABA degradation.
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Affiliation(s)
| | - Bettina Hause
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Halle, Germany
| | - Margret Sauter
- Plant Developmental Biology and Plant Physiology, University of Kiel, Kiel, Germany
| | - Romy R Schmidt-Schippers
- Department of Plant Biotechnology, University of Bielefeld, Institute of Biology, Bielefeld, Germany
- Center for Biotechnology, University of Bielefeld, Bielefeld, Germany
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López-Ruíz BA, García-Ponce B, de la Paz Sánchez M, Álvarez-Buylla ER, Urrutia AO, Garay-Arroyo A. Genome-wide association studies meta-analysis uncovers NOJO and SGS3 novel genes involved in Arabidopsis thaliana primary root development and plasticity. Mol Biol Rep 2024; 51:763. [PMID: 38874813 PMCID: PMC11178574 DOI: 10.1007/s11033-024-09623-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 05/08/2024] [Indexed: 06/15/2024]
Abstract
BACKGROUND Arabidopsis thaliana primary root growth has become a model for evo-devo studies due to its simplicity and facility to record cell proliferation and differentiation. To identify new genetic components relevant to primary root growth, we used a Genome-Wide Association Studies (GWAS) meta-analysis approach using data published in the last decade. In this work, we performed intra and inter-studies analyses to discover new genetic components that could participate in primary root growth. METHODS AND RESULTS We used 639 accessions from nine different studies under control conditions and performed different GWAS tests. We found that primary root growth changes were associated with 41 genes, of which six (14.6%) have been previously described as inhibitors or promoters of primary root growth. The knockdown lines of two genes, Suppressor of Gene Silencing (SGS3), involved in tasiRNA processing, and a gene with a Sterile Alpha Motif (SAM) motif named NOJOCH MOOTS (NOJO), confirmed their role as repressors of primary root growth, none has been shown to participate in this developmental process before. CONCLUSIONS In summary, our GWAS analysis of different available studies identified new genes that participate in primary root growth; two of them were identified as repressors of primary root growth.
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Affiliation(s)
- Brenda Anabel López-Ruíz
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Depto. de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México (UNAM), C. U. CDMX, México
| | - Berenice García-Ponce
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Depto. de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México (UNAM), C. U. CDMX, México
| | - María de la Paz Sánchez
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Depto. de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México (UNAM), C. U. CDMX, México
| | - Elena R Álvarez-Buylla
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Depto. de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México (UNAM), C. U. CDMX, México
- Centro de Ciencias de la Complejidad, UNAM, CDMX, México
| | - Araxi O Urrutia
- Laboratorio de Genómica Evolutiva y Funcional, Instituto de Ecología, UNAM, Mexico City, México.
- Milner Centre for Evolution, Department of Life Sciences, University of Bath, Bath, BA2 7AY, UK.
| | - Adriana Garay-Arroyo
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Depto. de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México (UNAM), C. U. CDMX, México.
- Centro de Ciencias de la Complejidad, UNAM, CDMX, México.
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Islam MS, Ghimire A, Lay L, Khan W, Lee JD, Song Q, Jo H, Kim Y. Identification of Quantitative Trait Loci Controlling Root Morphological Traits in an Interspecific Soybean Population Using 2D Imagery Data. Int J Mol Sci 2024; 25:4687. [PMID: 38731906 PMCID: PMC11083680 DOI: 10.3390/ijms25094687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 04/23/2024] [Accepted: 04/23/2024] [Indexed: 05/13/2024] Open
Abstract
Roots are the hidden and most important part of plants. They serve as stabilizers and channels for uptaking water and nutrients and play a crucial role in the growth and development of plants. Here, two-dimensional image data were used to identify quantitative trait loci (QTL) controlling root traits in an interspecific mapping population derived from a cross between wild soybean 'PI366121' and cultivar 'Williams 82'. A total of 2830 single-nucleotide polymorphisms were used for genotyping, constructing genetic linkage maps, and analyzing QTLs. Forty-two QTLs were identified on twelve chromosomes, twelve of which were identified as major QTLs, with a phenotypic variation range of 36.12% to 39.11% and a logarithm of odds value range of 12.01 to 17.35. Two significant QTL regions for the average diameter, root volume, and link average diameter root traits were detected on chromosomes 3 and 13, and both wild and cultivated soybeans contributed positive alleles. Six candidate genes, Glyma.03G027500 (transketolase/glycoaldehyde transferase), Glyma.03G014500 (dehydrogenases), Glyma.13G341500 (leucine-rich repeat receptor-like protein kinase), Glyma.13G341400 (AGC kinase family protein), Glyma.13G331900 (60S ribosomal protein), and Glyma.13G333100 (aquaporin transporter) showed higher expression in root tissues based on publicly available transcriptome data. These results will help breeders improve soybean genetic components and enhance soybean root morphological traits using desirable alleles from wild soybeans.
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Affiliation(s)
- Mohammad Shafiqul Islam
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea; (M.S.I.); (A.G.); (L.L.); (W.K.); (J.-D.L.); (H.J.)
- Department of Integrative Biology, Kyungpook National University, Daegu 41566, Republic of Korea
- Department of Agriculture, Noakhali Science and Technology University, Noakhali 3814, Bangladesh
| | - Amit Ghimire
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea; (M.S.I.); (A.G.); (L.L.); (W.K.); (J.-D.L.); (H.J.)
- Department of Integrative Biology, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Liny Lay
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea; (M.S.I.); (A.G.); (L.L.); (W.K.); (J.-D.L.); (H.J.)
- Department of Integrative Biology, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Waleed Khan
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea; (M.S.I.); (A.G.); (L.L.); (W.K.); (J.-D.L.); (H.J.)
- Department of Integrative Biology, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Jeong-Dong Lee
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea; (M.S.I.); (A.G.); (L.L.); (W.K.); (J.-D.L.); (H.J.)
- Department of Integrative Biology, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Qijian Song
- Soybean Genomics and Improvement Laboratory, USDA-ARS, Beltsville Agricultural Research Center, Beltsville, MD 20705, USA;
| | - Hyun Jo
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea; (M.S.I.); (A.G.); (L.L.); (W.K.); (J.-D.L.); (H.J.)
| | - Yoonha Kim
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea; (M.S.I.); (A.G.); (L.L.); (W.K.); (J.-D.L.); (H.J.)
- Department of Integrative Biology, Kyungpook National University, Daegu 41566, Republic of Korea
- Upland Field Machinery Research Center, Kyungpook National University, Daegu 41566, Republic of Korea
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Yu B, Chao DY, Zhao Y. How plants sense and respond to osmotic stress. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:394-423. [PMID: 38329193 DOI: 10.1111/jipb.13622] [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: 12/14/2023] [Revised: 01/12/2024] [Accepted: 01/18/2024] [Indexed: 02/09/2024]
Abstract
Drought is one of the most serious abiotic stresses to land plants. Plants sense and respond to drought stress to survive under water deficiency. Scientists have studied how plants sense drought stress, or osmotic stress caused by drought, ever since Charles Darwin, and gradually obtained clues about osmotic stress sensing and signaling in plants. Osmotic stress is a physical stimulus that triggers many physiological changes at the cellular level, including changes in turgor, cell wall stiffness and integrity, membrane tension, and cell fluid volume, and plants may sense some of these stimuli and trigger downstream responses. In this review, we emphasized water potential and movements in organisms, compared putative signal inputs in cell wall-containing and cell wall-free organisms, prospected how plants sense changes in turgor, membrane tension, and cell fluid volume under osmotic stress according to advances in plants, animals, yeasts, and bacteria, summarized multilevel biochemical and physiological signal outputs, such as plasma membrane nanodomain formation, membrane water permeability, root hydrotropism, root halotropism, Casparian strip and suberin lamellae, and finally proposed a hypothesis that osmotic stress responses are likely to be a cocktail of signaling mediated by multiple osmosensors. We also discussed the core scientific questions, provided perspective about the future directions in this field, and highlighted the importance of robust and smart root systems and efficient source-sink allocations for generating future high-yield stress-resistant crops and plants.
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Affiliation(s)
- Bo Yu
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, The Chinese Academy of Sciences, Shanghai, 200032, China
- Key Laboratory of Plant Carbon Capture, The Chinese Academy of Sciences, Shanghai, 200032, China
| | - Dai-Yin Chao
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, The Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yang Zhao
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, The Chinese Academy of Sciences, Shanghai, 200032, China
- Key Laboratory of Plant Carbon Capture, The Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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Kościelniak P, Glazińska P, Kęsy J, Mucha J, Zadworny M. Identification of genetics and hormonal factors involved in Quercus robur root growth regulation in different cultivation system. BMC PLANT BIOLOGY 2024; 24:123. [PMID: 38373900 PMCID: PMC10877882 DOI: 10.1186/s12870-024-04797-z] [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: 08/22/2023] [Accepted: 02/05/2024] [Indexed: 02/21/2024]
Abstract
Understanding the molecular processes and hormonal signals that govern root growth is of paramount importance for effective forest management. While Arabidopsis studies have shed light on the role of the primary root in root system development, the structure of root systems in trees is considerably more intricate, posing challenges to comprehend taproot growth in acorn-sown and nursery-cultivated seedlings. In this study, we investigated Quercus robur seedlings using rhizotrons, containers, and transplanted containers to rhizotrons, aiming to unravel the impact of forest nursery practices on processes governing taproot growth and root system development. Root samples were subjected to RNA-seq analysis to identify gene expression patterns and perform differential gene expression and phytohormone analysis. Among studied cultivation systems, differentially expressed genes (DEGs) exhibited significant diversity, where the number of co-occurring DEGs among cultivation systems was significantly smaller than the number of unique DEGs in different cultivation systems. Moreover, the results imply that container cultivation triggers the activation of several genes associated with linolenic acid and peptide synthesis in root growth. Upon transplantation from containers to rhizotrons, rapid enhancement in gene expression occurs, followed by gradual reduction as root growth progresses, ultimately reaching a similar expression pattern as observed in the taproot of rhizotron-cultivated seedlings. Phytohormone analysis revealed that taproot growth patterns under different cultivation systems are regulated by the interplay between auxin and cytokinin concentrations. Moreover, the diversification of hormone levels within the root zone and cultivation systems allows for taproot growth inhibition and prompt recovery in transplanted seedlings. Our study highlights the crucial role of hormone interactions during the early stages of taproot elongation, influencing root system formation across.
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Affiliation(s)
- Paulina Kościelniak
- Department of Ecology, Institute of Dendrology, Polish Academy of Sciences, 62-035, Kórnik, Poland.
| | - Paulina Glazińska
- Department of Plant Physiology and Biotechnology, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, 87-100, Toruń, Poland
| | - Jacek Kęsy
- Department of Plant Physiology and Biotechnology, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, 87-100, Toruń, Poland
| | - Joanna Mucha
- Department of Ecology, Institute of Dendrology, Polish Academy of Sciences, 62-035, Kórnik, Poland
- Faculty of Forestry and Wood Technology, Poznan University of Life Sciences, Wojska Polskiego 71a, 60-625, Poznań, Poland
| | - Marcin Zadworny
- Department of Ecology, Institute of Dendrology, Polish Academy of Sciences, 62-035, Kórnik, Poland
- Faculty of Forestry and Wood Technology, Poznan University of Life Sciences, Wojska Polskiego 71a, 60-625, Poznań, Poland
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6
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Safi A, Smagghe W, Gonçalves A, Wang Q, Xu K, Fernandez AI, Cappe B, Riquet FB, Mylle E, Eeckhout D, De Winne N, Van De Slijke E, Persyn F, Persiau G, Van Damme D, Geelen D, De Jaeger G, Beeckman T, Van Leene J, Vanneste S. Phase separation-based visualization of protein-protein interactions and kinase activities in plants. THE PLANT CELL 2023; 35:3280-3302. [PMID: 37378595 PMCID: PMC10473206 DOI: 10.1093/plcell/koad188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 05/23/2023] [Accepted: 06/23/2023] [Indexed: 06/29/2023]
Abstract
Protein activities depend heavily on protein complex formation and dynamic posttranslational modifications, such as phosphorylation. The dynamic nature of protein complex formation and posttranslational modifications is notoriously difficult to monitor in planta at cellular resolution, often requiring extensive optimization. Here, we generated and exploited the SYnthetic Multivalency in PLants (SYMPL)-vector set to assay protein-protein interactions (PPIs) (separation of phases-based protein interaction reporter) and kinase activities (separation of phases-based activity reporter of kinase) in planta, based on phase separation. This technology enabled easy detection of inducible, binary and ternary PPIs among cytoplasmic and nuclear proteins in plant cells via a robust image-based readout. Moreover, we applied the SYMPL toolbox to develop an in vivo reporter for SNF1-related kinase 1 activity, allowing us to visualize tissue-specific, dynamic SnRK1 activity in stable transgenic Arabidopsis (Arabidopsis thaliana) plants. The SYMPL cloning toolbox provides a means to explore PPIs, phosphorylation, and other posttranslational modifications with unprecedented ease and sensitivity.
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Affiliation(s)
- Alaeddine Safi
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Wouter Smagghe
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Amanda Gonçalves
- Cell Death and Inflammation Unit, VIB-UGent Center for Inflammation Research (IRC), Ghent, Belgium
- Department of Biomedical Molecular Biology (DBMB), Ghent University, Ghent, Belgium
- VIB, Bioimaging Core, B-9052 Ghent, Belgium
| | - Qing Wang
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Ke Xu
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Ana Ibis Fernandez
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Benjamin Cappe
- Cell Death and Inflammation Unit, VIB-UGent Center for Inflammation Research (IRC), Ghent, Belgium
- Department of Biomedical Molecular Biology (DBMB), Ghent University, Ghent, Belgium
| | - Franck B Riquet
- Cell Death and Inflammation Unit, VIB-UGent Center for Inflammation Research (IRC), Ghent, Belgium
- Department of Biomedical Molecular Biology (DBMB), Ghent University, Ghent, Belgium
- Université de Lille, CNRS, UMR 8523-PhLAM-Physique des Lasers Atomes et Molécules, 59000 Lille, France
| | - Evelien Mylle
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Dominique Eeckhout
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Nancy De Winne
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Eveline Van De Slijke
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Freya Persyn
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Geert Persiau
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Daniël Van Damme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Danny Geelen
- Department of Plants and Crops, Ghent University, 9000 Ghent, Belgium
| | - Geert De Jaeger
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Tom Beeckman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Jelle Van Leene
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Steffen Vanneste
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plants and Crops, Ghent University, 9000 Ghent, Belgium
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Fan S, Amombo E, Yin Y, Wang G, Avoga S, Wu N, Li Y. Root system architecture and genomic plasticity to salinity provide insights into salt-tolerant traits in tall fescue. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 262:115315. [PMID: 37542983 DOI: 10.1016/j.ecoenv.2023.115315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 07/25/2023] [Accepted: 07/30/2023] [Indexed: 08/07/2023]
Abstract
Salinity is detrimental to soil health, plant growth, and crop productivity. Understanding salt tolerance mechanisms offers the potential to introduce superior crops, especially in coastal regions. Root system architecture (RSA) plasticity is vital for plant salt stress adaptation. Tall fescue is a promising forage grass in saline regions with scarce RSA studies. Here, we used the computer-integrated and -automated programs EZ-Rhizo II and ROOT-Vis II to analyze and identify natural RSA variations and adaptability to high salt stress at physiological and genetic levels in 17 global tall fescue accessions. Total root length rather than the number of lateral roots contribute more to water uptake and could be used to separate salt-tolerant (LS-11) and -sensitive accessions (PI531230). Comparative evaluation of LS-11 and PI531230 demonstrated that the lateral root length rather than the main root contributed more towards the total root length in LS-11. Also, high water uptake was associated with a larger lateral root vector and position while low water intake was associated with an insignificant correlation between root length, vector, and position. To examine candidate gene expression, we performed transcriptome and transcription analyses using high-throughput RNA sequencing and real-time quantitative PCR, respectively of the lateral and main roots. The main root displayed more differentially expressed genes than the lateral root. A Poisson comparison of LS-11 vs PI531230 demonstrated significant upregulation of PLASMA MEMBRANE AQUAPORIN 1 and AUXIN RESPONSE FACTOR 22 in both the main and lateral root, which are associated with transmembrane water transport and the auxin-activated signaling system, respectively. There is also an upregulation of BASIC HELIX-LOOP-HELIX 5 in the main root and a downregulation in the lateral root, which is ascribed to sodium ion transmembrane transport, as well as an upregulation of THE MEDIATOR COMPLEX 1 assigned to water transport in the lateral root and a downregulation in the main root. Gene-protein interaction analysis found that more genes interacting with aquaporins proteins were upregulated in the lateral root than in the main root. We inferred that deeper main roots with longer lateral roots emanating from the bottom of the main root were ideal for tall fescue water uptake and salt tolerance, rather than many shallow roots, and that, while both main lateral roots may play similar roles in salt sensing and water uptake, there are intrinsic genomic differences.
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Affiliation(s)
- Shugao Fan
- School of Resources and Environmental Engineering, Ludong University, Yantai 264000, PR China
| | - Erick Amombo
- African Sustainable Agriculture Research Institute, Mohammed VI Polytechnic University, Laayoune 70000, Morocco
| | - Yanling Yin
- School of Resources and Environmental Engineering, Ludong University, Yantai 264000, PR China
| | - Gunagyang Wang
- School of Resources and Environmental Engineering, Ludong University, Yantai 264000, PR China
| | - Sheila Avoga
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Science, Wuhan 430061, PR China
| | - Nan Wu
- School of Resources and Environmental Engineering, Ludong University, Yantai 264000, PR China.
| | - Yating Li
- School of Resources and Environmental Engineering, Ludong University, Yantai 264000, PR China.
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Li C, Shi H, Xu L, Xing M, Wu X, Bai Y, Niu M, Gao J, Zhou Q, Cui C. Combining transcriptomics and metabolomics to identify key response genes for aluminum toxicity in the root system of Brassica napus L. seedlings. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:169. [PMID: 37418156 PMCID: PMC10328865 DOI: 10.1007/s00122-023-04412-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 06/22/2023] [Indexed: 07/08/2023]
Abstract
By integrating QTL mapping, transcriptomics and metabolomics, 138 hub genes were identified in rapeseed root response to aluminum stress and mainly involved in metabolism of lipids, carbohydrates and secondary metabolites. Aluminum (Al) toxicity has become one of the important abiotic stress factors in areas with acid soil, which hinders the absorption of water and nutrients by roots, and consequently retards the growth of crops. A deeper understanding of the stress-response mechanism of Brassica napus may allow us to identify the tolerance gene(s) and use this information in breeding-resistant crop varieties. In this study, a population of 138 recombinant inbred lines (RILs) was subjected to aluminum stress, and QTL (quantitative trait locus) mapping was used to preliminarily locate quantitative trait loci related to aluminum stress. Root tissues from seedlings of an aluminum-resistant (R) line and an aluminum-sensitive (S) line from the RIL population were harvested for transcriptome sequencing and metabolome determination. By combining the data on quantitative trait genes (QTGs), differentially expressed genes (DEGs), and differentially accumulated metabolites (DAMs), key candidate genes related to aluminum tolerance in rapeseed were determined. The results showed that there were 3186 QTGs in the RIL population, 14,232 DEGs and 457 DAMs in the comparison between R and S lines. Lastly, 138 hub genes were selected to have a strong positive or negative correlation with 30 important metabolites (|R|≥ 0.95). These genes were mainly involved in the metabolism of lipids, carbohydrates and secondary metabolites in response to Al toxicity stress. In summary, this study provides an effective method for screening key genes by combining QTLs, transcriptome sequencing and metabolomic analysis, but also lists key genes for exploring the molecular mechanism of Al tolerance in rapeseed seedling roots.
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Affiliation(s)
- Chenyang Li
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715, China
| | - Hongsong Shi
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715, China
| | - Lu Xu
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715, China
| | - Mingli Xing
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715, China
| | - Xiaoru Wu
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715, China
| | - Yansong Bai
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715, China
| | - Mengyuan Niu
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715, China
| | - Junqi Gao
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715, China
| | - Qingyuan Zhou
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715, China.
| | - Cui Cui
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715, China.
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Shishkova S, Huang L, Rodríguez RE, Ristova D, Dello Ioio R. Editorial: Root development: Towards understanding regulatory networks and complex interactions between cell populations. FRONTIERS IN PLANT SCIENCE 2023; 13:1108367. [PMID: 36684758 PMCID: PMC9854129 DOI: 10.3389/fpls.2022.1108367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Accepted: 12/23/2022] [Indexed: 06/17/2023]
Affiliation(s)
- Svetlana Shishkova
- Departamento de Biologa Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Ling Huang
- Integrative Genomics and Bioinformatics Core, Salk Institute for Biological Studies, La Jolla, CA, United States
| | - Ramiro Esteban Rodríguez
- Instituto de Biología Molecular y Celular de Rosario (IBR) - National Scientific and Technical Research Council and Universidad Nacional de Rosario, Rosario, Argentina
| | - Daniela Ristova
- Institute for Plant Sciences, Cologne Biocenter, University of Cologne, Cologne, Germany
| | - Raffaele Dello Ioio
- Dipartimento di Biologia e Biotecnologie, Sapienza Università di Roma, Rome, Italy
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10
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Wang Z, Huang C, Niu Y, Yung WS, Xiao Z, Wong FL, Huang M, Wang X, Man CK, Sze CC, Liu A, Wang Q, Chen Y, Liu S, Wu C, Liu L, Hou W, Han T, Li MW, Lam HM. QTL analyses of soybean root system architecture revealed genetic relationships with shoot-related traits. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:4507-4522. [PMID: 36422673 DOI: 10.1007/s00122-022-04235-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 10/09/2022] [Indexed: 06/16/2023]
Abstract
The genetic basis of soybean root system architecture (RSA) and the genetic relationship between shoot and RSA were revealed by integrating data from recombinant inbred population grafting and QTL mapping. Variations in root system architecture (RSA) affect the functions of roots and thus play vital roles in plant adaptations and agricultural productivity. The aim of this study was to unravel the genetic relationship between RSA traits and shoot-related traits in soybean. This study characterized RSA variability at seedling stage in a recombinant inbred population, derived from a cross between cultivated soybean C08 and wild soybean W05, and performed high-resolution quantitative trait locus (QTL) mapping. In total, 34 and 41 QTLs were detected for RSA-related and shoot-related traits, respectively, constituting eight QTL clusters. Significant QTL correspondence was found between shoot biomass and RSA-related traits, consistent with significant correlations between these phenotypes. RSA-related QTLs also overlapped with selection regions in the genome, suggesting the cultivar RSA could be a partial consequence of domestication. Using reciprocal grafting, we confirmed that shoot-derived signals affected root development and the effects were controlled by multiple loci. Meanwhile, RSA-related QTLs were found to co-localize with four soybean flowering-time loci. Consistent with the phenotypes of the parental lines of our RI population, diminishing the function of flowering controlling E1 family through RNA interference (RNAi) led to reduced root growth. This implies that the flowering time-related genes within the RSA-related QTLs are actually contributing to RSA. To conclude, this study identified the QTLs that determine RSA through controlling root growth indirectly via regulating shoot functions, and discovered superior alleles from wild soybean that could be used to improve the root structure in existing soybean cultivars.
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Affiliation(s)
- Zhili Wang
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Cheng Huang
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
| | - Yongchao Niu
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Wai-Shing Yung
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Zhixia Xiao
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Fuk-Ling Wong
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Mingkun Huang
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, 332900, Jiangxi, China
| | - Xin Wang
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
| | - Chun-Kuen Man
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Ching-Ching Sze
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Ailin Liu
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Qianwen Wang
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Yinglong Chen
- The UWA Institute of Agriculture, & School of Agriculture and Environment, The University of Western Australia, Perth, WA6001, Australia
- State Key Laboratory of Soil Erosion and Dryland Farming On the Loess Plateau, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Shuo Liu
- State Key Laboratory of Soil Erosion and Dryland Farming On the Loess Plateau, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Cunxiang Wu
- Ministry of Agriculture and Rural Affairs Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, The Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081, China
| | - Lifeng Liu
- Ministry of Agriculture and Rural Affairs Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, The Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081, China
| | - Wensheng Hou
- Ministry of Agriculture and Rural Affairs Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, The Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081, China
| | - Tianfu Han
- Ministry of Agriculture and Rural Affairs Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, The Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081, China
| | - Man-Wah Li
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China.
| | - Hon-Ming Lam
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China.
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11
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Bhattacharya S, Gröne F, Przesdzink F, Ziffer-Berger J, Barazani O, Mummenhoff K, Kappert N. 'Root of all success': Plasticity in root architecture of invasive wild radish for adaptive benefit. FRONTIERS IN PLANT SCIENCE 2022; 13:1035089. [PMID: 36466265 PMCID: PMC9709435 DOI: 10.3389/fpls.2022.1035089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 10/21/2022] [Indexed: 06/17/2023]
Abstract
Successful plant establishment in a particular environment depends on the root architecture of the seedlings and the extent of edaphic resource utilization. However, diverse habitats often pose a predicament on the suitability of the fundamental root structure of a species that evolved over a long period. We hypothesized that the plasticity in the genetically controlled root architecture in variable habitats provides an adaptive advantage to worldwide-distributed wild radish (Raphanus raphanistrum, Rr) over its close relative (R. pugioniformis, Rp) that remained endemic to the East Mediterranean region. To test the hypothesis, we performed a reciprocal comparative analysis between the two species, growing in a common garden experiment on their native soils (Hamra/Sandy for Rr, Terra Rossa for Rp) and complementary controlled experiments mimicking the major soil compositions. Additionally, we analyzed the root growth kinetics via semi-automated digital profiling and compared the architecture between Rr and Rp. In both experiments, the primary roots of Rr were significantly longer, developed fewer lateral roots, and showed slower growth kinetics than Rp. Multivariate analyses of seven significant root architecture variables revealed that Rr could successfully adapt to different surrogate growth conditions by only modulating their main root length and number of lateral roots. In contrast, Rp needs to modify several other root parameters, which are very resource-intensive, to grow on non-native soil. Altogether the findings suggest an evo-devo adaptive advantage for Rr as it can potentially establish in various habitats with the minimal tweak of key root parameters, hence allocating resources for other developmental requirements.
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Affiliation(s)
| | - Franziska Gröne
- Department of Biology, Botany, Osnabrück University, Osnabrück, Germany
| | - Felix Przesdzink
- Department of Biology, Botany, Osnabrück University, Osnabrück, Germany
| | - Jotham Ziffer-Berger
- Department of Biology, Levinsky College of Education, Tel-Aviv, Israel
- Herbarium, Steinhardt Museum of Natural History, Tel-Aviv, Israel
| | - Oz Barazani
- Institute of Plant Sciences, Agricultural Research Organization, Rishon LeZion, Israel
| | - Klaus Mummenhoff
- Department of Biology, Botany, Osnabrück University, Osnabrück, Germany
| | - Niels Kappert
- Department of Biology, Botany, Osnabrück University, Osnabrück, Germany
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12
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Fedoreyeva LI, Baranova EN, Chaban IA, Dilovarova TA, Vanyushin BF, Kononenko NV. Elongating Effect of the Peptide AEDL on the Root of Nicotiana tabacum under Salinity. PLANTS 2022; 11:plants11101352. [PMID: 35631778 PMCID: PMC9147445 DOI: 10.3390/plants11101352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 05/12/2022] [Accepted: 05/13/2022] [Indexed: 11/18/2022]
Abstract
The overall survival of a plant depends on the development, growth, and functioning of the roots. Root development and growth are not only genetically programmed but are constantly influenced by environmental factors, with the roots adapting to such changes. The peptide AEDL (alanine–glutamine acid–asparagine acid–leucine) at a concentration of 10−7 M had an elongating effect on the root cells of Nicotiana tabacum seedlings. The action of this peptide at such a low concentration is similar to that of peptide phytohormones. In the presence of 150 mM NaCl, a strong distortion in the development and architecture of the tobacco roots was observed. However, the combined presence of AEDL and NaCl resulted in normal root development. In the presence of AEDL, reactive oxygen species (ROS) were detected in the elongation and root hair zones of the roots. The ROS marker fluorescence intensity in plant cells grown with AEDL was much lower than that of plant cells grown without the peptide. Thus, AEDL protected the root tissue from damage by oxidative stress caused by the toxic effects of NaCl. Localization and accumulation of AEDL at the root were tissue-specific. Fluorescence microscopy showed that FITC-AEDL predominantly localized in the zones of elongation and root hairs, with insignificant localization in the meristem zone. AEDL induced a change in the structural organization of chromatin. Structural changes in chromatin caused significant changes in the expression of numerous genes associated with the development and differentiation of the root system. In the roots of tobacco seedlings grown in the presence of AEDL, the expression of WOX family genes decreased, and differentiation of stem cells increased, which led to root elongation. However, in the presence of NaCl, elongation of the tobacco root occurred via a different mechanism involving genes of the expansin family that weaken the cell wall in the elongation zone. Root elongation of plants is of fundamental importance in biology and is especially relevant to crop production as it can affect crop yields.
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Affiliation(s)
- Larisa I. Fedoreyeva
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya 42, 127550 Moscow, Russia; (E.N.B.); (I.A.C.); (T.A.D.); (B.F.V.); (N.V.K.)
- Correspondence:
| | - Ekaterina N. Baranova
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya 42, 127550 Moscow, Russia; (E.N.B.); (I.A.C.); (T.A.D.); (B.F.V.); (N.V.K.)
- N.V. Tsitsin Main Botanical Garden of Russian Academy of Sciences, Botanicheskaya 4, 127276 Moscow, Russia
| | - Inn A. Chaban
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya 42, 127550 Moscow, Russia; (E.N.B.); (I.A.C.); (T.A.D.); (B.F.V.); (N.V.K.)
| | - Tatyana A. Dilovarova
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya 42, 127550 Moscow, Russia; (E.N.B.); (I.A.C.); (T.A.D.); (B.F.V.); (N.V.K.)
| | - Boris F. Vanyushin
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya 42, 127550 Moscow, Russia; (E.N.B.); (I.A.C.); (T.A.D.); (B.F.V.); (N.V.K.)
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia
| | - Neonila V. Kononenko
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya 42, 127550 Moscow, Russia; (E.N.B.); (I.A.C.); (T.A.D.); (B.F.V.); (N.V.K.)
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13
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Matthes MS, Darnell Z, Best NB, Guthrie K, Robil JM, Amstutz J, Durbak A, McSteen P. Defects in meristem maintenance, cell division, and cytokinin signaling are early responses in the boron deficient maize mutant tassel-less1. PHYSIOLOGIA PLANTARUM 2022; 174:e13670. [PMID: 35292977 DOI: 10.1111/ppl.13670] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 02/28/2022] [Accepted: 03/10/2022] [Indexed: 06/14/2023]
Abstract
Meristems house the stem cells needed for the developmental plasticity observed in adverse environmental conditions and are crucial for determining plant architecture. Meristem development is particularly sensitive to deficiencies of the micronutrient boron, yet how boron integrates into meristem development pathways is unknown. We addressed this question using the boron-deficient maize mutant, tassel-less1 (tls1). Reduced boron uptake in tls1 leads to a progressive impairment of meristem development that manifests in vegetative and reproductive defects. We show, that the tls1 tassel phenotype (male reproductive structure) was partially suppressed by mutations in the CLAVATA1 (CLV1)-ortholog, thick tassel dwarf1 (td1), but not by other mutants in the well characterized CLV-WUSCHEL pathway, which controls meristem size. The suppression of tls1 by td1 correlates with altered signaling of the phytohormone cytokinin. In contrast, mutations in the meristem maintenance gene knotted1 (kn1) enhanced both vegetative and reproductive defects in tls1. In addition, reduced transcript levels of kn1 and cell cycle genes are early defects in tls1 tassel meristems. Our results show that specific meristem maintenance and hormone pathways are affected in tls1, and suggest that reduced boron levels induced by tls1 are the underlying cause of the observed defects. We, therefore, provide new insights into the molecular mechanisms affected by boron deficiency in maize, leading to a better understanding of how genetic and environmental factors integrate during shoot meristem development.
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Affiliation(s)
- Michaela S Matthes
- Division of Biological Sciences, Bond Life Sciences Center, Interdisciplinary Plant Group, and Missouri Maize Center, University of Missouri, Columbia, Missouri, USA
| | - Zoe Darnell
- Division of Biological Sciences, Bond Life Sciences Center, Interdisciplinary Plant Group, and Missouri Maize Center, University of Missouri, Columbia, Missouri, USA
| | - Norman B Best
- Division of Biological Sciences, Bond Life Sciences Center, Interdisciplinary Plant Group, and Missouri Maize Center, University of Missouri, Columbia, Missouri, USA
| | - Katy Guthrie
- Division of Biological Sciences, Bond Life Sciences Center, Interdisciplinary Plant Group, and Missouri Maize Center, University of Missouri, Columbia, Missouri, USA
| | - Janlo M Robil
- Division of Biological Sciences, Bond Life Sciences Center, Interdisciplinary Plant Group, and Missouri Maize Center, University of Missouri, Columbia, Missouri, USA
| | - Jen Amstutz
- Division of Biological Sciences, Bond Life Sciences Center, Interdisciplinary Plant Group, and Missouri Maize Center, University of Missouri, Columbia, Missouri, USA
| | - Amanda Durbak
- Division of Biological Sciences, University of Missouri, Columbia, Missouri, USA
| | - Paula McSteen
- Division of Biological Sciences, Bond Life Sciences Center, Interdisciplinary Plant Group, and Missouri Maize Center, University of Missouri, Columbia, Missouri, USA
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14
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Motto M, Sahay S. Energy plants (crops): potential natural and future designer plants. HANDBOOK OF BIOFUELS 2022:73-114. [DOI: 10.1016/b978-0-12-822810-4.00004-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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15
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Montagnoli A, Chiatante D, Godbold DL, Koike T, Rewald B, Dumroese RK. Editorial: Modulation of Growth and Development of Tree Roots in Forest Ecosystems. FRONTIERS IN PLANT SCIENCE 2022; 13:850163. [PMID: 35242162 PMCID: PMC8886106 DOI: 10.3389/fpls.2022.850163] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 01/17/2022] [Indexed: 05/02/2023]
Affiliation(s)
- Antonio Montagnoli
- Laboratory of Environmental and Applied Botany, Department of Biotechnology and Life Science, University of Insubria, Varese, Italy
- *Correspondence: Antonio Montagnoli
| | - Donato Chiatante
- Laboratory of Environmental and Applied Botany, Department of Biotechnology and Life Science, University of Insubria, Varese, Italy
| | - Douglas L. Godbold
- Department of Forest and Soil Sciences, Institute of Forest Ecology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
- Department of Landscape Carbon Deposition, Global Change Research Institute, Academy of Sciences of the Czech Republic, Ceske Budejovice, Czechia
| | - Takayoshi Koike
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Boris Rewald
- Department of Forest and Soil Sciences, Institute of Forest Ecology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
| | - R. Kasten Dumroese
- Rocky Mountain Research Station, U.S. Department of Agriculture Forest Service, Moscow, ID, United States
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16
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Kościelniak P, Glazińska P, Kȩsy J, Zadworny M. Formation and Development of Taproots in Deciduous Tree Species. FRONTIERS IN PLANT SCIENCE 2021; 12:772567. [PMID: 34925417 PMCID: PMC8675582 DOI: 10.3389/fpls.2021.772567] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 10/27/2021] [Indexed: 06/14/2023]
Abstract
Trees are generally long-lived and are therefore exposed to numerous episodes of external stimuli and adverse environmental conditions. In certain trees e.g., oaks, taproots evolved to increase the tree's ability to acquire water from deeper soil layers. Despite the significant role of taproots, little is known about the growth regulation through internal factors (genes, phytohormones, and micro-RNAs), regulating taproot formation and growth, or the effect of external factors, e.g., drought. The interaction of internal and external stimuli, involving complex signaling pathways, regulates taproot growth during tip formation and the regulation of cell division in the root apical meristem (RAM). Assuming that the RAM is the primary regulatory center responsible for taproot growth, factors affecting the RAM function provide fundamental information on the mechanisms affecting taproot development.
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Affiliation(s)
| | - Paulina Glazińska
- Department of Plant Physiology and Biotechnology, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, Toruń, Poland
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Toruń, Poland
| | - Jacek Kȩsy
- Department of Plant Physiology and Biotechnology, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, Toruń, Poland
| | - Marcin Zadworny
- Institute of Dendrology, Polish Academy of Sciences, Kórnik, Poland
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17
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Yamoune A, Cuyacot AR, Zdarska M, Hejatko J. Hormonal orchestration of root apical meristem formation and maintenance in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:6768-6788. [PMID: 34343283 DOI: 10.1093/jxb/erab360] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 08/02/2021] [Indexed: 06/13/2023]
Abstract
Plant hormones are key regulators of a number of developmental and adaptive responses in plants, integrating the control of intrinsic developmental regulatory circuits with environmental inputs. Here we provide an overview of the molecular mechanisms underlying hormonal regulation of root development. We focus on key events during both embryonic and post-embryonic development, including specification of the hypophysis as a future organizer of the root apical meristem (RAM), hypophysis asymmetric division, specification of the quiescent centre (QC) and the stem cell niche (SCN), RAM maturation and maintenance of QC/SCN activity, and RAM size. We address both well-established and newly proposed concepts, highlight potential ambiguities in recent terminology and classification criteria of longitudinal root zonation, and point to contrasting results and alternative scenarios for recent models. In the concluding remarks, we summarize the common principles of hormonal control during root development and the mechanisms potentially explaining often antagonistic outputs of hormone action, and propose possible future research directions on hormones in the root.
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Affiliation(s)
- Amel Yamoune
- Functional Genomics and Proteomics of Plants, Central European Institute of Technology and National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic
| | - Abigail Rubiato Cuyacot
- Functional Genomics and Proteomics of Plants, Central European Institute of Technology and National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic
| | - Marketa Zdarska
- Functional Genomics and Proteomics of Plants, Central European Institute of Technology and National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic
| | - Jan Hejatko
- Functional Genomics and Proteomics of Plants, Central European Institute of Technology and National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic
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18
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Ahmad Z, Bashir K, Matsui A, Tanaka M, Sasaki R, Oikawa A, Hirai MY, Zu Y, Kawai-Yamada M, Rashid B, Husnain T, Seki M. Overexpression of nicotinamidase 3 (NIC3) gene and the exogenous application of nicotinic acid (NA) enhance drought tolerance and increase biomass in Arabidopsis. PLANT MOLECULAR BIOLOGY 2021; 107:63-84. [PMID: 34460049 DOI: 10.1007/s11103-021-01179-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 08/02/2021] [Indexed: 05/27/2023]
Abstract
Overexpressing Nicotinamidase 3 gene, and the exogenous application of its metabolite nicotinic acid (NA), enhance drought stress tolerance and increase biomass in Arabidopsis thaliana. With progressive global climatic changes, plant productivity is threatened severely by drought stress. Deciphering the molecular mechanisms regarding genes responsible for balancing plant growth and stress amelioration could imply multiple possibilities for future sustainable goals. Nicotinamide adenine dinucleotide (NAD) biosynthesis and recycling/ distribution is a crucial feature for plant growth. The current study focuses on the functional characterization of nicotinamidase 3 (NIC3) gene, which is involved in the biochemical conversion of nicotinamide (NAM) to nicotinic acid (NA) in the salvage pathway of NAD biosynthesis. Our data show that overexpression of NIC3 gene enhances drought stress tolerance and increases plant growth. NIC3-OX plants accumulated more NA as compared to WT plants. Moreover, the upregulation of several genes related to plant growth/stress tolerance indicates that regulating the NAD salvage pathway could significantly enhance plant growth and drought stress tolerance. The exogenous application of nicotinic acid (NA) showed a similar phenotype as the effect of overexpressing NIC3 gene. In short, we contemplated the role of NIC3 gene and NA application in drought stress tolerance and plant growth. Our results would be helpful in engineering plants with enhanced drought stress tolerance and increased growth potential.
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Affiliation(s)
- Zarnab Ahmad
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science (CSRS), Yokohama, 230-0045, Japan
- Plant Genomics Laboratory, Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Khurram Bashir
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science (CSRS), Yokohama, 230-0045, Japan
- Laboratory of Plant Biotechnology, Department of Biology, Syed Babar Ali School of Science and Engineering, Lahore University of Management Sciences (LUMS), Lahore, Pakistan
| | - Akihiro Matsui
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science (CSRS), Yokohama, 230-0045, Japan
- Plant Epigenome Regulation Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, 351-0198, Japan
| | - Maho Tanaka
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science (CSRS), Yokohama, 230-0045, Japan
- Plant Epigenome Regulation Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, 351-0198, Japan
| | - Ryosuke Sasaki
- Mass Spectrometry and Microscopy Unit, RIKEN Center for Sustainable Resource Science (CSRS), Yokohama, 230-0045, Japan
| | - Akira Oikawa
- Mass Spectrometry and Microscopy Unit, RIKEN Center for Sustainable Resource Science (CSRS), Yokohama, 230-0045, Japan
- Faculty of Agriculture, Yamagata University, Tsuruoka, 997-8555, Japan
| | - Masami Yokota Hirai
- Mass Spectrometry and Microscopy Unit, RIKEN Center for Sustainable Resource Science (CSRS), Yokohama, 230-0045, Japan
- Metabolic Systems Research Team, RIKEN Center for Sustainable Resource Science (CSRS), Yokohama, 230-0045, Japan
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, 464-8601, Japan
| | - Yanhui Zu
- Graduate School of Science and Engineering, Saitama University, 225 Shimo-Okubo, Sakura-ku, Saitama, 338-8570, Japan
| | - Maki Kawai-Yamada
- Graduate School of Science and Engineering, Saitama University, 225 Shimo-Okubo, Sakura-ku, Saitama, 338-8570, Japan
| | - Bushra Rashid
- Plant Genomics Laboratory, Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Tayyab Husnain
- Plant Genomics Laboratory, Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Motoaki Seki
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science (CSRS), Yokohama, 230-0045, Japan.
- Plant Epigenome Regulation Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, 351-0198, Japan.
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, 244-0813, Japan.
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19
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Kumar J, Sen Gupta D, Djalovic I, Kumar S, Siddique KHM. Root-omics for drought tolerance in cool-season grain legumes. PHYSIOLOGIA PLANTARUM 2021; 172:629-644. [PMID: 33314181 DOI: 10.1111/ppl.13313] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 12/02/2020] [Indexed: 06/12/2023]
Abstract
Root traits can be exploited to increase the physiological efficiency of crop water use under drought. Root length, root hairs, root branching, root diameter, and root proliferation rate are genetically defined traits that can help to improve the water productivity potential of crops. Recently, high-throughput phenotyping techniques/platforms have been used to screen the germplasm of major cool-season grain legumes for root traits and their impact on different physiological processes, including nutrient uptake and yield potential. Advances in omics approaches have led to the dissection of genomic, proteomic, and metabolomic structures of these traits. This knowledge facilitates breeders to improve the water productivity and nutrient uptake of cultivars under limited soil moisture conditions in major cool-season grain legumes that usually face terminal drought. This review discusses the advances in root traits and their potential for developing drought-tolerant cultivars in cool-season grain legumes.
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Affiliation(s)
- Jitendra Kumar
- Division of Crop Improvement, ICAR-Indian Institute of Pulses Research, Kanpur, India
| | - Debjyoti Sen Gupta
- Division of Crop Improvement, ICAR-Indian Institute of Pulses Research, Kanpur, India
| | - Ivica Djalovic
- Maize Department, Institute of Field and Vegetable Crops, Novi Sad, Serbia
| | - Shiv Kumar
- Biodiversity and Crop Improvement Program, International Centre for Agricultural Research in the Dry Areas (ICARDA), Rabat, Morocco
| | - Kadambot H M Siddique
- The UWA Institute of Agriculture and School of Agriculture and Environment, The University of Western Australia, Perth, Western Australia, Australia
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20
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Allelign Ashagre H, Zaltzman D, Idan-Molakandov A, Romano H, Tzfadia O, Harpaz-Saad S. FASCICLIN-LIKE 18 Is a New Player Regulating Root Elongation in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2021; 12:645286. [PMID: 33897736 PMCID: PMC8058476 DOI: 10.3389/fpls.2021.645286] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 02/19/2021] [Indexed: 05/26/2023]
Abstract
The plasticity of root development represents a key trait that enables plants to adapt to diverse environmental cues. The pattern of cell wall deposition, alongside other parameters, affects the extent, and direction of root growth. In this study, we report that FASCICLIN-LIKE ARABINOGALACTAN PROTEIN 18 (FLA18) plays a role during root elongation in Arabidopsis thaliana. Using root-specific co-expression analysis, we identified FLA18 to be co-expressed with a sub-set of genes required for root elongation. FLA18 encodes for a putative extra-cellular arabinogalactan protein from the FLA-gene family. Two independent T-DNA insertion lines, named fla18-1 and fla18-2, display short and swollen lateral roots (LRs) when grown on sensitizing condition of high-sucrose containing medium. Unlike fla4/salt overly sensitive 5 (sos5), previously shown to display short and swollen primary root (PR) and LRs under these conditions, the PR of the fla18 mutants is slightly longer compared to the wild-type. Overexpression of the FLA18 CDS complemented the fla18 root phenotype. Genetic interaction between either of the fla18 alleles and sos5 reveals a more severe perturbation of anisotropic growth in both PR and LRs, as compared to the single mutants and the wild-type under restrictive conditions of high sucrose or high-salt containing medium. Additionally, under salt-stress conditions, fla18sos5 had a small, chlorotic shoot phenotype, that was not observed in any of the single mutants or the wild type. As previously shown for sos5, the fla18-1 and fla18-1sos5 root-elongation phenotype is suppressed by abscisic acid (ABA) and display hypersensitivity to the ABA synthesis inhibitor, Fluridon. Last, similar to other cell wall mutants, fla18 root elongation is hypersensitive to the cellulose synthase inhibitor, Isoxaben. Altogether, the presented data assign a new role for FLA18 in the regulation of root elongation. Future studies of the unique vs. redundant roles of FLA proteins during root elongation is anticipated to shed a new light on the regulation of root architecture during plant adaptation to different growth conditions.
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Affiliation(s)
- Hewot Allelign Ashagre
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - David Zaltzman
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Anat Idan-Molakandov
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Hila Romano
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Oren Tzfadia
- Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, Institute for Tropical Medicine, Antwerp, Belgium
| | - Smadar Harpaz-Saad
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Jerusalem, Israel
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21
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López-Ruiz BA, Zluhan-Martínez E, Sánchez MDLP, Álvarez-Buylla ER, Garay-Arroyo A. Interplay between Hormones and Several Abiotic Stress Conditions on Arabidopsis thaliana Primary Root Development. Cells 2020; 9:E2576. [PMID: 33271980 PMCID: PMC7759812 DOI: 10.3390/cells9122576] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 11/18/2020] [Accepted: 11/18/2020] [Indexed: 01/17/2023] Open
Abstract
As sessile organisms, plants must adjust their growth to withstand several environmental conditions. The root is a crucial organ for plant survival as it is responsible for water and nutrient acquisition from the soil and has high phenotypic plasticity in response to a lack or excess of them. How plants sense and transduce their external conditions to achieve development, is still a matter of investigation and hormones play fundamental roles. Hormones are small molecules essential for plant growth and their function is modulated in response to stress environmental conditions and internal cues to adjust plant development. This review was motivated by the need to explore how Arabidopsis thaliana primary root differentially sense and transduce external conditions to modify its development and how hormone-mediated pathways contribute to achieve it. To accomplish this, we discuss available data of primary root growth phenotype under several hormone loss or gain of function mutants or exogenous application of compounds that affect hormone concentration in several abiotic stress conditions. This review shows how different hormones could promote or inhibit primary root development in A. thaliana depending on their growth in several environmental conditions. Interestingly, the only hormone that always acts as a promoter of primary root development is gibberellins.
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Affiliation(s)
- Brenda Anabel López-Ruiz
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de Mexico, Mexico City 04510, Mexico; (B.A.L.-R.); (E.Z.-M.); (M.d.l.P.S.); (E.R.Á.-B.)
| | - Estephania Zluhan-Martínez
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de Mexico, Mexico City 04510, Mexico; (B.A.L.-R.); (E.Z.-M.); (M.d.l.P.S.); (E.R.Á.-B.)
| | - María de la Paz Sánchez
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de Mexico, Mexico City 04510, Mexico; (B.A.L.-R.); (E.Z.-M.); (M.d.l.P.S.); (E.R.Á.-B.)
| | - Elena R. Álvarez-Buylla
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de Mexico, Mexico City 04510, Mexico; (B.A.L.-R.); (E.Z.-M.); (M.d.l.P.S.); (E.R.Á.-B.)
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de Mexico, Mexico City 04510, Mexico
| | - Adriana Garay-Arroyo
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de Mexico, Mexico City 04510, Mexico; (B.A.L.-R.); (E.Z.-M.); (M.d.l.P.S.); (E.R.Á.-B.)
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de Mexico, Mexico City 04510, Mexico
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22
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Montesinos JC, Abuzeineh A, Kopf A, Juanes-Garcia A, Ötvös K, Petrášek J, Sixt M, Benková E. Phytohormone cytokinin guides microtubule dynamics during cell progression from proliferative to differentiated stage. EMBO J 2020; 39:e104238. [PMID: 32667089 PMCID: PMC7459425 DOI: 10.15252/embj.2019104238] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 06/12/2020] [Accepted: 06/22/2020] [Indexed: 12/22/2022] Open
Abstract
Cell production and differentiation for the acquisition of specific functions are key features of living systems. The dynamic network of cellular microtubules provides the necessary platform to accommodate processes associated with the transition of cells through the individual phases of cytogenesis. Here, we show that the plant hormone cytokinin fine‐tunes the activity of the microtubular cytoskeleton during cell differentiation and counteracts microtubular rearrangements driven by the hormone auxin. The endogenous upward gradient of cytokinin activity along the longitudinal growth axis in Arabidopsis thaliana roots correlates with robust rearrangements of the microtubule cytoskeleton in epidermal cells progressing from the proliferative to the differentiation stage. Controlled increases in cytokinin activity result in premature re‐organization of the microtubule network from transversal to an oblique disposition in cells prior to their differentiation, whereas attenuated hormone perception delays cytoskeleton conversion into a configuration typical for differentiated cells. Intriguingly, cytokinin can interfere with microtubules also in animal cells, such as leukocytes, suggesting that a cytokinin‐sensitive control pathway for the microtubular cytoskeleton may be at least partially conserved between plant and animal cells.
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Affiliation(s)
| | - Anas Abuzeineh
- Department of Plant Biotechnology and Bioinformatics, Ghent University and Center for Plant Systems Biology, VIB, Gent, Belgium
| | - Aglaja Kopf
- Institute of Science and Technology Austria (IST Austria), Klosterneuburg, Austria
| | - Alba Juanes-Garcia
- Institute of Science and Technology Austria (IST Austria), Klosterneuburg, Austria
| | - Krisztina Ötvös
- Institute of Science and Technology Austria (IST Austria), Klosterneuburg, Austria.,Bioresources Unit, Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, Tulln, Austria
| | - Jan Petrášek
- Institute of Experimental Botany, The Czech Academy of Sciences, Praha, Czech Republic
| | - Michael Sixt
- Institute of Science and Technology Austria (IST Austria), Klosterneuburg, Austria
| | - Eva Benková
- Institute of Science and Technology Austria (IST Austria), Klosterneuburg, Austria
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23
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Auxin-Abscisic Acid Interactions in Plant Growth and Development. Biomolecules 2020; 10:biom10020281. [PMID: 32059519 PMCID: PMC7072425 DOI: 10.3390/biom10020281] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Revised: 02/06/2020] [Accepted: 02/07/2020] [Indexed: 01/10/2023] Open
Abstract
Plant hormones regulate many aspects of plant growth, development, and response to biotic and abiotic stress. Much research has gone into our understanding of individual plant hormones, focusing primarily on their mechanisms of action and the processes that they regulate. However, recent research has begun to focus on a more complex problem; how various plant hormones work together to regulate growth and developmental processes. In this review, we focus on two phytohormones, abscisic acid (ABA) and auxin. We begin with brief overviews of the hormones individually, followed by in depth analyses of interactions between auxin and ABA, focusing on interactions in individual tissues and how these interactions are occurring where possible. Finally, we end with a brief discussion and future prospects for the field.
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24
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Moisseyev G, Park K, Cui A, Freitas D, Rajagopal D, Konda AR, Martin-Olenski M, Mcham M, Liu K, Du Q, Schnable JC, Moriyama EN, Cahoon EB, Zhang C. RGPDB: database of root-associated genes and promoters in maize, soybean, and sorghum. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2020; 2020:5851117. [PMID: 32500918 PMCID: PMC7273057 DOI: 10.1093/database/baaa038] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 03/02/2020] [Accepted: 05/06/2020] [Indexed: 12/21/2022]
Abstract
Root-associated genes play an important role in plants. Despite the fact that there have been studies on root biology, information on genes that are specifically expressed or upregulated in roots is poorly collected. There exist very few databases dedicated to genes and promoters associated with root biology, preventing effective root-related studies. Therefore, we analyzed multiple types of omics data to identify root-associated genes in maize, soybean, and sorghum and constructed a comprehensive online database of these genes and their promoter sequences. This database creates a pivotal platform capable of stimulating and facilitating further studies on manipulating root growth and development.
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Affiliation(s)
- Gleb Moisseyev
- Young Nebraska Scientists Program, University of Nebraska (EPSCoR), Lincoln, NE 68588, USA
| | - Kiyoul Park
- Department of Biochemistry, University of Nebraska, Lincoln, NE 68588 USA.,Center for Plant Science Innovation, University of Nebraska, Lincoln, NE 68588, USA
| | - Alix Cui
- Young Nebraska Scientists Program, University of Nebraska (EPSCoR), Lincoln, NE 68588, USA
| | - Daniel Freitas
- Young Nebraska Scientists Program, University of Nebraska (EPSCoR), Lincoln, NE 68588, USA
| | - Divith Rajagopal
- Young Nebraska Scientists Program, University of Nebraska (EPSCoR), Lincoln, NE 68588, USA
| | - Anji Reddy Konda
- Department of Biochemistry, University of Nebraska, Lincoln, NE 68588 USA.,Center for Plant Science Innovation, University of Nebraska, Lincoln, NE 68588, USA
| | | | - Mackenzie Mcham
- Young Nebraska Scientists Program, University of Nebraska (EPSCoR), Lincoln, NE 68588, USA
| | - Kan Liu
- School of Biological Sciences, University of Nebraska, Lincoln, NE 68588 USA.,Center for Plant Science Innovation, University of Nebraska, Lincoln, NE 68588, USA
| | - Qian Du
- School of Biological Sciences, University of Nebraska, Lincoln, NE 68588 USA.,Center for Plant Science Innovation, University of Nebraska, Lincoln, NE 68588, USA
| | - James C Schnable
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE 68583 USA.,Center for Plant Science Innovation, University of Nebraska, Lincoln, NE 68588, USA
| | - Etsuko N Moriyama
- School of Biological Sciences, University of Nebraska, Lincoln, NE 68588 USA.,Center for Plant Science Innovation, University of Nebraska, Lincoln, NE 68588, USA
| | - Edgar B Cahoon
- Department of Biochemistry, University of Nebraska, Lincoln, NE 68588 USA.,Center for Plant Science Innovation, University of Nebraska, Lincoln, NE 68588, USA
| | - Chi Zhang
- School of Biological Sciences, University of Nebraska, Lincoln, NE 68588 USA.,Center for Plant Science Innovation, University of Nebraska, Lincoln, NE 68588, USA
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25
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Ripoll JJ, Zhu M, Brocke S, Hon CT, Yanofsky MF, Boudaoud A, Roeder AHK. Growth dynamics of the Arabidopsis fruit is mediated by cell expansion. Proc Natl Acad Sci U S A 2019; 116:25333-25342. [PMID: 31757847 PMCID: PMC6911193 DOI: 10.1073/pnas.1914096116] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Fruit have evolved a sophisticated tissue and cellular architecture to secure plant reproductive success. Postfertilization growth is perhaps the most dramatic event during fruit morphogenesis. Several studies have proposed that fertilized ovules and developing seeds initiate signaling cascades to coordinate and promote the growth of the accompanying fruit tissues. This dynamic process allows the fruit to conspicuously increase its size and acquire its final shape and means for seed dispersal. All these features are key for plant survival and crop yield. Despite its importance, we lack a high-resolution spatiotemporal map of how postfertilization fruit growth proceeds at the cellular level. In this study, we have combined live imaging, mutant backgrounds in which fertilization can be controlled, and computational modeling to monitor and predict postfertilization fruit growth in Arabidopsis We have uncovered that, unlike leaves, sepals, or roots, fruit do not exhibit a spatial separation of cell division and expansion domains; instead, there is a separation into temporal stages with fertilization as the trigger for transitioning to cell expansion, which drives postfertilization fruit growth. We quantified the coordination between fertilization and fruit growth by imaging no transmitting tract (ntt) mutants, in which fertilization fails in the bottom half of the fruit. By combining our experimental data with computational modeling, we delineated the mobility properties of the seed-derived signaling cascades promoting growth in the fruit. Our study provides the basis for generating a comprehensive understanding of the molecular and cellular mechanisms governing fruit growth and shape.
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Affiliation(s)
- Juan-José Ripoll
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA 92093-0116;
- Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, CA 92093-0116
| | - Mingyuan Zhu
- School of Integrative Plant Science, Section of Plant Biology, Cornell University, Ithaca, NY 14853
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853
| | - Stephanie Brocke
- School of Integrative Plant Science, Section of Plant Biology, Cornell University, Ithaca, NY 14853
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853
| | - Cindy T Hon
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA 92093-0116
| | - Martin F Yanofsky
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA 92093-0116
- Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, CA 92093-0116
| | - Arezki Boudaoud
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, École Normale Supérieur de Lyon, Claud Bernard University Lyon 1, CNRS, Institut National de la Recherche Agronomique, F-69342 Lyon, France
| | - Adrienne H K Roeder
- School of Integrative Plant Science, Section of Plant Biology, Cornell University, Ithaca, NY 14853;
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853
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26
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Jiang N, Floro E, Bray AL, Laws B, Duncan KE, Topp CN. Three-Dimensional Time-Lapse Analysis Reveals Multiscale Relationships in Maize Root Systems with Contrasting Architectures. THE PLANT CELL 2019; 31:1708-1722. [PMID: 31123089 PMCID: PMC6713302 DOI: 10.1105/tpc.19.00015] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 05/08/2019] [Accepted: 07/01/2019] [Indexed: 05/22/2023]
Abstract
Understanding how an organism's phenotypic traits are conditioned by genetic and environmental variation is a central goal of biology. Root systems are one of the most important but poorly understood aspects of plants, largely due to the three-dimensional (3D), dynamic, and multiscale phenotyping challenge they pose. A critical gap in our knowledge is how root systems build in complexity from a single primary root to a network of thousands of roots that collectively compete for ephemeral, heterogeneous soil resources. We used time-lapse 3D imaging and mathematical modeling to assess root system architectures (RSAs) of two maize (Zea mays) inbred genotypes and their hybrid as they grew in complexity from a few to many roots. Genetically driven differences in root branching zone size and lateral branching densities along a single root, combined with differences in peak growth rate and the relative allocation of carbon resources to new versus existing roots, manifest as sharply distinct global RSAs over time. The 3D imaging of mature field-grown root crowns showed that several genetic differences in seedling architectures could persist throughout development and across environments. This approach connects individual and system-wide scales of root growth dynamics, which could eventually be used to predict genetic variation for complex RSAs and their functions.
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Affiliation(s)
- Ni Jiang
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132
| | - Eric Floro
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132
| | - Adam L Bray
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132
- Division of Plant Sciences, University of Missouri, Columbia, Missouri 65211
| | - Benjamin Laws
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132
| | - Keith E Duncan
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132
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27
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Jiang N, Floro E, Bray AL, Laws B, Duncan KE, Topp CN. Three-Dimensional Time-Lapse Analysis Reveals Multiscale Relationships in Maize Root Systems with Contrasting Architectures. THE PLANT CELL 2019; 31:1708-1722. [PMID: 31123089 DOI: 10.1101/381046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 05/08/2019] [Accepted: 07/01/2019] [Indexed: 05/28/2023]
Abstract
Understanding how an organism's phenotypic traits are conditioned by genetic and environmental variation is a central goal of biology. Root systems are one of the most important but poorly understood aspects of plants, largely due to the three-dimensional (3D), dynamic, and multiscale phenotyping challenge they pose. A critical gap in our knowledge is how root systems build in complexity from a single primary root to a network of thousands of roots that collectively compete for ephemeral, heterogeneous soil resources. We used time-lapse 3D imaging and mathematical modeling to assess root system architectures (RSAs) of two maize (Zea mays) inbred genotypes and their hybrid as they grew in complexity from a few to many roots. Genetically driven differences in root branching zone size and lateral branching densities along a single root, combined with differences in peak growth rate and the relative allocation of carbon resources to new versus existing roots, manifest as sharply distinct global RSAs over time. The 3D imaging of mature field-grown root crowns showed that several genetic differences in seedling architectures could persist throughout development and across environments. This approach connects individual and system-wide scales of root growth dynamics, which could eventually be used to predict genetic variation for complex RSAs and their functions.
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Affiliation(s)
- Ni Jiang
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132
| | - Eric Floro
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132
| | - Adam L Bray
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132
- Division of Plant Sciences, University of Missouri, Columbia, Missouri 65211
| | - Benjamin Laws
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132
| | - Keith E Duncan
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132
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28
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Solanki S, Richards J, Ameen G, Wang X, Khan A, Ali H, Stangel A, Tamang P, Gross T, Gross P, Fetch TG, Brueggeman RS. Characterization of genes required for both Rpg1 and rpg4-mediated wheat stem rust resistance in barley. BMC Genomics 2019; 20:495. [PMID: 31200635 PMCID: PMC6570958 DOI: 10.1186/s12864-019-5858-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Accepted: 05/29/2019] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Puccinia graminis f. sp. tritici (Pgt) race TTKSK and its lineage pose a threat to barley production world-wide justifying the extensive efforts to identify, clone, and characterize the rpg4-mediated resistance locus (RMRL), the only effective resistance to virulent Pgt races in the TTKSK lineage. The RMRL contains two nucleotide-binding domain and leucine-rich repeat (NLR) resistance genes, Rpg5 and HvRga1, which are required for resistance. The two NLRs have head-to-head genome architecture with one NLR, Rpg5, containing an integrated C-terminal protein kinase domain, characteristic of an "integrated sensory domain" resistance mechanism. Fast neutron mutagenesis of line Q21861 was utilized in a forward genetics approach to identify genetic components that function in the RMRL or Rpg1 resistance mechanisms, as Q21861 contains both genes. A mutant was identified that compromises both RMRL and Rpg1-mediated resistances and had stunted seedling roots, designated required for P. graminis resistance 9 (rpr9). RESULTS The rpr9 mutant generated in the Q21861 background was crossed with the Swiss landrace Hv584, which carries RMRL but contains polymorphism across the genome compared to Q21861. To map Rpr9, a Hv584 x rpr9 F6:7 recombinant inbred line (RIL) population was developed. The RIL population was phenotyped with Pgt race QCCJB. The Hv584 x rpr9 RIL population was genotyped with the 9 k Illumina Infinium iSelect marker panel, producing 2701 polymorphic markers. A robust genetic map consisting of 563 noncosegregating markers was generated and used to map Rpr9 to an ~ 3.4 cM region on barley chromosome 3H. The NimbleGen barley exome capture array was utilized to capture rpr9 and wild type Q21861 exons, followed by Illumina sequencing. Comparative analysis, resulting in the identification of a 1.05 Mbp deletion at the chromosome 3H rpr9 locus. The identified deletion contains ten high confidence annotated genes with the best rpr9 candidates encoding a SKP1-like 9 protein and a F-box family protein. CONCLUSION Genetic mapping and exome capture rapidly identified candidate gene/s that function in RMRL and Rpg1 mediated resistance pathway/s. One or more of the identified candidate rpr9 genes are essential in the only two known effective stem rust resistance mechanisms, present in domesticated barley.
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Affiliation(s)
- Shyam Solanki
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58108-6050 USA
| | - Jonathan Richards
- Department of Plant Pathology and Crop Physiology, Louisiana State University AgCenter, Baton Rouge, LA 70803 USA
| | - Gazala Ameen
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58108-6050 USA
| | - Xue Wang
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58108-6050 USA
| | - Atiya Khan
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58108-6050 USA
| | - Harris Ali
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58108-6050 USA
| | - Alex Stangel
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58108-6050 USA
| | - Prabin Tamang
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58108-6050 USA
| | - Thomas Gross
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58108-6050 USA
| | - Patrick Gross
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58108-6050 USA
| | - Thomas G. Fetch
- Cereal Research Centre, Agriculture and Agri-Food Canada, 101 Route 100, Morden, MB R6M 1Y5 Canada
| | - Robert S. Brueggeman
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58108-6050 USA
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29
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Xu Y, Zou J, Zheng H, Xu M, Zong X, Wang L. RNA-Seq Transcriptome Analysis of Rice Primary Roots Reveals the Role of Flavonoids in Regulating the Rice Primary Root Growth. Genes (Basel) 2019; 10:genes10030213. [PMID: 30871177 PMCID: PMC6470995 DOI: 10.3390/genes10030213] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 03/06/2019] [Accepted: 03/07/2019] [Indexed: 01/02/2023] Open
Abstract
Flavonoids play important roles in root development and in its tropic responses, whereas the flavonoids-mediated changes of the global transcription levels during root growth remain unclear. Here, the global transcription changes in quercetin-treated rice primary roots were analyzed. Quercetin treatment significantly induced the inhibition of root growth and the reduction of H2O2 and O2− levels. In addition, the RNA-seq analysis revealed that there are 1243 differentially expressed genes (DEGs) identified in quercetin-treated roots, including 1032 up-regulated and 211 down-regulated genes. A gene ontology (GO) enrichment analysis showed that the enriched GO terms are mainly associated with the cell wall organization, response to oxidative stress, and response to hormone stimulus. The Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment pathway analysis showed that the enriched DEGs are involved in phenylpropanoid biosynthesis, glutathione metabolism, and plant hormone signal transduction. Moreover, the quercetin treatment led to an increase of the antioxidant enzyme activities of catalase (CAT), peroxidase (POD), and superoxide dismutase (SOD) in rice roots. Also, the quercetin treatment altered the DR5:GUS expression pattern in the root tips. All of these data indicated that the flavonoids-mediated transcription changes of genes are related to the genes involved in cell wall remodeling, redox homeostasis, and auxin signaling, leading to a reduced cell division in the meristem zone and cell elongation in the elongation zone of roots.
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Affiliation(s)
- Yu Xu
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China.
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Junjie Zou
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Hongyan Zheng
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Miaoyun Xu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Xuefeng Zong
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China.
| | - Lei Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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Fonouni-Farde C, Miassod A, Laffont C, Morin H, Bendahmane A, Diet A, Frugier F. Gibberellins negatively regulate the development of Medicago truncatula root system. Sci Rep 2019; 9:2335. [PMID: 30787350 PMCID: PMC6382856 DOI: 10.1038/s41598-019-38876-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 01/10/2019] [Indexed: 01/10/2023] Open
Abstract
The root system displays a remarkable plasticity that enables plants to adapt to changing environmental conditions. This plasticity is tightly linked to the activity of root apical meristems (RAMs) and to the formation of lateral roots, both controlled by related hormonal crosstalks. In Arabidopsis thaliana, gibberellins (GAs) were shown to positively control RAM growth and the formation of lateral roots. However, we showed in Medicago truncatula that GAs negatively regulate root growth and RAM size as well as the number of lateral roots depending at least on the MtDELLA1 protein. By using confocal microscopy and molecular analyses, we showed that GAs primarily regulate RAM size by affecting cortical cell expansion and additionally negatively regulate a subset of cytokinin-induced root expansin encoding genes. Moreover, GAs reduce the number of cortical cell layers, resulting in the formation of both shorter and thinner roots. These results suggest contrasting effects of GA regulations on the root system architecture depending on plant species.
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Affiliation(s)
- Camille Fonouni-Farde
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, Univ Paris Diderot, INRA, Univ Paris Sud, Univ d'Evry, Université Paris-Saclay, Rue de Noetzlin, 91190, Gif-sur-Yvette, France
| | - Ambre Miassod
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, Univ Paris Diderot, INRA, Univ Paris Sud, Univ d'Evry, Université Paris-Saclay, Rue de Noetzlin, 91190, Gif-sur-Yvette, France
| | - Carole Laffont
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, Univ Paris Diderot, INRA, Univ Paris Sud, Univ d'Evry, Université Paris-Saclay, Rue de Noetzlin, 91190, Gif-sur-Yvette, France
| | - Halima Morin
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, Univ Paris Diderot, INRA, Univ Paris Sud, Univ d'Evry, Université Paris-Saclay, Rue de Noetzlin, 91190, Gif-sur-Yvette, France
| | - Abdelhafid Bendahmane
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, Univ Paris Diderot, INRA, Univ Paris Sud, Univ d'Evry, Université Paris-Saclay, Rue de Noetzlin, 91190, Gif-sur-Yvette, France
| | - Anouck Diet
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, Univ Paris Diderot, INRA, Univ Paris Sud, Univ d'Evry, Université Paris-Saclay, Rue de Noetzlin, 91190, Gif-sur-Yvette, France
| | - Florian Frugier
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, Univ Paris Diderot, INRA, Univ Paris Sud, Univ d'Evry, Université Paris-Saclay, Rue de Noetzlin, 91190, Gif-sur-Yvette, France.
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Hong L, Zhang L, Liu M, Wang S, He L, Yang W, Li J, Yu Q, Li QQ, Zhou K. Heavy metal rich stone-processing wastewater inhibits the growth and development of plants. INTERNATIONAL JOURNAL OF PHYTOREMEDIATION 2018; 21:479-486. [PMID: 30560684 DOI: 10.1080/15226514.2018.1537241] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Large amounts of wastewater are generated from stone processing, which are toxic and cause serious environmental and health risks. To quantify the content of stone processing wastewater and estimate its effects on plant growth, we collected water samples from sewage outfall of four stone processing factories and nearby water bodies. The concentration of potential toxic metals were much higher in the wastewater than background controls. Wastewater inhibited plant primary root elongation, lateral root formation, and growth of aerial part. Seedlings treated with the effluents were unhealthy with deep purple leaves and usually died before flowering. Chlorophyll a/b contents and chloroplast number were reduced in those abnormal mesophyll cells. Transcriptional levels were decreased for chloroplast formation genes, but increased for those participated in chloroplast degradation and catabolism. Six out of nine tested senescence-associated genes were up-regulated. Furthermore, our results show that endogenous toxic metal levels indeed increased after wastewater treatment. Altogether, these results indicated that the potential toxic metals rich wastewater had significant inhibition on plant growth and led to senescence-associated program cell death, which could be helpful for the government and enterprises to understand the environmental risks and formulate reasonable wastewater emission standards for the stone processing industry.
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Affiliation(s)
- Liwei Hong
- a Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems , College of the Environment and Ecology, Xiamen University , Xiamen , Fujian , China
| | - Liangjie Zhang
- a Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems , College of the Environment and Ecology, Xiamen University , Xiamen , Fujian , China
| | - Meiling Liu
- a Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems , College of the Environment and Ecology, Xiamen University , Xiamen , Fujian , China
| | - Shengjie Wang
- a Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems , College of the Environment and Ecology, Xiamen University , Xiamen , Fujian , China
| | - Linjun He
- a Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems , College of the Environment and Ecology, Xiamen University , Xiamen , Fujian , China
| | - Wanyu Yang
- a Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems , College of the Environment and Ecology, Xiamen University , Xiamen , Fujian , China
| | - Jingli Li
- a Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems , College of the Environment and Ecology, Xiamen University , Xiamen , Fujian , China
| | - Qiaojie Yu
- a Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems , College of the Environment and Ecology, Xiamen University , Xiamen , Fujian , China
| | - Qingshun Q Li
- a Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems , College of the Environment and Ecology, Xiamen University , Xiamen , Fujian , China
- b Graduate College , Western University of Health Science , Pomona , CA , USA
| | - Kefu Zhou
- a Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems , College of the Environment and Ecology, Xiamen University , Xiamen , Fujian , China
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Wei C, Zhu L, Wen J, Yi B, Ma C, Tu J, Shen J, Fu T. Morphological, transcriptomics and biochemical characterization of new dwarf mutant of Brassica napus. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 270:97-113. [PMID: 29576090 DOI: 10.1016/j.plantsci.2018.01.021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2017] [Revised: 01/16/2018] [Accepted: 01/19/2018] [Indexed: 05/08/2023]
Abstract
Plant height is a key trait of plant architecture, and is responsible for both yield and lodging resistance in Brassica napus. A dwarf mutant line (bnaC.dwf) was obtained by chemical mutagenesis of an inbred line T6. However, the molecular mechanisms and changed biological processes of the dwarf mutant remain to be determined. In this study, a comparative transcriptome analysis between bnaC.dwf and T6 plants was performed to identify genome-wide differentially expressed genes (DEGs) and possible biological processes that may explain the phenotype variations in bnaC.dwf. As a result of this analysis, 60,134,746-60,301,384 clean reads were aligned to 60,074 genes in the B. napus genome, and accounted for 60.03% of the annotated genes. In total, 819 differentially expressed genes were used for GO (Gene Ontology) term and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway enrichment analyses with a FDR (false discovery rate) criterion of <0.001, |log2Ratio| ≥ 1. We focused on plant hormone signal transduction pathways, plant-pathogen interaction pathway, protein phosphorylation and degradation pathways and sugar metabolism pathways. Taken together, the decrease in local auxin (IAA) levels, the variation in BnTCH4, BnKAN1, BnERF109, COI1-JAZ9-MYC2, auxin response genes (BnGH3.11, BnSAUR78, and AUX/IAA19), and ABA (abscisic acid) signaling genes (BnADP5, BnSnRK2.1, BnABF3.1) partially accounted for variations of cell proliferation in internodes, shoot and root apical meristem maintenance, abiotic and biotic stress resistance, and pre-harvest sprouting. As a comprehensive consequence of the cross-talk between plant hormones, sugar metabolism, plant-pathogen interactions and protein metabolism, bnaC.dwf presents distinct phenotypes from T6. These results will be helpful for shedding light on molecular mechanisms in the dwarf mutant, and give insight into further molecular breeding of semi-dwarf B. napus.
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Affiliation(s)
- Chao Wei
- Tingdong Fu National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement in Wuhan, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China.
| | - Lixia Zhu
- Tingdong Fu National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement in Wuhan, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China.
| | - Jing Wen
- Tingdong Fu National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement in Wuhan, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China.
| | - Bin Yi
- Tingdong Fu National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement in Wuhan, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China.
| | - Chaozhi Ma
- Tingdong Fu National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement in Wuhan, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China.
| | - Jinxing Tu
- Tingdong Fu National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement in Wuhan, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China.
| | - Jinxiong Shen
- Tingdong Fu National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement in Wuhan, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China.
| | - Tingdong Fu
- Tingdong Fu National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement in Wuhan, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China.
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Tandonnet JP, Marguerit E, Cookson SJ, Ollat N. Genetic architecture of aerial and root traits in field-grown grafted grapevines is largely independent. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:903-915. [PMID: 29305700 DOI: 10.1007/s00122-017-3046-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 12/21/2017] [Indexed: 05/21/2023]
Abstract
QTLs were identified for traits assessed on field-grown grafted grapevines. Root number and section had the largest phenotypic variance explained. Genetic control of root and aerial traits was independent. Breeding new rootstocks for perennial crops remains challenging, mainly because of the number of desirable traits which have to be combined, these traits include good rooting ability and root development. Consequently, the present study analyzes the genetic architecture of root traits in grapevine. A segregating progeny of 138 F1 genotypes issued from an inter-specific cross between Vitis vinifera cv. Cabernet-Sauvignon × V. riparia cv. Gloire de Montpellier, used as rootstock, was phenotyped in grafted plants grown for 2 years in the field. Seven traits, related to aerial and root development, were quantified. Heritability ranged between 0.44 for aerial biomass to 0.7 for root number. Total root number was related to the number of fine roots, while root biomass was related to the number of coarse roots. Significant quantitative trait loci (QTLs) were identified for all the traits studied with some of them explaining approximately 20% of phenotypic variance. Only a single QTL co-localized for root and aerial biomass. Identified QTLs for aerial-to-root biomass ratio suggest that aerial and root traits are controlled independently. Genes known to be involved in auxin signaling pathways and phosphorus nutrition, whose orthologues were previously shown to regulate root development in Arabidopsis, were located in the confidence intervals of several QTLs. This study opens new perspectives for breeding rootstocks with improved root development capacities.
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Affiliation(s)
- Jean-Pascal Tandonnet
- EGFV, Bordeaux Sciences Agro, INRA, University of Bordeaux, 33140, Villenave d'Ornon, France
| | - Elisa Marguerit
- EGFV, Bordeaux Sciences Agro, INRA, University of Bordeaux, 33140, Villenave d'Ornon, France
| | - Sarah J Cookson
- EGFV, Bordeaux Sciences Agro, INRA, University of Bordeaux, 33140, Villenave d'Ornon, France
| | - Nathalie Ollat
- EGFV, Bordeaux Sciences Agro, INRA, University of Bordeaux, 33140, Villenave d'Ornon, France.
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Egea I, Albaladejo I, Meco V, Morales B, Sevilla A, Bolarin MC, Flores FB. The drought-tolerant Solanum pennellii regulates leaf water loss and induces genes involved in amino acid and ethylene/jasmonate metabolism under dehydration. Sci Rep 2018; 8:2791. [PMID: 29434236 PMCID: PMC5809557 DOI: 10.1038/s41598-018-21187-2] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 01/31/2018] [Indexed: 12/29/2022] Open
Abstract
Breeding for drought-tolerant crops is a pressing issue due to the increasing frequency and duration of droughts caused by climate change. Although important sources of variation for drought tolerance exist in wild relatives, the mechanisms and the key genes controlling tolerance in tomato are little known. The aim of this study is to determine the drought response of the tomato wild relative Solanum pennellii (Sp) compared with the cultivated tomato Solanum lycopersicum (Sl). The paper investigates the physiological and molecular responses in leaves of Sp and Sl plants without stress and moderate drought stress. Significant physiological differences between species were found, with Sp leaves showing greater ability to avoid water loss and oxidative damage. Leaf transcriptomic analysis carried out when leaves did not as yet show visual dehydration symptoms revealed important constitutive expression differences between Sp and Sl species. Genes linked to different physiological and metabolic processes were induced by drought in Sp, especially those involved in N assimilation, GOGAT/GS cycle and GABA-shunt. Up-regulation in Sp of genes linked to JA/ET biosynthesis and signaling pathways was also observed. In sum, genes involved in the amino acid metabolism together with genes linked to ET/JA seem to be key actors in the drought tolerance of the wild tomato species.
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Affiliation(s)
- Isabel Egea
- Department of stress biology and plant pathology, CEBAS-CSIC, P.O. Box 164, 30100, Espinardo-Murcia, Spain
| | - Irene Albaladejo
- Department of stress biology and plant pathology, CEBAS-CSIC, P.O. Box 164, 30100, Espinardo-Murcia, Spain
| | - Victoriano Meco
- Department of stress biology and plant pathology, CEBAS-CSIC, P.O. Box 164, 30100, Espinardo-Murcia, Spain.,Department of Molecular Biology and Biochemistry, Instituto de Hortofruticultura Subtropical y Mediterránea, University of Malaga-CSIC, 29071, Malaga, Spain
| | - Belén Morales
- Department of stress biology and plant pathology, CEBAS-CSIC, P.O. Box 164, 30100, Espinardo-Murcia, Spain
| | - Angel Sevilla
- Inbionova Biotech S.L., Edif. CEEIM.University of Murcia, Campus de Espinardo, 30100, Espinardo-Murcia, Spain
| | - Maria C Bolarin
- Department of stress biology and plant pathology, CEBAS-CSIC, P.O. Box 164, 30100, Espinardo-Murcia, Spain
| | - Francisco B Flores
- Department of stress biology and plant pathology, CEBAS-CSIC, P.O. Box 164, 30100, Espinardo-Murcia, Spain.
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Arnao MB, Hernández-Ruiz J. Melatonin and its relationship to plant hormones. ANNALS OF BOTANY 2018; 121:195-207. [PMID: 29069281 PMCID: PMC5808790 DOI: 10.1093/aob/mcx114] [Citation(s) in RCA: 265] [Impact Index Per Article: 44.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 08/17/2017] [Indexed: 05/18/2023]
Abstract
BACKGROUND Plant melatonin appears to be a multi-regulatory molecule, similar to those observed in animals, with many specific functions in plant physiology. In recent years, the number of studies on melatonin in plants has increased significantly. One of the most studied actions of melatonin in plants is its effect on biotic and abiotic stress, such as that produced by drought, extreme temperatures, salinity, chemical pollution and UV radiation, among others. SCOPE This review looks at studies in which some aspects of the relationship between melatonin and the plant hormones auxin, cytokinin, gibberellins, abscisic acid, ethylene, jasmonic acid and salicylic acid are presented. The effects that some melatonin treatments have on endogenous plant hormone levels, their related genes (biosynthesis, catabolism, receptors and transcription factors) and the physiological actions induced by melatonin, mainly in stress conditions, are discussed. CONCLUSIONS Melatonin is an important modulator of gene expression related to plant hormones, e.g. in auxin carrier proteins, as well as in metabolism of indole-3-acetic acid (IAA), gibberellins, cytokinins, abscisic acid and ethylene. Most of the studies performed have dealt with the auxin-like activity of melatonin which, in a similar way to IAA, is able to induce growth in shoots and roots and stimulate root generation, giving rise to new lateral and adventitious roots. Melatonin is also able to delay senescence, protecting photosynthetic systems and related sub-cellular structures and processes. Also, its role in fruit ripening and post-harvest processes as a gene regulator of ethylene-related factors is relevant. Another decisive aspect is its role in the pathogen-plant interaction. Melatonin appears to act as a key molecule in the plant immune response, together with other well-known molecules such as nitric oxide and hormones, such as jasmonic acid and salicylic acid. In this sense, the discovery of elevated levels of melatonin in endophytic organisms associated with plants has thrown light on a possible novel form of communication between beneficial endophytes and host plants via melatonin.
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Affiliation(s)
- M B Arnao
- Department of Plant Biology (Plant Physiology), Faculty of Biology, University of Murcia, Murcia, Spain
| | - J Hernández-Ruiz
- Department of Plant Biology (Plant Physiology), Faculty of Biology, University of Murcia, Murcia, Spain
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Proust H, Hartmann C, Crespi M, Lelandais-Brière C. Root Development in Medicago truncatula: Lessons from Genetics to Functional Genomics. Methods Mol Biol 2018; 1822:205-239. [PMID: 30043307 DOI: 10.1007/978-1-4939-8633-0_15] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
This decade introduced "omics" approaches, such as genomics, transcriptomics, proteomics, and metabolomics in association with reverse and forward genetic approaches, developed earlier, to try to identify molecular pathways involved in the development or in the response to environmental conditions as well as in animals and plants. This review summarizes studies that utilized "omics" strategies to unravel the root development in the model legume Medicago truncatula and how external factors such as soil mineral status or the presence of bacteria and fungi affect root system architecture in this species. We also compare these "omics" data to the knowledges concerning the Arabidopsis thaliana root development, nowadays considered as the model of allorhiz root systems. However, unlike legumes, this species is unable to interact with soil nitrogen-fixing rhizobia and arbuscular-mycorrhizal (AM) fungi to develop novel root-derived symbiotic structures. Differences in root organization, development, and regulatory pathways between these two model species have been highlighted.
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Affiliation(s)
- Hélène Proust
- Institute of Plant Sciences Paris-Saclay, IPS2, Univ. Paris-Diderot, CNRS, INRA, Univ. Paris-Sud, Univ. Evry Val d'Essonne, Sorbonne Paris-Cité, University of Paris-Saclay, Orsay, France
| | - Caroline Hartmann
- Institute of Plant Sciences Paris-Saclay, IPS2, Univ. Paris-Diderot, CNRS, INRA, Univ. Paris-Sud, Univ. Evry Val d'Essonne, Sorbonne Paris-Cité, University of Paris-Saclay, Orsay, France
| | - Martin Crespi
- Institute of Plant Sciences Paris-Saclay, IPS2, Univ. Paris-Diderot, CNRS, INRA, Univ. Paris-Sud, Univ. Evry Val d'Essonne, Sorbonne Paris-Cité, University of Paris-Saclay, Orsay, France
| | - Christine Lelandais-Brière
- Institute of Plant Sciences Paris-Saclay, IPS2, Univ. Paris-Diderot, CNRS, INRA, Univ. Paris-Sud, Univ. Evry Val d'Essonne, Sorbonne Paris-Cité, University of Paris-Saclay, Orsay, France.
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Fonouni-Farde C, Kisiala A, Brault M, Emery RJN, Diet A, Frugier F. DELLA1-Mediated Gibberellin Signaling Regulates Cytokinin-Dependent Symbiotic Nodulation. PLANT PHYSIOLOGY 2017; 175:1795-1806. [PMID: 29046420 PMCID: PMC5717729 DOI: 10.1104/pp.17.00919] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 10/17/2017] [Indexed: 05/06/2023]
Abstract
In legume plants, low-nitrogen soils promote symbiotic interactions with rhizobial bacteria, leading to the formation of nitrogen-fixing root nodules. Among critical signals regulating this developmental process are bacterial Nod Factors (NFs) and several plant hormones, including cytokinins (CKs) and gibberellins (GAs). Here, we show in Medicago truncatula that GA signaling mediated by DELLA1 decreases the amount of bioactive CKs in roots and negatively impacts the Cytokinin Response1 (CRE1)-dependent NF activation of a subset of CK-signaling genes as well as of the CK-regulated Nodulation Signaling Pathway2 and Ethylene Response Factor Required for Nodulation1 early nodulation genes. Consistently, a dominant-active DELLA1 protein can partially rescue the reduced nodulation of the cre1 mutant and triggers the formation of nodule-like structures when expressed in the root cortex or in the root epidermis. This suggests a model where the DELLA1-mediated GA signaling interplays with the CRE1-dependent CK pathway to regulate early nodulation in response to both NF and CK signals critical for this symbiotic interaction.
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Affiliation(s)
- Camille Fonouni-Farde
- Institute of Plant Sciences Paris-Saclay (IPS2), Centre National de la Recherche Scientifique, Université Paris Sud, Université Paris Diderot, Institut National de la Recherche Agronomique, Université Evry, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Anna Kisiala
- Biology Department, Trent University, Peterborough K9J 7B8, Canada
| | - Mathias Brault
- Institute of Plant Sciences Paris-Saclay (IPS2), Centre National de la Recherche Scientifique, Université Paris Sud, Université Paris Diderot, Institut National de la Recherche Agronomique, Université Evry, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - R J Neil Emery
- Biology Department, Trent University, Peterborough K9J 7B8, Canada
| | - Anouck Diet
- Institute of Plant Sciences Paris-Saclay (IPS2), Centre National de la Recherche Scientifique, Université Paris Sud, Université Paris Diderot, Institut National de la Recherche Agronomique, Université Evry, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Florian Frugier
- Institute of Plant Sciences Paris-Saclay (IPS2), Centre National de la Recherche Scientifique, Université Paris Sud, Université Paris Diderot, Institut National de la Recherche Agronomique, Université Evry, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
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Klikno J, Kutschera U. Regulation of root development in Arabidopsis thaliana by phytohormone-secreting epiphytic methylobacteria. PROTOPLASMA 2017; 254:1867-1877. [PMID: 28054231 DOI: 10.1007/s00709-016-1067-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 12/19/2016] [Indexed: 05/20/2023]
Abstract
In numerous experimental studies, seedlings of the model dicot Arabidopsis thaliana have been raised on sterile mineral salt agar. However, under natural conditions, no plant has ever grown in an environment without bacteria. Here, we document that germ-free (gnotobiotic) seedlings, raised on mineral salt agar without sucrose, develop very short root hairs. In the presence of a soil extract that contains naturally occurring microbes, root hair elongation is promoted; this effect can be mimicked by the addition of methylobacteria to germ-free seedlings. Using five different bacterial species (Methylobacterium mesophilicum, Methylobacterium extorquens, Methylobacterium oryzae, Methylobacterium podarium, and Methylobacterium radiotolerans), we show that, over 9 days of seedling development in a light-dark cycle, root development (hair elongation, length of the primary root, branching patterns) is regulated by these epiphytic microbes that occur in the rhizosphere of field-grown plants. In a sterile liquid culture test system, auxin (IAA) inhibited root growth with little effect on hair elongation and significantly stimulated hypocotyl enlargement. Cytokinins (trans-zeatin, kinetin) and ethylene (application of the precursor ACC) likewise exerted an inhibitory effect on root growth but, in contrast to IAA, drastically stimulated root hair elongation. Methylobacteria are phytosymbionts that produce/secrete cytokinins. We conclude that, under real-world conditions (soil), the provision of these phytohormones by methylobacteria (and other epiphytic microbes) regulates root development during seedling establishment.
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Affiliation(s)
- Jana Klikno
- Institute of Biology, University of Kassel, Heinrich-Plett-Str. 40, 34132, Kassel, Germany
| | - Ulrich Kutschera
- Institute of Biology, University of Kassel, Heinrich-Plett-Str. 40, 34132, Kassel, Germany.
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Moubayidin L, Østergaard L. Gynoecium formation: an intimate and complicated relationship. Curr Opin Genet Dev 2017; 45:15-21. [DOI: 10.1016/j.gde.2017.02.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 02/07/2017] [Accepted: 02/09/2017] [Indexed: 02/02/2023]
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Kushwah S, Laxmi A. The interaction between glucose and cytokinin signaling in controlling Arabidopsis thaliana seedling root growth and development. PLANT SIGNALING & BEHAVIOR 2017; 12:e1312241. [PMID: 28467152 PMCID: PMC5501229 DOI: 10.1080/15592324.2017.1312241] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Cytokinin (CK) and glucose (GLC) control several common responses in plants. There is an extensive overlap between CK and GLC signal transduction pathways in Arabidopsis. Physiologically, both GLC and CK could regulate root length in light. CK interacts with GLC via HXK1 dependent pathway for root length control. Wild-type (WT) roots cannot elongate in the GLC free medium while CK-receptor mutant ARABIDOPSIS HISTIDINE KINASE4 (ahk4) and type B ARR triple mutant ARABIDOPSIS RESPONSE REGULATOR1, 10,11 (arr1, 10,11) roots could elongate even in the absence of GLC as compared with the WT. The root hair initiation was also found defective in CK signaling mutants ahk4, arr1,10,11 and arr3,4,5,6,8,9 on increasing GLC concentration (up to 3%); and lesser number of root hairs were visible even at 5% GLC as compared with the WT. Out of 941 BAP regulated genes, 103 (11%) genes were involved in root growth and development. Out of these 103 genes, 60 (58%) genes were also regulated by GLC. GLC could regulate 5736 genes, which include 327 (6%) genes involved in root growth and development. Out of these 327 genes, 60 (18%) genes were also regulated by BAP. Both GLC and CK signaling cannot alter root length in light in auxin signaling mutant AUXIN RESPONSE3/INDOLE-3-ACETIC ACID17 (axr3/iaa17) suggesting that they may involve auxin signaling component as a nodal point. Therefore CK- and GLC- signaling are involved in controlling different aspects of root growth and development such as root length, with auxin signaling components working as downstream target.
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Affiliation(s)
- Sunita Kushwah
- National Institute of Plant Genome Research, New Delhi, India
| | - Ashverya Laxmi
- National Institute of Plant Genome Research, New Delhi, India
- CONTACT Ashverya Laxmi National Institute of Plant Genome Research, Aruna Asaf Ali Road, New Delhi-110067, India
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41
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Bruno L, Pacenza M, Forgione I, Lamerton LR, Greco M, Chiappetta A, Bitonti MB. In Arabidopsis thaliana Cadmium Impact on the Growth of Primary Root by Altering SCR Expression and Auxin-Cytokinin Cross-Talk. FRONTIERS IN PLANT SCIENCE 2017; 8:1323. [PMID: 28798767 PMCID: PMC5529362 DOI: 10.3389/fpls.2017.01323] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 07/14/2017] [Indexed: 05/21/2023]
Abstract
Cadmium is one of the most widespread pollutant in both terrestrial and marine environment, and its inhibitory effect on plant growth has been largely demonstrated. However, the molecular mechanisms underlying Cd toxicity in plant and mainly in root, as the first organ sensing soil heavy metals, need to be better investigated. To this aim, in the present work we analyzed the growth and the organization of Arabidopsis thaliana primary root in seedlings exposed to Cd (25 and 50 μM) for 8 days starting from germination. Root length, root meristem size, and organization were evaluated together with the behavior of some of the major molecular players in root growth and patterning. In particular, by using different GFP transgenic lines, we monitored: (i) the expression pattern of WOX5 and SCR transcription factors involved in the establishment and maintenance of stem cell niche and in the control of meristem size; (ii) the expression pattern of the IAA-inducible pDR5::GFP reporter, PIN 1, 2, 3, 7 auxin carriers and TCSn::GFP cytokinin-sensitive sensor as relevant components of hormone circuit controlling root growth. We report that Cd exposure inhibits primary root growth via affecting RAM stem cell niche and root radial pattern. At the molecular level, an impairment of auxin maximum accumulation at the root tip, related to a down-regulation and mislocalisation of PIN proteins, and an enhancement of TCSn::GFP cytokinin-sensitive sensor signal is also detected under Cd treatment, thus suggesting an alteration in the homeostasis of auxin/cytokinin signaling. Moreover, and for the first time Cd toxicity on root growth and pattern has been related to a misexpression of SCR transcription factors which is known to interplay with auxin/cytokinin cross-talk in the control of RAM maintenance and activity.
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Affiliation(s)
- Leonardo Bruno
- Dipartimento di Biologia, Ecologia e Scienze della Terra, Università della CalabriaArcavacata di Rende, Italy
- *Correspondence: Leonardo Bruno,
| | - Marianna Pacenza
- Dipartimento di Biologia, Ecologia e Scienze della Terra, Università della CalabriaArcavacata di Rende, Italy
| | - Ivano Forgione
- Dipartimento di Biologia, Ecologia e Scienze della Terra, Università della CalabriaArcavacata di Rende, Italy
| | - Liam R. Lamerton
- Dipartimento di Biologia, Ecologia e Scienze della Terra, Università della CalabriaArcavacata di Rende, Italy
- School of Biosciences, University of CardiffCardiff, United Kingdom
| | - Maria Greco
- Dipartimento di Biologia, Ecologia e Scienze della Terra, Università della CalabriaArcavacata di Rende, Italy
| | - Adriana Chiappetta
- Dipartimento di Biologia, Ecologia e Scienze della Terra, Università della CalabriaArcavacata di Rende, Italy
| | - Maria B. Bitonti
- Dipartimento di Biologia, Ecologia e Scienze della Terra, Università della CalabriaArcavacata di Rende, Italy
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Birnbaum KD. How many ways are there to make a root? CURRENT OPINION IN PLANT BIOLOGY 2016; 34:61-67. [PMID: 27780106 DOI: 10.1016/j.pbi.2016.10.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2016] [Revised: 09/27/2016] [Accepted: 10/03/2016] [Indexed: 05/11/2023]
Abstract
Plants often make the same organ in different development contexts. Roots are a quintessential example, with embryonic, primary, lateral, adventitious, and regenerative roots common to many plants. The cellular origins and early morphologies of different roots can vary greatly, but the adult structures can be remarkably similar. Recent studies have highlighted the diversity of mechanisms that can initiate roots while late patterning mechanisms are frequently shared. In the middle stages when patterning emerges, evidence shows that antagonistic auxin-cytokinin interactions regulate tissue patterns in root embryogenesis, vascular organization, and regeneration but it is not yet clear if a common ontogeny for the root body plan exists.
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Affiliation(s)
- Kenneth D Birnbaum
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York 10003, USA.
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Koevoets IT, Venema JH, Elzenga JTM, Testerink C. Roots Withstanding their Environment: Exploiting Root System Architecture Responses to Abiotic Stress to Improve Crop Tolerance. FRONTIERS IN PLANT SCIENCE 2016; 7:1335. [PMID: 27630659 PMCID: PMC5005332 DOI: 10.3389/fpls.2016.01335] [Citation(s) in RCA: 194] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 08/18/2016] [Indexed: 05/18/2023]
Abstract
To face future challenges in crop production dictated by global climate changes, breeders and plant researchers collaborate to develop productive crops that are able to withstand a wide range of biotic and abiotic stresses. However, crop selection is often focused on shoot performance alone, as observation of root properties is more complex and asks for artificial and extensive phenotyping platforms. In addition, most root research focuses on development, while a direct link to the functionality of plasticity in root development for tolerance is often lacking. In this paper we review the currently known root system architecture (RSA) responses in Arabidopsis and a number of crop species to a range of abiotic stresses, including nutrient limitation, drought, salinity, flooding, and extreme temperatures. For each of these stresses, the key molecular and cellular mechanisms underlying the RSA response are highlighted. To explore the relevance for crop selection, we especially review and discuss studies linking root architectural responses to stress tolerance. This will provide a first step toward understanding the relevance of adaptive root development for a plant's response to its environment. We suggest that functional evidence on the role of root plasticity will support breeders in their efforts to include root properties in their current selection pipeline for abiotic stress tolerance, aimed to improve the robustness of crops.
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Affiliation(s)
- Iko T. Koevoets
- Swammerdam Institute for Life Sciences, Plant Cell Biology, University of AmsterdamAmsterdam, Netherlands
| | - Jan Henk Venema
- Genomics Research in Ecology and Evolution in Nature – Plant Physiology, Groningen Institute for Evolutionary Life Sciences, University of GroningenGroningen, Netherlands
| | - J. Theo. M. Elzenga
- Genomics Research in Ecology and Evolution in Nature – Plant Physiology, Groningen Institute for Evolutionary Life Sciences, University of GroningenGroningen, Netherlands
| | - Christa Testerink
- Swammerdam Institute for Life Sciences, Plant Cell Biology, University of AmsterdamAmsterdam, Netherlands
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Aceves-García P, Álvarez-Buylla ER, Garay-Arroyo A, García-Ponce B, Muñoz R, Sánchez MDLP. Root Architecture Diversity and Meristem Dynamics in Different Populations of Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2016; 7:858. [PMID: 27379140 PMCID: PMC4910468 DOI: 10.3389/fpls.2016.00858] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 05/31/2016] [Indexed: 05/26/2023]
Abstract
Arabidopsis thaliana has been an excellent model system for molecular genetic approaches to development and physiology. More recently, the potential of studying various accessions collected from diverse habitats has been started to exploit. Col-0 has been the best-studied accession but we now know that several traits show significant divergences among them. In this work, we focused in the root that has become a key system for development. We studied root architecture and growth dynamics of 12 Arabidopsis accessions. Our data reveal a wide variability in root architecture and root length among accessions. We also found variability in the root apical meristem (RAM), explained mainly by cell size at the RAM transition domain and possibly by peculiar forms of organization at the stem cell niche in some accessions. Contrary to Col-0 reports, in some accessions the RAM size not always explains the variations in the root length; indicating that elongated cell size could be more relevant in the determination of root length than the RAM size itself. This study contributes to investigations dealing with understanding the molecular and cellular basis of phenotypic variation, the role of plasticity on adaptation, and the developmental mechanisms that may restrict phenotypic variation in response to contrasting environmental conditions.
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Affiliation(s)
- Pamela Aceves-García
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, MéxicoMexico
| | - Elena R. Álvarez-Buylla
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, MéxicoMexico
| | - Adriana Garay-Arroyo
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, MéxicoMexico
| | - Berenice García-Ponce
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, MéxicoMexico
| | - Rodrigo Muñoz
- Departamento de Ecología y Recursos Naturales, Facultad de Ciencias, Universidad Nacional Autónoma de México, MéxicoMexico
| | - María de la Paz Sánchez
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, MéxicoMexico
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Della Rovere F, Fattorini L, Ronzan M, Falasca G, Altamura MM. The quiescent center and the stem cell niche in the adventitious roots of Arabidopsis thaliana. PLANT SIGNALING & BEHAVIOR 2016; 11:e1176660. [PMID: 27089118 PMCID: PMC4973785 DOI: 10.1080/15592324.2016.1176660] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Adventitious rooting is essential for the survival of numerous species from vascular cryptogams to monocots, and is required for successful micropropagation. The tissues involved in AR initiation may differ in planta and in in vitro systems. For example, in Arabidopsis thaliana, ARs originate from the hypocotyl pericycle in planta and the stem endodermis in in vitro cultured thin cell layers. The formation of adventitious roots (ARs) depends on numerous factors, among which the hormones, auxin, in particular. In both primary and lateral roots, growth depends on a functional stem cell niche in the apex, maintained by an active quiescent center (QC), and involving the expression of genes controlled by auxin and cytokinin. This review summarizes current knowledge about auxin and cytokinin control on genes involved in the definition and maintenance of QC, and stem cell niche, in the apex of Arabidopsis ARs in planta and in longitudinal thin cell layers.
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Affiliation(s)
- Federica Della Rovere
- Department of Environmental Biology, Sapienza University of Rome, P.le Aldo Moro, Rome, Italy
| | - Laura Fattorini
- Department of Environmental Biology, Sapienza University of Rome, P.le Aldo Moro, Rome, Italy
| | - Marilena Ronzan
- Department of Environmental Biology, Sapienza University of Rome, P.le Aldo Moro, Rome, Italy
| | - Giuseppina Falasca
- Department of Environmental Biology, Sapienza University of Rome, P.le Aldo Moro, Rome, Italy
| | - Maria Maddalena Altamura
- Department of Environmental Biology, Sapienza University of Rome, P.le Aldo Moro, Rome, Italy
- Maria Maddalena Altamura
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