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Méndez T, Guajardo J, Cruz N, Gutiérrez RA, Norambuena L, Vega A, Moya-León MA, Herrera R. The Characterization of a Novel PrMADS11 Transcription Factor from Pinus radiata Induced Early in Bent Pine Stem. Int J Mol Sci 2024; 25:7245. [PMID: 39000352 PMCID: PMC11241540 DOI: 10.3390/ijms25137245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 06/19/2024] [Accepted: 06/21/2024] [Indexed: 07/16/2024] Open
Abstract
A novel MADS-box transcription factor from Pinus radiata D. Don was characterized. PrMADS11 encodes a protein of 165 amino acids for a MADS-box transcription factor belonging to group II, related to the MIKC protein structure. PrMADS11 was differentially expressed in the stems of pine trees in response to 45° inclination at early times (1 h). Arabidopsis thaliana was stably transformed with a 35S::PrMADS11 construct in an effort to identify the putative targets of PrMADS11. A massive transcriptome analysis revealed 947 differentially expressed genes: 498 genes were up-regulated, and 449 genes were down-regulated due to the over-expression of PrMADS11. The gene ontology analysis highlighted a cell wall remodeling function among the differentially expressed genes, suggesting the active participation of cell wall modification required during the response to vertical stem loss. In addition, the phenylpropanoid pathway was also indicated as a PrMADS11 target, displaying a marked increment in the expression of the genes driven to the biosynthesis of monolignols. The EMSA assays confirmed that PrMADS11 interacts with CArG-box sequences. This TF modulates the gene expression of several molecular pathways, including other TFs, as well as the genes involved in cell wall remodeling. The increment in the lignin content and the genes involved in cell wall dynamics could be an indication of the key role of PrMADS11 in the response to trunk inclination.
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Affiliation(s)
- Tamara Méndez
- Instituto de Ciencias Biológicas, Universidad de Talca, Av. Lircay s/n, Talca 3465548, Chile; (T.M.); (J.G.); (M.A.M.-L.)
| | - Joselin Guajardo
- Instituto de Ciencias Biológicas, Universidad de Talca, Av. Lircay s/n, Talca 3465548, Chile; (T.M.); (J.G.); (M.A.M.-L.)
| | - Nicolás Cruz
- Facultad de Ciencias Agrarias y Forestales, Universidad Técnica Estatal de Quevedo, Quevedo 120313, Ecuador;
| | - Rodrigo A. Gutiérrez
- Millennium Institute Center for Genome Regulation, Millennium Institute for Integrative Biology, Instituto de Ecología y Biodiversidad, Facultad Ciencias Biológicas, P. Universidad Católica de Chile, Avda, Libertador Bernardo O’Higgins 340, Santiago 8331150, Chile;
| | - Lorena Norambuena
- Plant Molecular Biology Centre, Department of Biology, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Santiago 7750000, Chile;
| | - Andrea Vega
- Facultad de Ingeniería y Ciencias, Universidad Adolfo Ibáñez, Peñalolen 7940000, Chile;
| | - María A. Moya-León
- Instituto de Ciencias Biológicas, Universidad de Talca, Av. Lircay s/n, Talca 3465548, Chile; (T.M.); (J.G.); (M.A.M.-L.)
| | - Raúl Herrera
- Instituto de Ciencias Biológicas, Universidad de Talca, Av. Lircay s/n, Talca 3465548, Chile; (T.M.); (J.G.); (M.A.M.-L.)
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Alrajhi A, Alharbi S, Beecham S, Alotaibi F. Regulation of root growth and elongation in wheat. FRONTIERS IN PLANT SCIENCE 2024; 15:1397337. [PMID: 38835859 PMCID: PMC11148372 DOI: 10.3389/fpls.2024.1397337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Accepted: 05/06/2024] [Indexed: 06/06/2024]
Abstract
Currently, the control of rhizosphere selection on farms has been applied to achieve enhancements in phenotype, extending from improvements in single root characteristics to the dynamic nature of entire crop systems. Several specific signals, regulatory elements, and mechanisms that regulate the initiation, morphogenesis, and growth of new lateral or adventitious root species have been identified, but much more work remains. Today, phenotyping technology drives the development of root traits. Available models for simulation can support all phenotyping decisions (root trait improvement). The detection and use of markers for quantitative trait loci (QTLs) are effective for enhancing selection efficiency and increasing reproductive genetic gains. Furthermore, QTLs may help wheat breeders select the appropriate roots for efficient nutrient acquisition. Single-nucleotide polymorphisms (SNPs) or alignment of sequences can only be helpful when they are associated with phenotypic variation for root development and elongation. Here, we focus on major root development processes and detail important new insights recently generated regarding the wheat genome. The first part of this review paper discusses the root morphology, apical meristem, transcriptional control, auxin distribution, phenotyping of the root system, and simulation models. In the second part, the molecular genetics of the wheat root system, SNPs, TFs, and QTLs related to root development as well as genome editing (GE) techniques for the improvement of root traits in wheat are discussed. Finally, we address the effect of omics strategies on root biomass production and summarize existing knowledge of the main molecular mechanisms involved in wheat root development and elongation.
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Affiliation(s)
- Abdullah Alrajhi
- King Abdulaziz City for Science and Technology (KACST), Riyadh, Saudi Arabia
- Sustainable Infrastructure and Resource Management, University of South Australia, University of South Australia Science, Technology, Engineering, and Mathematics (UniSA STEM), Mawson Lakes, SA, Australia
| | - Saif Alharbi
- The National Research and Development Center for Sustainable Agriculture (Estidamah), Riyadh, Saudi Arabia
| | - Simon Beecham
- Sustainable Infrastructure and Resource Management, University of South Australia, University of South Australia Science, Technology, Engineering, and Mathematics (UniSA STEM), Mawson Lakes, SA, Australia
| | - Fahad Alotaibi
- King Abdulaziz City for Science and Technology (KACST), Riyadh, Saudi Arabia
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Aluko OO, Kant S, Adedire OM, Li C, Yuan G, Liu H, Wang Q. Unlocking the potentials of nitrate transporters at improving plant nitrogen use efficiency. FRONTIERS IN PLANT SCIENCE 2023; 14:1074839. [PMID: 36895876 PMCID: PMC9989036 DOI: 10.3389/fpls.2023.1074839] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 01/16/2023] [Indexed: 05/27/2023]
Abstract
Nitrate ( NO 3 - ) transporters have been identified as the primary targets involved in plant nitrogen (N) uptake, transport, assimilation, and remobilization, all of which are key determinants of nitrogen use efficiency (NUE). However, less attention has been directed toward the influence of plant nutrients and environmental cues on the expression and activities of NO 3 - transporters. To better understand how these transporters function in improving plant NUE, this review critically examined the roles of NO 3 - transporters in N uptake, transport, and distribution processes. It also described their influence on crop productivity and NUE, especially when co-expressed with other transcription factors, and discussed these transporters' functional roles in helping plants cope with adverse environmental conditions. We equally established the possible impacts of NO 3 - transporters on the uptake and utilization efficiency of other plant nutrients while suggesting possible strategic approaches to improving NUE in plants. Understanding the specificity of these determinants is crucial to achieving better N utilization efficiency in crops within a given environment.
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Affiliation(s)
- Oluwaseun Olayemi Aluko
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
- Graduate School of Chinese Academy of Agricultural Sciences, Beijing, China
| | - Surya Kant
- Agriculture Victoria, Grains Innovation Park, Horsham, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| | | | - Chuanzong Li
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
- Graduate School of Chinese Academy of Agricultural Sciences, Beijing, China
| | - Guang Yuan
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
- Graduate School of Chinese Academy of Agricultural Sciences, Beijing, China
| | - Haobao Liu
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Qian Wang
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
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Wu X, Xie X, Yang S, Yin Q, Cao H, Dong X, Hui J, Liu Z, Jia Z, Mao C, Yuan L. OsAMT1;1 and OsAMT1;2 Coordinate Root Morphological and Physiological Responses to Ammonium for Efficient Nitrogen Foraging in Rice. PLANT & CELL PHYSIOLOGY 2022; 63:1309-1320. [PMID: 35861152 DOI: 10.1093/pcp/pcac104] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 06/28/2022] [Accepted: 07/20/2022] [Indexed: 06/15/2023]
Abstract
Optimal plant growth and development rely on morphological and physiological adaptions of the root system to forage heterogeneously distributed nitrogen (N) in soils. Rice grows mainly in the paddy soil where ammonium (NH4+) is present as the major N source. Although root NH4+ foraging behaviors are expected to be agronomically relevant, the underlying mechanism remains largely unknown. Here, we showed that NH4+ supply transiently enhanced the high-affinity NH4+ uptake and stimulated lateral root (LR) branching and elongation. These synergistic physiological and morphological responses were closely related to NH4+-induced expression of NH4+ transporters OsAMT1;1 and OsAMT1;2 in roots. The two independent double mutants (dko) defective in OsAMT1;1 and OsAMT1;2 failed to induce NH4+ uptake and stimulate LR formation, suggesting that OsAMT1s conferred the substrate-dependent root NH4+ foraging. In dko plants, NH4+ was unable to activate the expression of OsPIN2, and the OsPIN2 mutant (lra1) exhibited a strong reduction in NH4+-triggered LR branching, suggesting that the auxin pathway was likely involved in OsAMT1s-dependent LR branching. Importantly, OsAMT1s-dependent root NH4+ foraging behaviors facilitated rice growth and N acquisition under fluctuating NH4+ supply. These results revealed an essential role of OsAMT1s in synergizing root morphological and physiological processes, allowing for efficient root NH4+ foraging to optimize N capture under fluctuating N availabilities.
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Affiliation(s)
- Xiangyu Wu
- Key Laboratory of Plant-Soil Interactions, MOE, College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing 100193, China
| | - Xiaoxiao Xie
- Key Laboratory of Plant-Soil Interactions, MOE, College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing 100193, China
| | - Shan Yang
- Key Laboratory of Plant-Soil Interactions, MOE, College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing 100193, China
| | - Qianyu Yin
- Key Laboratory of Plant-Soil Interactions, MOE, College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing 100193, China
| | - Huairong Cao
- Key Laboratory of Plant-Soil Interactions, MOE, College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing 100193, China
| | - Xiaonan Dong
- Key Laboratory of Plant-Soil Interactions, MOE, College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing 100193, China
| | - Jing Hui
- Key Laboratory of Plant-Soil Interactions, MOE, College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing 100193, China
| | - Zhi Liu
- Key Laboratory of Plant-Soil Interactions, MOE, College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing 100193, China
| | - Zhongtao Jia
- Key Laboratory of Plant-Soil Interactions, MOE, College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing 100193, China
| | - Chuanzao Mao
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, No. 866 Yuhangtang Road, Xihu District, Hangzhou City, Zhejiang Province 310058, China
| | - Lixing Yuan
- Key Laboratory of Plant-Soil Interactions, MOE, College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing 100193, China
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Gao Y, Qi S, Wang Y. Nitrate signaling and use efficiency in crops. PLANT COMMUNICATIONS 2022; 3:100353. [PMID: 35754172 PMCID: PMC9483113 DOI: 10.1016/j.xplc.2022.100353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 06/06/2022] [Accepted: 06/23/2022] [Indexed: 06/15/2023]
Abstract
Nitrate (NO3-) is not only an essential nutrient but also an important signaling molecule for plant growth. Low nitrogen use efficiency (NUE) of crops is causing increasingly serious environmental and ecological problems. Understanding the molecular mechanisms of NO3- regulation in crops is crucial for NUE improvement in agriculture. During the last several years, significant progress has been made in understanding the regulation of NO3- signaling in crops, and some key NO3- signaling factors have been shown to play important roles in NO3- utilization. However, no detailed reviews have yet summarized these advances. Here, we focus mainly on recent advances in crop NO3- signaling, including short-term signaling, long-term signaling, and the impact of environmental factors. We also review the regulation of crop NUE by crucial genes involved in NO3- signaling. This review provides useful information for further research on NO3- signaling in crops and a theoretical basis for breeding new crop varieties with high NUE, which has great significance for sustainable agriculture.
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Affiliation(s)
- Yangyang Gao
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong 271018, China
| | - Shengdong Qi
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong 271018, China
| | - Yong Wang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong 271018, China.
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GWAS and Transcriptome Analysis Reveal Key Genes Affecting Root Growth under Low Nitrogen Supply in Maize. Genes (Basel) 2022; 13:genes13091632. [PMID: 36140800 PMCID: PMC9498817 DOI: 10.3390/genes13091632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/06/2022] [Accepted: 09/08/2022] [Indexed: 11/24/2022] Open
Abstract
Nitrogen (N) is one of the most important factors affecting crop production. Root morphology exhibits a high degree of plasticity to nitrogen deficiency. However, the mechanisms underlying the root foraging response under low-N conditions remain poorly understood. In this study, we analyzed 213 maize inbred lines using hydroponic systems and regarding their natural variations in 22 root traits and 6 shoot traits under normal (2 mM nitrate) and low-N (0 mM nitrate) conditions. Substantial phenotypic variations were detected for all traits. N deficiency increased the root length and decreased the root diameter and shoot related traits. A total of 297 significant marker-trait associations were identified by a genome-wide association study involving different N levels and the N response value. A total of 51 candidate genes with amino acid variations in coding regions or differentially expressed under low nitrogen conditions were identified. Furthermore, a candidate gene ZmNAC36 was resequenced in all tested lines. A total of 38 single nucleotide polymorphisms and 12 insertions and deletions were significantly associated with lateral root length of primary root, primary root length between 0 and 0.5 mm in diameter, primary root surface area, and total length of primary root under a low-N condition. These findings help us to improve our understanding of the genetic mechanism of root plasticity to N deficiency, and the identified loci and candidate genes will be useful for the genetic improvement of maize tolerance cultivars to N deficiency.
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zmm28 transgenic maize increases both N uptake- and N utilization-efficiencies. Commun Biol 2022; 5:555. [PMID: 35672405 PMCID: PMC9174173 DOI: 10.1038/s42003-022-03501-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 05/18/2022] [Indexed: 12/14/2022] Open
Abstract
Biotechnology has emerged as a valuable tool in the development of maize (Zea mays L.) hybrids with enhanced nitrogen (N) use efficiency. Recent work has described the positive effects of an increased and extended expression of the zmm28 transcription factor (Event DP202216) on maize yield productivity. In this study, we expand on the previous findings studying maize N uptake and utilization in DP202216 transgenic hybrids compared to wild-type (WT) controls. Isotope 15N labeling demonstrates that DP202216 hybrids have an improved N uptake during late-vegetative stages (inducing N storage in lower leaves of the canopy) and, thus, N uptake efficiency (N uptake to applied N ratio) relative to WT. Through both greater N harvest index and reproductive N remobilization, transgenic plants were able to achieve better N utilization efficiency (yield to N uptake ratio). Our findings suggest the DP202216 trait could open new avenues for improving N uptake and utilization efficiencies in maize.
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8
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Muktar MS, Habte E, Teshome A, Assefa Y, Negawo AT, Lee KW, Zhang J, Jones CS. Insights Into the Genetic Architecture of Complex Traits in Napier Grass ( Cenchrus purpureus) and QTL Regions Governing Forage Biomass Yield, Water Use Efficiency and Feed Quality Traits. FRONTIERS IN PLANT SCIENCE 2022; 12:678862. [PMID: 35069609 PMCID: PMC8776657 DOI: 10.3389/fpls.2021.678862] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 12/06/2021] [Indexed: 05/14/2023]
Abstract
Napier grass is the most important perennial tropical grass native to Sub-Saharan Africa and widely grown in tropical and subtropical regions around the world, primarily as a forage crop for animal feed, but with potential as an energy crop and in a wide range of other areas. Genomic resources have recently been developed for Napier grass that need to be deployed for genetic improvement and molecular dissection of important agro-morphological and feed quality traits. From a diverse set of Napier grass genotypes assembled from two independent collections, a subset of 84 genotypes (although a small population size, the genotypes were selected to best represent the genetic diversity of the collections) were selected and evaluated for 2 years in dry (DS) and wet (WS) seasons under three soil moisture conditions: moderate water stress in DS (DS-MWS); severe water stress in DS (DS-SWS) and, under rainfed (RF) conditions in WS (WS-RF). Data for agro-morphological and feed quality traits, adjusted for the spatial heterogeneity in the experimental blocks, were collected over a 2-year period from 2018 to 2020. A total of 135,706 molecular markers were filtered, after removing markers with missing values >10% and a minor allele frequency (MAF) <5%, from the high-density genome-wide markers generated previously using the genotyping by sequencing (GBS) method of the DArTseq platform. A genome-wide association study (GWAS), using two different mixed linear model algorithms implemented in the GAPIT R package, identified more than 35 QTL regions and markers associated with agronomic, morphological, and water-use efficiency traits. QTL regions governing purple pigmentation and feed quality traits were also identified. The identified markers will be useful in the genetic improvement of Napier grass through the application of marker-assisted selection and for further characterization and map-based cloning of the QTLs.
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Affiliation(s)
- Meki S. Muktar
- Feed and Forage Development, International Livestock Research Institute, Addis Ababa, Ethiopia
| | - Ermias Habte
- Feed and Forage Development, International Livestock Research Institute, Addis Ababa, Ethiopia
| | - Abel Teshome
- Feed and Forage Development, International Livestock Research Institute, Addis Ababa, Ethiopia
| | - Yilikal Assefa
- Feed and Forage Development, International Livestock Research Institute, Addis Ababa, Ethiopia
| | - Alemayehu T. Negawo
- Feed and Forage Development, International Livestock Research Institute, Addis Ababa, Ethiopia
| | - Ki-Won Lee
- Grassland and Forages Division, National Institute of Animal Science, Rural Development Administration, Cheonan, South Korea
| | - Jiyu Zhang
- State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Chris S. Jones
- Feed and Forage Development, International Livestock Research Institute, Nairobi, Kenya
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Jia Z, Giehl RFH, von Wirén N. Nutrient-hormone relations: Driving root plasticity in plants. MOLECULAR PLANT 2022; 15:86-103. [PMID: 34920172 DOI: 10.1016/j.molp.2021.12.004] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 12/04/2021] [Accepted: 12/14/2021] [Indexed: 05/25/2023]
Abstract
Optimal plant development requires root uptake of 14 essential mineral elements from the soil. Since the bioavailability of these nutrients underlies large variation in space and time, plants must dynamically adjust their root architecture to optimize nutrient access and acquisition. The information on external nutrient availability and whole-plant demand is translated into cellular signals that often involve phytohormones as intermediates to trigger a systemic or locally restricted developmental response. Timing and extent of such local root responses depend on the overall nutritional status of the plant that is transmitted from shoots to roots in the form of phytohormones or other systemic long-distance signals. The integration of these systemic and local signals then determines cell division or elongation rates in primary and lateral roots, the initiation, emergence, or elongation of lateral roots, as well as the formation of root hairs. Here, we review the cascades of nutrient-related sensing and signaling events that involve hormones and highlight nutrient-hormone relations that coordinate root developmental plasticity in plants.
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Affiliation(s)
- Zhongtao Jia
- Molecular Plant Nutrition, Department of Physiology & Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466 Stadt Seeland, OT Gatersleben, Germany
| | - Ricardo F H Giehl
- Molecular Plant Nutrition, Department of Physiology & Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466 Stadt Seeland, OT Gatersleben, Germany
| | - Nicolaus von Wirén
- Molecular Plant Nutrition, Department of Physiology & Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466 Stadt Seeland, OT Gatersleben, Germany.
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Zhao D, Chen Z, Xu L, Zhang L, Zou Q. Genome-Wide Analysis of the MADS-Box Gene Family in Maize: Gene Structure, Evolution, and Relationships. Genes (Basel) 2021; 12:genes12121956. [PMID: 34946905 PMCID: PMC8701013 DOI: 10.3390/genes12121956] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 11/24/2021] [Accepted: 12/02/2021] [Indexed: 12/24/2022] Open
Abstract
The MADS-box gene family is one of the largest families in plants and plays an important roles in floral development. The MADS-box family includes the SRF-like domain and K-box domain. It is considered that the MADS-box gene family encodes a DNA-binding domain that is generally related to transcription factors, and plays important roles in regulating floral development. Our study identified 211 MADS-box protein sequences in the Zea mays proteome and renamed all the genes based on the gene annotations. All the 211 MADS-box protein sequences were coded by 98 expressed genes. Phylogenetic analysis of the MADS-box genes showed that all the family members were categorized into five subfamilies: MIKC-type, Mα, Mβ, Mγ, and Mδ. Gene duplications are regarded as products of several types of errors during the period of DNA replication and reconstruction; in our study all the 98 MADS-box genes contained 22 pairs of segmentally duplicated events which were distributed on 10 chromosomes. We compared expression data in different tissues from the female spikelet, silk, pericarp aleurone, ear primordium, leaf zone, vegetative meristem, internode, endosperm crown, mature pollen, embryo, root cortex, secondary root, germination kernels, primary root, root elongation zone, and root meristem. According to analysis of gene ontology pathways, we found a total of 41 pathways in which MADS-box genes in maize are involved. All the studies we conducted provided an overview of MADS-box gene family members in maize and showed multiple functions as transcription factors. The related research of MADS-box domains has provided the theoretical basis of MADS-box domains for agricultural applications.
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Affiliation(s)
- Da Zhao
- School of Applied Chemistry and Biological Technology, Shenzhen Polytechnic, Shenzhen 518055, China; (D.Z.); (Z.C.); (L.Z.)
| | - Zheng Chen
- School of Applied Chemistry and Biological Technology, Shenzhen Polytechnic, Shenzhen 518055, China; (D.Z.); (Z.C.); (L.Z.)
| | - Lei Xu
- School of Electronic and Communication Engineering, Shenzhen Polytechnic, Shenzhen 518055, China
- Correspondence: (L.X.); (Q.Z.)
| | - Lijun Zhang
- School of Applied Chemistry and Biological Technology, Shenzhen Polytechnic, Shenzhen 518055, China; (D.Z.); (Z.C.); (L.Z.)
| | - Quan Zou
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu 610054, China
- Correspondence: (L.X.); (Q.Z.)
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Xu J, Wang X, Zhu H, Yu F. Maize Genotypes With Different Zinc Efficiency in Response to Low Zinc Stress and Heterogeneous Zinc Supply. FRONTIERS IN PLANT SCIENCE 2021; 12:736658. [PMID: 34691112 PMCID: PMC8531504 DOI: 10.3389/fpls.2021.736658] [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: 07/05/2021] [Accepted: 08/30/2021] [Indexed: 06/13/2023]
Abstract
All over the world, a common problem in the soil is the low content of available zinc (Zn), which is unevenly distributed and difficult to move. However, information on the foraging strategies of roots in response to heterogeneous Zn supply is still very limited. Few studies have analyzed the adaptability of maize inbred lines with different Zn efficiencies to different low Zn stress time lengths in maize. This study analyzed the effects of different time lengths of low Zn stress on various related traits in different inbred lines. In addition, morphological plasticity of roots and the response of Zn-related important gene iron-regulated transporter-like proteins (ZIPs) were studied via simulating the heterogeneity of Zn nutrition in the soil. In this report, when Zn deficiency stress duration was extended (from 14 to 21 days), under Zn-deficient supply (0.5 μM), Zn efficiency (ZE) based on shoot dry weight of Wu312 displayed no significant difference, and ZE for Ye478 was increased by 92.9%. Under longer-term Zn deficiency, shoot, and root dry weights of Ye478 were 6.5 and 2.1-fold higher than those of Wu312, respectively. Uneven Zn supply strongly inhibited the development of some root traits in the -Zn region. Difference in shoot dry weights between Wu312 and Ye478 was larger in T1 (1.97 times) than in T2 (1.53 times). Under heterogeneous condition of Zn supply, both the -Zn region and the +Zn region upregulated the expressions of ZmZIP3, ZmZIP4, ZmZIP5, ZmZIP7, and ZmZIP8 in the roots of two inbred lines. These results indicate that extended time length of low-Zn stress will enlarge the difference of multiple physiological traits, especially biomass, between Zn-sensitive and Zn-tolerant inbred lines. There were significant genotypic differences of root morphology in response to heterogeneous Zn supply. Compared with split-supply with +Zn/+Zn, the difference of above-ground biomass between Zn-sensitive and Zn-tolerant inbred lines under split-supply with -Zn/+Zn was higher. Under the condition of heterogeneous Zn supply, several ZmZIP genes may play important roles in tolerance to low Zn stress, which can provide a basis for further functional characterization.
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Local auxin biosynthesis acts downstream of brassinosteroids to trigger root foraging for nitrogen. Nat Commun 2021; 12:5437. [PMID: 34521826 PMCID: PMC8440578 DOI: 10.1038/s41467-021-25250-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 07/29/2021] [Indexed: 12/31/2022] Open
Abstract
Lateral roots (LRs) dominate the overall root surface of adult plants and are crucial for soil exploration and nutrient acquisition. When grown under mild nitrogen (N) deficiency, flowering plants develop longer LRs to enhance nutrient acquisition. This response is partly mediated by brassinosteroids (BR) and yet unknown mechanisms. Here, we show that local auxin biosynthesis modulates LR elongation while allelic coding variants of YUCCA8 determine the extent of elongation under N deficiency. By up-regulating the expression of YUCCA8/3/5/7 and of Tryptophan Aminotransferase of Arabidopsis 1 (TAA1) under mild N deficiency auxin accumulation increases in LR tips. We further demonstrate that N-dependent auxin biosynthesis in LRs acts epistatic to and downstream of a canonical BR signaling cascade. The uncovered BR-auxin hormonal module and its allelic variants emphasize the importance of fine-tuning hormonal crosstalk to boost adaptive root responses to N availability and offer a path to improve soil exploration by expanded root systems in plants.
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Xia Y, Xue B, Shi M, Zhan F, Wu D, Jing D, Wang S, Guo Q, Liang G, He Q. Comparative transcriptome analysis of flower bud transition and functional characterization of EjAGL17 involved in regulating floral initiation in loquat. PLoS One 2020; 15:e0239382. [PMID: 33031442 PMCID: PMC7544058 DOI: 10.1371/journal.pone.0239382] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 09/08/2020] [Indexed: 11/18/2022] Open
Abstract
Floral initiation plays a critical role for reproductive success in plants, especially fruit trees. However, little information is known on the mechanism of the initiation in loquat (Eriobotrya japonica Lindl.). Here, we used transcriptomic, expression and functional analysis to investigate the candidate genes in floral initiation in loquat. Comparative transcriptome analysis showed differentially expressed genes (DEGs) were mainly enriched in the metabolic pathways of plant hormone signal transduction. The DEGs were mainly involved in the gibberellin, auxin, cytokinin, abscisic acid, salicylic acid and ethylene signaling pathways. Meanwhile, some transcription factors, including MADS-box (MCM1, AGAMOUS, DEFICIENS and SRF), MYB (Myeloblastosis), TCP (TEOSINTE BRANCHED 1, CYCLOIDEA and PCF1), WOX (WUSCHEL-related homeobox) and WRKY (WRKY DNA-binding protein), were significantly differentially expressed. Among these key DEGs, we confirmed that an AGL17 ortholog EjAGL17 was significantly upregulated at the flower bud transition stage. Phylogenetic tree analysis revealed that EjAGL17 was grouped into an AGL17 clade of MADS-box transcription factors. Protein sequence alignment showed that EjAGL17 included a distinctive C-terminal domain. Subcellular localization of EjAGL17 was found only in the nucleus. Expression levels of EjAGL17 reached the highest at the development stage of flower bud transition. Moreover, ectopic expression of EjAGL17 in Arabidopsis significantly exhibited early flowering. Our study provides abundant resources of candidate genes for studying the mechanisms underlying the floral initiation in loquat and other Rosaceae species.
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Affiliation(s)
- Yan Xia
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing, China
- Academy of Agricultural Sciences of Southwest University, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Beibei, Chongqing, China
| | - Baogui Xue
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing, China
- Academy of Agricultural Sciences of Southwest University, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Beibei, Chongqing, China
| | - Min Shi
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing, China
- Academy of Agricultural Sciences of Southwest University, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Beibei, Chongqing, China
| | - Feng Zhan
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing, China
| | - Di Wu
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing, China
- Academy of Agricultural Sciences of Southwest University, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Beibei, Chongqing, China
| | - Danlong Jing
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing, China
- Academy of Agricultural Sciences of Southwest University, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Beibei, Chongqing, China
| | - Shuming Wang
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing, China
- Academy of Agricultural Sciences of Southwest University, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Beibei, Chongqing, China
| | - Qigao Guo
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing, China
- Academy of Agricultural Sciences of Southwest University, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Beibei, Chongqing, China
| | - Guolu Liang
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing, China
- Academy of Agricultural Sciences of Southwest University, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Beibei, Chongqing, China
- * E-mail: (GL); (QH)
| | - Qiao He
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing, China
- Academy of Agricultural Sciences of Southwest University, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Beibei, Chongqing, China
- * E-mail: (GL); (QH)
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Xu G, Takahashi H. Improving nitrogen use efficiency: from cells to plant systems. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:4359-4364. [PMID: 32710784 DOI: 10.1093/jxb/eraa309] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Affiliation(s)
- Guohua Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
- China MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Nanjing, China
| | - Hideki Takahashi
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, USA
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Jia Z, Giehl RFH, von Wirén N. The Root Foraging Response under Low Nitrogen Depends on DWARF1-Mediated Brassinosteroid Biosynthesis. PLANT PHYSIOLOGY 2020; 183:998-1010. [PMID: 32398320 PMCID: PMC7333712 DOI: 10.1104/pp.20.00440] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 04/30/2020] [Indexed: 05/04/2023]
Abstract
Root developmental plasticity enables plants to adapt to limiting or fluctuating nutrient conditions in the soil. When grown under nitrogen (N) deficiency, plants develop a more exploratory root system by increasing primary and lateral root length. However, mechanisms underlying this so-called foraging response remain poorly understood. We performed a genome-wide association study in Arabidopsis (Arabidopsis thaliana) and we show here that noncoding variations of the brassinosteroid (BR) biosynthesis gene DWARF1 (DWF1) lead to variation of the DWF1 transcript level that contributes to natural variation of root elongation under low N. In addition to DWF1, other central BR biosynthesis genes upregulated under low N include CONSTITUTIVE PHOTOMORPHOGENIC DWARF, DWF4, and BRASSINOSTEROID-6-OXIDASE 2 Phenotypic characterization of knockout and knockdown mutants of these genes showed significant reduction of their root elongation response to low N, suggesting a systemic stimulation of BR biosynthesis to promote root elongation. Moreover, we show that low N-induced root elongation is associated with aboveground N content and that overexpression of DWF1 significantly improves plant growth and overall N accumulation. Our study reveals that mild N deficiency induces key genes in BR biosynthesis and that natural variation in BR synthesis contributes to the root foraging response, complementing the impact of enhanced BR signaling observed recently. Furthermore, these results suggest a considerable potential of BR biosynthesis to genetically engineer plants with improved N uptake.
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Affiliation(s)
- Zhongtao Jia
- Molecular Plant Nutrition, Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research, 06466 Gatersleben, Germany
| | - Ricardo F H Giehl
- Molecular Plant Nutrition, Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research, 06466 Gatersleben, Germany
| | - Nicolaus von Wirén
- Molecular Plant Nutrition, Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research, 06466 Gatersleben, Germany
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