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Shen D, Wippel K, Remmel S, Zhang Y, Kuertoes N, Neumann U, Kopriva S, Andersen TG. The Arabidopsis SGN3/GSO1 receptor kinase integrates soil nitrogen status into shoot development. EMBO J 2024:10.1038/s44318-024-00107-3. [PMID: 38698215 DOI: 10.1038/s44318-024-00107-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 03/18/2024] [Accepted: 04/04/2024] [Indexed: 05/05/2024] Open
Abstract
The Casparian strip is a barrier in the endodermal cell walls of plants that allows the selective uptake of nutrients and water. In the model plant Arabidopsis thaliana, its development and establishment are under the control of a receptor-ligand mechanism termed the Schengen pathway. This pathway facilitates barrier formation and activates downstream compensatory responses in case of dysfunction. However, due to a very tight functional association with the Casparian strip, other potential signaling functions of the Schengen pathway remain obscure. In this work, we created a MYB36-dependent synthetic positive feedback loop that drives Casparian strip formation independently of Schengen-induced signaling. We evaluated this by subjecting plants in which the Schengen pathway has been uncoupled from barrier formation, as well as a number of established barrier-mutant plants, to agar-based and soil conditions that mimic agricultural settings. Under the latter conditions, the Schengen pathway is necessary for the establishment of nitrogen-deficiency responses in shoots. These data highlight Schengen signaling as an essential hub for the adaptive integration of signaling from the rhizosphere to aboveground tissues.
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Affiliation(s)
- Defeng Shen
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
| | - Kathrin Wippel
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Cologne, Germany
- Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098XH, Amsterdam, The Netherlands
| | - Simone Remmel
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
| | - Yuanyuan Zhang
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
| | - Noah Kuertoes
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
| | - Ulla Neumann
- Central Microscopy, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
| | - Stanislav Kopriva
- Cluster of Excellence on Plant Sciences (CEPLAS), Cologne, Germany
- Institute for Plant Sciences, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | - Tonni Grube Andersen
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany.
- Cluster of Excellence on Plant Sciences (CEPLAS), Cologne, Germany.
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Mandal SN, Sanchez J, Bhowmick R, Bello OR, Van-Beek CR, de Los Reyes BG. Novel genes and alleles of the BTB/POZ protein family in Oryza rufipogon. Sci Rep 2023; 13:15466. [PMID: 37726366 PMCID: PMC10509276 DOI: 10.1038/s41598-023-41269-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 08/24/2023] [Indexed: 09/21/2023] Open
Abstract
The BTB/POZ family of proteins is widespread in plants and animals, playing important roles in development, growth, metabolism, and environmental responses. Although members of the expanded BTB/POZ gene family (OsBTB) have been identified in cultivated rice (Oryza sativa), their conservation, novelty, and potential applications for allele mining in O. rufipogon, the direct progenitor of O. sativa ssp. japonica and potential wide-introgression donor, are yet to be explored. This study describes an analysis of 110 BTB/POZ encoding gene loci (OrBTB) across the genome of O. rufipogon as outcomes of tandem duplication events. Phylogenetic grouping of duplicated OrBTB genes was supported by the analysis of gene sequences and protein domain architecture, shedding some light on their evolution and functional divergence. The O. rufipogon genome encodes nine novel BTB/POZ genes with orthologs in its distant cousins in the family Poaceae (Sorghum bicolor, Brachypodium distachyon), but such orthologs appeared to have been lost in its domesticated descendant, O. sativa ssp. japonica. Comparative sequence analysis and structure comparisons of novel OrBTB genes revealed that diverged upstream regulatory sequences and regulon restructuring are the key features of the evolution of this large gene family. Novel genes from the wild progenitor serve as a reservoir of potential new alleles that can bring novel functions to cultivars when introgressed by wide hybridization. This study establishes a foundation for hypothesis-driven functional genomic studies and their applications for widening the genetic base of rice cultivars through the introgression of novel genes or alleles from the exotic gene pool.
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Affiliation(s)
- Swarupa Nanda Mandal
- Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, 79409, USA
| | - Jacobo Sanchez
- Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, 79409, USA
| | - Rakesh Bhowmick
- ICAR-Vivekananda Parvatiya Krishi Anusandhan Sansthan, Almora, Uttarakhand, 263601, India
| | - Oluwatobi R Bello
- Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, 79409, USA
| | - Coenraad R Van-Beek
- Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, 79409, USA
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Liao Z, Xia X, Zhang Z, Nong B, Guo H, Feng R, Chen C, Xiong F, Qiu Y, Li D, Yang X. Genome-wide association study using specific-locus amplified fragment sequencing identifies new genes influencing nitrogen use efficiency in rice landraces. FRONTIERS IN PLANT SCIENCE 2023; 14:1126254. [PMID: 37521918 PMCID: PMC10375723 DOI: 10.3389/fpls.2023.1126254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Accepted: 04/28/2023] [Indexed: 08/01/2023]
Abstract
Nitrogen is essential for crop production. It is a critical macronutrient for plant growth and development. However, excessive application of nitrogen fertilizer is not only a waste of resources but also pollutes the environment. An effective approach to solving this problem is to breed rice varieties with high nitrogen use efficiency (NUE). In this study, we performed a genome-wide association study (GWAS) on 419 rice landraces using 208,993 single nucleotide polymorphisms (SNPs). With the mixed linear model (MLM) in the Tassel software, we identified 834 SNPs associated with root surface area (RSA), root length (RL), root branch number (RBN), root number (RN), plant dry weight (PDW), plant height (PH), root volume (RL), plant fresh weight (PFW), root fractal dimension (RFD), number of root nodes (NRN), and average root diameter (ARD), with a significant level of p < 2.39×10-7. In addition, we found 49 SNPs that were correlated with RL, RBN, RN, PDW, PH, PFW, RFD, and NRN using genome-wide efficient mixed-model association (GEMMA), with a significant level of p < 1×10-6. Additionally, the final results for eight traits associated with 193 significant SNPs by using multi-locus random-SNP-effect mixed linear model (mrMLM) model and 272 significant SNPs associated with 11 traits by using IIIVmrMLM. Within the linkage intervals of significantly associated SNP, we identified eight known related genes to NUE in rice, namely, OsAMT2;3, OsGS1, OsNR2, OsNPF7.4, OsPTR9, OsNRT1.1B, OsNRT2.3, and OsNRT2.2. According to the linkage disequilibrium (LD) decay value of this population, there were 75 candidate genes within the 150-kb regions upstream and downstream of the most significantly associated SNP (Chr5_29804690, Chr5_29956584, and Chr10_17540654). These candidate genes included 22 transposon genes, 25 expressed genes, and 28 putative functional genes. The expression levels of these candidate genes were measured by real-time quantitative PCR (RT-qPCR), and the expression levels of LOC_Os05g51700 and LOC_Os05g51710 in C347 were significantly lower than that in C117; the expression levels of LOC_Os05g51740, LOC_Os05g51780, LOC_Os05g51960, LOC_Os05g51970, and LOC_Os10g33210 were significantly higher in C347 than C117. Among them, LOC_Os10g33210 encodes a peptide transporter, and LOC_Os05g51690 encodes a CCT domain protein and responds to NUE in rice. This study identified new loci related to NUE in rice, providing new genetic resources for the molecular breeding of rice landraces with high NUE.
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Affiliation(s)
- Zuyu Liao
- College of Agriculture, Guangxi University, Nanning, China
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Xiuzhong Xia
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Zongqiong Zhang
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Baoxuan Nong
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Hui Guo
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Rui Feng
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Can Chen
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Faqian Xiong
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Yongfu Qiu
- College of Agriculture, Guangxi University, Nanning, China
| | - Danting Li
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Xinghai Yang
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
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4
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Li P, Du R, Li Z, Chen Z, Li J, Du H. An integrated nitrogen utilization gene network and transcriptome analysis reveal candidate genes in response to nitrogen deficiency in Brassica napus. FRONTIERS IN PLANT SCIENCE 2023; 14:1187552. [PMID: 37229128 PMCID: PMC10203523 DOI: 10.3389/fpls.2023.1187552] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 04/21/2023] [Indexed: 05/27/2023]
Abstract
Nitrogen (N) is an essential factor for crop yield. Here, we characterized 605 genes from 25 gene families that form the complex gene networks of N utilization pathway in Brassica napus. We found unequal gene distribution between the An- and Cn-sub-genomes, and that genes derived from Brassica rapa were more retained. Transcriptome analysis indicated that N utilization pathway gene activity shifted in a spatio-temporal manner in B. napus. A low N (LN) stress RNA-seq of B. napus seedling leaves and roots was generated, which proved that most N utilization related genes were sensitive to LN stress, thereby forming co-expression network modules. Nine candidate genes in N utilization pathway were confirmed to be significantly induced under N deficiency conditions in B. napus roots, indicating their potential roles in LN stress response process. Analyses of 22 representative species confirmed that the N utilization gene networks were widely present in plants ranging from Chlorophyta to angiosperms with a rapid expansion trend. Consistent with B. napus, the genes in this pathway commonly showed a wide and conserved expression profile in response to N stress in other plants. The network, genes, and gene-regulatory modules identified here represent resources that may enhance the N utilization efficiency or the LN tolerance of B. napus.
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Affiliation(s)
- Pengfeng Li
- College of Agronomy and Biotechnology, Chongqing Engineering Research Center for Rapeseed, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Runjie Du
- College of Agronomy and Biotechnology, Chongqing Engineering Research Center for Rapeseed, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Zhaopeng Li
- College of Agronomy and Biotechnology, Chongqing Engineering Research Center for Rapeseed, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Zhuo Chen
- College of Agronomy and Biotechnology, Chongqing Engineering Research Center for Rapeseed, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Jiana Li
- College of Agronomy and Biotechnology, Chongqing Engineering Research Center for Rapeseed, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Hai Du
- College of Agronomy and Biotechnology, Chongqing Engineering Research Center for Rapeseed, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
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5
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Das S, Singh D, Meena HS, Jha SK, Kumari J, Chinnusamy V, Sathee L. Long term nitrogen deficiency alters expression of miRNAs and alters nitrogen metabolism and root architecture in Indian dwarf wheat (Triticum sphaerococcum Perc.) genotypes. Sci Rep 2023; 13:5002. [PMID: 36973317 PMCID: PMC10043004 DOI: 10.1038/s41598-023-31278-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 03/09/2023] [Indexed: 03/29/2023] Open
Abstract
The important roles of plant microRNAs (miRNAs) in adaptation to nitrogen (N) deficiency in different crop species especially cereals (rice, wheat, maize) have been under discussion since last decade with little focus on potential wild relatives and landraces. Indian dwarf wheat (Triticum sphaerococcum Percival) is an important landrace native to the Indian subcontinent. Several unique features, especially high protein content and resistance to drought and yellow rust, make it a very potent landrace for breeding. Our aim in this study is to identify the contrasting Indian dwarf wheat genotypes based on nitrogen use efficiency (NUE) and nitrogen deficiency tolerance (NDT) traits and the associated miRNAs differentially expressed under N deficiency in selected genotypes. Eleven Indian dwarf wheat genotypes and a high NUE bread wheat genotype (for comparison) were evaluated for NUE under control and N deficit field conditions. Based on NUE, selected genotypes were further evaluated under hydroponics and miRNome was compared by miRNAseq under control and N deficit conditions. Among the identified, differentially expressed miRNAs in control and N starved seedlings, the target gene functions were associated with N metabolism, root development, secondary metabolism and cell-cycle associated pathways. The key findings on miRNA expression, changes in root architecture, root auxin abundance and changes in N metabolism reveal new information on the N deficiency response of Indian dwarf wheat and targets for genetic improvement of NUE.
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Affiliation(s)
- Samrat Das
- Division of Plant Physiology, ICAR-IARI, New Delhi, India
| | - Dalveer Singh
- Division of Plant Physiology, ICAR-IARI, New Delhi, India
| | - Hari S Meena
- Division of Plant Physiology, ICAR-IARI, New Delhi, India
| | | | - Jyoti Kumari
- Division of Germplasm Evaluation, ICAR-NBPGR, New Delhi, India
| | | | - Lekshmy Sathee
- Division of Plant Physiology, ICAR-IARI, New Delhi, India.
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6
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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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7
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Chattha MS, Ali Q, Haroon M, Afzal MJ, Javed T, Hussain S, Mahmood T, Solanki MK, Umar A, Abbas W, Nasar S, Schwartz-Lazaro LM, Zhou L. Enhancement of nitrogen use efficiency through agronomic and molecular based approaches in cotton. FRONTIERS IN PLANT SCIENCE 2022; 13:994306. [PMID: 36237509 PMCID: PMC9552886 DOI: 10.3389/fpls.2022.994306] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 08/22/2022] [Indexed: 05/22/2023]
Abstract
Cotton is a major fiber crop grown worldwide. Nitrogen (N) is an essential nutrient for cotton production and supports efficient crop production. It is a crucial nutrient that is required more than any other. Nitrogen management is a daunting task for plants; thus, various strategies, individually and collectively, have been adopted to improve its efficacy. The negative environmental impacts of excessive N application on cotton production have become harmful to consumers and growers. The 4R's of nutrient stewardship (right product, right rate, right time, and right place) is a newly developed agronomic practice that provides a solid foundation for achieving nitrogen use efficiency (NUE) in cotton production. Cropping systems are equally crucial for increasing production, profitability, environmental growth protection, and sustainability. This concept incorporates the right fertilizer source at the right rate, time, and place. In addition to agronomic practices, molecular approaches are equally important for improving cotton NUE. This could be achieved by increasing the efficacy of metabolic pathways at the cellular, organ, and structural levels and NUE-regulating enzymes and genes. This is a potential method to improve the role of N transporters in plants, resulting in better utilization and remobilization of N in cotton plants. Therefore, we suggest effective methods for accelerating NUE in cotton. This review aims to provide a detailed overview of agronomic and molecular approaches for improving NUE in cotton production, which benefits both the environment and growers.
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Affiliation(s)
- Muhammad Sohaib Chattha
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- School of Plant, Environmental and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA, United States
| | - Qurban Ali
- Laboratory of Integrated Management of Crop Diseases and Pests, Department of Plant Pathology, College of Plant Protection, Ministry of Education, Nanjing Agricultural University, Nanjing, China
| | - Muhammad Haroon
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | | | - Talha Javed
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Sadam Hussain
- Department of Agronomy, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Tahir Mahmood
- Department of Plant Breeding & Genetics, Pir Mehr Ali Shah Arid Agriculture University, Rawalpindi, Pakistan
| | - Manoj K. Solanki
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Aisha Umar
- Institute of Botany, University of the Punjab, Lahore, Pakistan
| | - Waseem Abbas
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Shanza Nasar
- Department of Botany, University of Gujrat Hafiz Hayat Campus, Gujrat, Pakistan
| | - Lauren M. Schwartz-Lazaro
- School of Plant, Environmental and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA, United States
| | - Lei Zhou
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
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Ahmad N, Ibrahim S, Tian Z, Kuang L, Wang X, Wang H, Dun X. Quantitative trait loci mapping reveals important genomic regions controlling root architecture and shoot biomass under nitrogen, phosphorus, and potassium stress in rapeseed ( Brassica napus L.). FRONTIERS IN PLANT SCIENCE 2022; 13:994666. [PMID: 36172562 PMCID: PMC9511887 DOI: 10.3389/fpls.2022.994666] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 08/15/2022] [Indexed: 06/16/2023]
Abstract
Plants rely on root systems for nutrient uptake from soils. Marker-assisted selection helps breeders to select desirable root traits for effective nutrient uptake. Here, 12 root and biomass traits were investigated at the seedling stage under low nitrogen (LN), low phosphorus (LP), and low potassium (LK) conditions, respectively, in a recombinant inbred line (RIL) population, which was generated from Brassica napus L. Zhongshuang11 and 4D122 with significant differences in root traits and nutrient efficiency. Significant differences for all the investigated traits were observed among RILs, with high heritabilities (0.43-0.74) and high correlations between the different treatments. Quantitative trait loci (QTL) mapping identified 57, 27, and 36 loci, explaining 4.1-10.9, 4.6-10.8, and 4.9-17.4% phenotypic variances under LN, LP, and LK, respectively. Through QTL-meta analysis, these loci were integrated into 18 significant QTL clusters. Four major QTL clusters involved 25 QTLs that could be repeatedly detected and explained more than 10% phenotypic variances, including two NPK-common and two specific QTL clusters (K and NK-specific), indicating their critical role in cooperative nutrients uptake of N, P, and K. Moreover, 264 genes within the four major QTL clusters having high expressions in roots and SNP/InDel variations between two parents were identified as potential candidate genes. Thirty-eight of them have been reported to be associated with root growth and development and/or nutrient stress tolerance. These key loci and candidate genes lay the foundation for deeper dissection of the NPK starvation response mechanisms in B. napus.
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Affiliation(s)
- Nazir Ahmad
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Wuhan, China
| | - Sani Ibrahim
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Wuhan, China
| | - Ze Tian
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Wuhan, China
| | - Lieqiong Kuang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Wuhan, China
| | - Xinfa Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Hanzhong Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Xiaoling Dun
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Wuhan, China
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9
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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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10
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Kang H, Zhang TT, Li YY, Lin-Wang K, Espley RV, Du YP, Guan QM, Ma FW, Hao YJ, You CX, Wang XF. The apple BTB protein MdBT2 positively regulates MdCOP1 abundance to repress anthocyanin biosynthesis. PLANT PHYSIOLOGY 2022; 190:305-318. [PMID: 35674376 PMCID: PMC9434159 DOI: 10.1093/plphys/kiac279] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 05/11/2022] [Indexed: 05/27/2023]
Abstract
The ubiquitin ligase CONSTITUTIVELY PHOTOMORPHOGENIC 1 (COP1) plays a central role in light-induced anthocyanin biosynthesis. However, the upstream regulatory factors of COP1 remain poorly understood, particularly in horticultural plants. Here, we identified an MdCOP1-interacting protein, BROAD-COMPLEX, TRAMTRACK AND BRIC A BRAC2 (MdBT2), in apple (Malus domestica). MdBT2 is a BTB protein that directly interacts with and stabilizes MdCOP1 by inhibiting self-ubiquitination. Fluorescence observation and cell fractionation assays showed that MdBT2 increased the abundance of MdCOP1 in the nucleus. Moreover, a series of phenotypic analyses indicated that MdBT2 promoted MdCOP1-mediated ubiquitination and degradation of the MdMYB1 transcription factor, inhibiting the expression of anthocyanin biosynthesis genes and anthocyanin accumulation. Overall, our findings reveal a molecular mechanism by which MdBT2 positively regulates MdCOP1, providing insight into MdCOP1-mediated anthocyanin biosynthesis.
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Affiliation(s)
- Hui Kang
- State Key Laboratory of Crop Biology, Shandong Collaborative Innovation Center for Fruit and Vegetable Production with High Quality and Efficiency, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong 271018, China
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yang-Ling, Shaanxi 712100, China
| | - Ting-Ting Zhang
- State Key Laboratory of Crop Biology, Shandong Collaborative Innovation Center for Fruit and Vegetable Production with High Quality and Efficiency, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong 271018, China
| | - Yuan-Yuan Li
- State Key Laboratory of Crop Biology, Shandong Collaborative Innovation Center for Fruit and Vegetable Production with High Quality and Efficiency, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong 271018, China
| | - Kui Lin-Wang
- The New Zealand Institute for Plant and Food Research Limited, Mt. Albert, Auckland 92169, New Zealand
| | - Richard V Espley
- The New Zealand Institute for Plant and Food Research Limited, Mt. Albert, Auckland 92169, New Zealand
| | - Yuan-Peng Du
- State Key Laboratory of Crop Biology, Shandong Collaborative Innovation Center for Fruit and Vegetable Production with High Quality and Efficiency, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong 271018, China
| | - Qing-Mei Guan
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yang-Ling, Shaanxi 712100, China
| | - Feng-Wang Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yang-Ling, Shaanxi 712100, China
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11
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Wen B, Gong X, Deng W, Chen X, Li D, Fu X, Li L, Tan Q. The apple GARP family gene MdHHO3 regulates the nitrate response and leaf senescence. FRONTIERS IN PLANT SCIENCE 2022; 13:932767. [PMID: 36017256 PMCID: PMC9398197 DOI: 10.3389/fpls.2022.932767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 07/19/2022] [Indexed: 06/15/2023]
Abstract
The regulation of plant gene expression by nitrate is a complex regulatory process. Here, we identified 90 GARP family genes in apples by genome-wide analysis. As a member of the GARP gene family, the expression of MdHHO3 (Malus domestica HYPERSENSITIVITY TO LOW PHOSPHATE-ELICITED PRIMARY ROOT SHORTENING1 HOMOLOG 3) is upregulated under N (nitrogen) supply. The results of DNA-binding site analysis and electrophoretic mobility shift assays (EMSA) showed that MdHHO3 binds to the motif-containing GAATC. Furthermore, MdHHO3 binds to its promoter sequence and inhibits its activity. In addition, the overexpression of MdHHO3 in apple calli resulted in less accumulation of nitrate in 35S:MdHHO3-GFP calli and downregulated the expression of the nitrate transport-related genes but upregulated the expression of the nitrate assimilation-related genes. Similarly, the expression of the nitrate transport-related genes was downregulated and the expression of the nitrate assimilation-related genes was upregulated in MdHHO3 overexpression Arabidopsis and tobacco plants. Interaction experiments showed that MdHHO3 could bind to the promoter MdNRT2.1 (NITRATE TRANSPORTER 2.1) and negatively regulate its expression. Moreover, the exposure of MdHHO3-overexpressing Arabidopsis and tobacco to nitrate deficiency resulted in an early senescence phenotype as compared to the WT plants. These results show that MdHHO3 can not only negatively regulate nitrate accumulation in response to nitrate but also promote early leaf senescence under nitrate deficiency. This information may be useful to further reveal the mechanism of the nitrate response and demonstrates that nitrate deficiency induces leaf senescence in apples.
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Affiliation(s)
- Binbin Wen
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, China
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, China
| | - Xingyao Gong
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, China
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, China
| | - Wenpeng Deng
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, China
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, China
| | - Xiude Chen
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, China
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, China
- Shandong Collaborative Innovation Center for Fruit and Vegetable Production With High Quality and Efficiency, Shandong Agricultural University, Tai’an, China
| | - Dongmei Li
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, China
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, China
- Shandong Collaborative Innovation Center for Fruit and Vegetable Production With High Quality and Efficiency, Shandong Agricultural University, Tai’an, China
| | - Xiling Fu
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, China
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, China
- Shandong Collaborative Innovation Center for Fruit and Vegetable Production With High Quality and Efficiency, Shandong Agricultural University, Tai’an, China
| | - Ling Li
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, China
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, China
- Shandong Collaborative Innovation Center for Fruit and Vegetable Production With High Quality and Efficiency, Shandong Agricultural University, Tai’an, China
| | - Qiuping Tan
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, China
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, China
- Shandong Collaborative Innovation Center for Fruit and Vegetable Production With High Quality and Efficiency, Shandong Agricultural University, Tai’an, China
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12
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Ji XL, Li HL, Qiao ZW, Zhang JC, Sun WJ, You CX, Hao YJ, Wang XF. The BTB protein MdBT2 recruits auxin signaling components to regulate adventitious root formation in apple. PLANT PHYSIOLOGY 2022; 189:1005-1020. [PMID: 35218363 PMCID: PMC9157121 DOI: 10.1093/plphys/kiac084] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 01/28/2022] [Indexed: 05/27/2023]
Abstract
Ubiquitination is an important post-translational protein modification. Although BROAD-COMPLEX, TRAMTRACK AND BRIC A BRAC and TRANSCRIPTION ADAPTOR PUTATIVE ZINC FINGER domain protein 2 (BT2) is involved in many biological processes, its role in apple (Malus domestic) root formation remains unclear. Here, we revealed that MdBT2 inhibits adventitious root (AR) formation through interacting with AUXIN RESPONSE FACTOR8 (MdARF8) and INDOLE-3-ACETIC ACID INDUCIBLE3 (MdIAA3). MdBT2 facilitated MdARF8 ubiquitination and degradation through the 26S proteasome pathway and negatively regulated GRETCHEN HAGEN 3.1 (MdGH3.1) and MdGH3.6 expression. MdARF8 regulates AR formation through inducing transcription of MdGH3s (MdGH3.1, MdGH3.2, MdGH3.5, and MdGH3.6). In addition, MdBT2 facilitated MdIAA3 stability and slightly promoted its interaction with MdARF8. MdIAA3 inhibited AR formation by forming heterodimers with MdARF8 as well as other MdARFs (MdARF5, MdARF6, MdARF7, and MdARF19). Our findings reveal that MdBT2 acts as a negative regulator of AR formation in apple.
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Affiliation(s)
- Xing-Long Ji
- State Key Laboratory of Crop Biology, Shandong Collaborative Innovation Center of Fruit and Vegetable Quality and Efficient Production, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An 271018, China
- Institute of Grape Science and Engineering, College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China
| | - Hong-Liang Li
- State Key Laboratory of Crop Biology, Shandong Collaborative Innovation Center of Fruit and Vegetable Quality and Efficient Production, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An 271018, China
| | - Zhi-Wen Qiao
- State Key Laboratory of Crop Biology, Shandong Collaborative Innovation Center of Fruit and Vegetable Quality and Efficient Production, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An 271018, China
| | - Jiu-Cheng Zhang
- State Key Laboratory of Crop Biology, Shandong Collaborative Innovation Center of Fruit and Vegetable Quality and Efficient Production, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An 271018, China
| | - Wei-Jian Sun
- State Key Laboratory of Crop Biology, Shandong Collaborative Innovation Center of Fruit and Vegetable Quality and Efficient Production, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An 271018, China
| | - Chun-Xiang You
- State Key Laboratory of Crop Biology, Shandong Collaborative Innovation Center of Fruit and Vegetable Quality and Efficient Production, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An 271018, China
| | - Yu-Jin Hao
- State Key Laboratory of Crop Biology, Shandong Collaborative Innovation Center of Fruit and Vegetable Quality and Efficient Production, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An 271018, China
| | - Xiao-Fei Wang
- State Key Laboratory of Crop Biology, Shandong Collaborative Innovation Center of Fruit and Vegetable Quality and Efficient Production, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An 271018, China
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13
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Irigoyen S, Ramasamy M, Misra A, McKnight TD, Mandadi KK. A BTB-TAZ protein is required for gene activation by Cauliflower mosaic virus 35S multimerized enhancers. PLANT PHYSIOLOGY 2022; 188:397-410. [PMID: 34597402 PMCID: PMC8774732 DOI: 10.1093/plphys/kiab450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 08/27/2021] [Indexed: 06/13/2023]
Abstract
The Arabidopsis (Arabidopsis thaliana) BTB-TAZ DOMAIN PROTEIN 2 (BT2) contains an N-terminal BTB domain, a central TAZ zinc-finger protein-protein interaction domain, and a C-terminal calmodulin-binding domain. We previously demonstrated that BT2 regulates telomerase activity and mediates multiple responses to nutrients, hormones, and abiotic stresses in Arabidopsis. Here, we describe the essential role of BT2 in activation of genes by multimerized Cauliflower mosaic virus 35S (35S) enhancers. Loss of BT2 function in several well-characterized 35S enhancer activation-tagged lines resulted in suppression of the activation phenotypes. Suppression of the phenotypes was associated with decreased transcript abundance of the tagged genes. Nuclear run-on assays, mRNA decay studies, and bisulfite sequencing revealed that BT2 is required to maintain the transcriptionally active state of the multimerized 35S enhancers, and lack of BT2 leads to hypermethylation of the 35S enhancers. The TAZ domain and the Ca++/calmodulin-binding domain of BT2 are critical for its function and 35S enhancer activity. We further demonstrate that BT2 requires CULLIN3 and two bromodomain-containing Global Transcription factor group E proteins (GTE9 and GTE11), to regulate 35S enhancer activity. We propose that the BT2-CULLIN3 ubiquitin ligase, through interactions with GTE9 and GTE11, regulates 35S enhancer activity in Arabidopsis.
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Affiliation(s)
- Sonia Irigoyen
- Texas A&M AgriLife Research and Extension Center, Weslaco, Texas 79596, USA
| | | | - Anjali Misra
- Department of Biology, Texas A&M University, College Station, Texas 77843, USA
| | - Thomas D McKnight
- Department of Biology, Texas A&M University, College Station, Texas 77843, USA
| | - Kranthi K Mandadi
- Texas A&M AgriLife Research and Extension Center, Weslaco, Texas 79596, USA
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas 77843, USA
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14
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Transporters and transcription factors gene families involved in improving nitrogen use efficiency (NUE) and assimilation in rice (Oryza sativa L.). Transgenic Res 2021; 31:23-42. [PMID: 34524604 DOI: 10.1007/s11248-021-00284-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 09/06/2021] [Indexed: 12/18/2022]
Abstract
Nitrogen (N) as a macronutrient is an important determinant of plant growth. The excessive usage of chemical fertilizers is increasing environmental pollution; hence, the improvement of crop's nitrogen use efficiency (NUE) is imperative for sustainable agriculture. N uptake, transportation, assimilation, and remobilization are four important determinants of plant NUE. Oryza sativa L. (rice) is a staple food for approximately half of the human population, around the globe and improvement in rice yield is pivotal for rice breeders. The N transporters, enzymes indulged in N assimilation, and several transcription factors affect the rice NUE and subsequent yield. Although, a couple of improvements have been made regarding rice NUE, the knowledge about regulatory mechanisms operating NUE is scarce. The current review provides a precise knowledge of how rice plants detect soil N and how this detection is translated into the language of responses that regulate the growth. Additionally, the transcription factors that control N-associated genes in rice are discussed in detail. This mechanistic insight will help the researchers to improve rice yield with minimized use of chemical fertilizers.
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Moseley RC, Motta F, Tuskan GA, Haase SB, Yang X. Inference of Gene Regulatory Network Uncovers the Linkage between Circadian Clock and Crassulacean Acid Metabolism in Kalanchoë fedtschenkoi. Cells 2021; 10:2217. [PMID: 34571864 PMCID: PMC8471846 DOI: 10.3390/cells10092217] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 08/18/2021] [Accepted: 08/23/2021] [Indexed: 02/01/2023] Open
Abstract
The circadian clock drives time-specific gene expression, enabling biological processes to be temporally controlled. Plants that conduct crassulacean acid metabolism (CAM) photosynthesis represent an interesting case of circadian regulation of gene expression as stomatal movement is temporally inverted relative to stomatal movement in C3 plants. The mechanisms behind how the circadian clock enabled physiological differences at the molecular level is not well understood. Recently, the rescheduling of gene expression was reported as a mechanism to explain how CAM evolved from C3. Therefore, we investigated whether core circadian clock genes in CAM plants were re-phased during evolution, or whether networks of phase-specific genes were simply re-wired to different core clock genes. We identified candidate core clock genes based on gene expression features and then applied the Local Edge Machine (LEM) algorithm to infer regulatory relationships between this new set of core candidates and known core clock genes in Kalanchoë fedtschenkoi. We further inferred stomata-related gene targets for known and candidate core clock genes and constructed a gene regulatory network for core clock and stomata-related genes. Our results provide new insight into the mechanism of circadian control of CAM-related genes in K. fedtschenkoi, facilitating the engineering of CAM machinery into non-CAM plants for sustainable crop production in water-limited environments.
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Affiliation(s)
- Robert C. Moseley
- Department of Biology, Duke University, Durham, NC 27708, USA; (R.C.M.); (S.B.H.)
| | - Francis Motta
- Department of Mathematical Sciences, Florida Atlantic University, Boca Raton, FL 33431, USA;
| | - Gerald A. Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA;
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Steven B. Haase
- Department of Biology, Duke University, Durham, NC 27708, USA; (R.C.M.); (S.B.H.)
- Department of Medicine, Duke University, Durham, NC 27708, USA
| | - Xiaohan Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA;
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
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16
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Heerah S, Molinari R, Guerrier S, Marshall-Colon A. Granger-causal testing for irregularly sampled time series with application to nitrogen signalling in Arabidopsis. BIOINFORMATICS (OXFORD, ENGLAND) 2021; 37:2450-2460. [PMID: 33693548 DOI: 10.1101/2020.06.15.152819] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 02/18/2021] [Accepted: 03/03/2021] [Indexed: 05/27/2023]
Abstract
MOTIVATION Identification of system-wide causal relationships can contribute to our understanding of long-distance, intercellular signalling in biological organisms. Dynamic transcriptome analysis holds great potential to uncover coordinated biological processes between organs. However, many existing dynamic transcriptome studies are characterized by sparse and often unevenly spaced time points that make the identification of causal relationships across organs analytically challenging. Application of existing statistical models, designed for regular time series with abundant time points, to sparse data may fail to reveal biologically significant, causal relationships. With increasing research interest in biological time series data, there is a need for new statistical methods that are able to determine causality within and between time series data sets. Here, a statistical framework was developed to identify (Granger) causal gene-gene relationships of unevenly spaced, multivariate time series data from two different tissues of Arabidopsis thaliana in response to a nitrogen signal. RESULTS This work delivers a statistical approach for modelling irregularly sampled bivariate signals which embeds functions from the domain of engineering that allow to adapt the model's dependence structure to the specific sampling time. Using maximum-likelihood to estimate the parameters of this model for each bivariate time series, it is then possible to use bootstrap procedures for small samples (or asymptotics for large samples) in order to test for Granger-Causality. When applied to the A.thaliana data, the proposed approach produced 3078 significant interactions, in which 2012 interactions have root causal genes and 1066 interactions have shoot causal genes. Many of the predicted causal and target genes are known players in local and long-distance nitrogen signalling, including genes encoding transcription factors, hormones and signalling peptides. Of the 1007 total causal genes (either organ), 384 are either known or predicted mobile transcripts, suggesting that the identified causal genes may be directly involved in long-distance nitrogen signalling through intercellular interactions. The model predictions and subsequent network analysis identified nitrogen-responsive genes that can be further tested for their specific roles in long-distance nitrogen signalling. AVAILABILITY AND IMPLEMENTATION The method was developed with the R statistical software and is made available through the R package 'irg' hosted on the GitHub repository https://github.com/SMAC-Group/irg where also a running example vignette can be found (https://smac-group.github.io/irg/articles/vignette.html). A few signals from the original data set are made available in the package as an example to apply the method and the complete A.thaliana data can be found at: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE97500. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Sachin Heerah
- Department of Plant Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Roberto Molinari
- Department of Mathematics and Statistics, Auburn University, Auburn, AL 36849, USA
| | - Stéphane Guerrier
- Faculty of Science & Geneva School of Economics and Management, University of Geneva, Geneva 1205, Switzerland
| | - Amy Marshall-Colon
- Department of Plant Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
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17
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Ren YR, Zhao Q, Yang YY, Zhang R, Wang XF, Zhang TE, You CX, Huo HQ, Hao YJ. Interaction of BTB-TAZ protein MdBT2 and DELLA protein MdRGL3a regulates nitrate-mediated plant growth. PLANT PHYSIOLOGY 2021; 186:750-766. [PMID: 33764451 PMCID: PMC8154073 DOI: 10.1093/plphys/kiab065] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 01/15/2021] [Indexed: 06/01/2023]
Abstract
Nitrate acts as a vital signal molecule in the modulation of plant growth and development. The phytohormones gibberellin (GA) is also involved in this process. However, the exact molecular mechanism of how nitrate and GA signaling pathway work together in regulating plant growth remains poorly understood. In this study, we found that a nitrate-responsive BTB/TAZ protein MdBT2 participates in regulating nitrate-induced plant growth in apple (Malus × domestica). Yeast two-hybridization, protein pull-down, and bimolecular fluorescence complementation (BiFC) assays showed that MdBT2 interacts with a DELLA protein MdRGL3a, which is required for the ubiquitination and degradation of MdRGL3a proteins via a 26S proteasome-dependent pathway. Furthermore, heterologous expression of MdBT2 partially rescued growth inhibition caused by overexpression of MdRGL3a in Arabidopsis. Taken together, our findings indicate that MdBT2 promotes nitrate-induced plant growth partially through reducing the abundance of the DELLA protein MdRGL3a.
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Affiliation(s)
- Yi-Ran Ren
- State Key Laboratory of Crop Biology, Shandong Collaborative Innovation Center for Fruit and Vegetable Production with High Quality and Efficiency, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong, 271018, China
| | - Qiang Zhao
- Qingdao Agricultural University, Qingdao, Shandong, 266109, China
| | - Yu-Ying Yang
- State Key Laboratory of Crop Biology, Shandong Collaborative Innovation Center for Fruit and Vegetable Production with High Quality and Efficiency, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong, 271018, China
| | - Rui Zhang
- State Key Laboratory of Crop Biology, Shandong Collaborative Innovation Center for Fruit and Vegetable Production with High Quality and Efficiency, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong, 271018, China
| | - Xiao-Fei Wang
- State Key Laboratory of Crop Biology, Shandong Collaborative Innovation Center for Fruit and Vegetable Production with High Quality and Efficiency, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong, 271018, China
| | - Tian-En Zhang
- State Key Laboratory of Crop Biology, Shandong Collaborative Innovation Center for Fruit and Vegetable Production with High Quality and Efficiency, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong, 271018, China
| | - Chun-Xiang You
- State Key Laboratory of Crop Biology, Shandong Collaborative Innovation Center for Fruit and Vegetable Production with High Quality and Efficiency, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong, 271018, China
| | - He-Qiang Huo
- Mid-Florida Research and Education Center, University of Florida, Apopka, FL 32703, USA
| | - Yu-Jin Hao
- State Key Laboratory of Crop Biology, Shandong Collaborative Innovation Center for Fruit and Vegetable Production with High Quality and Efficiency, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong, 271018, China
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18
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Ruffel S, Chaput V, Przybyla-Toscano J, Fayos I, Ibarra C, Moyano T, Fizames C, Tillard P, O’Brien JA, Gutiérrez RA, Gojon A, Lejay L. Genome-wide analysis in response to nitrogen and carbon identifies regulators for root AtNRT2 transporters. PLANT PHYSIOLOGY 2021; 186:696-714. [PMID: 33582801 PMCID: PMC8154064 DOI: 10.1093/plphys/kiab047] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 01/19/2021] [Indexed: 05/14/2023]
Abstract
In Arabidopsis (Arabidopsis thaliana), the High-Affinity Transport System (HATS) for root nitrate (NO3-) uptake depends mainly on four NRT2 NO3- transporters, namely NRT2.1, NRT2.2, NRT2.4, and NRT2.5. The HATS is the target of many regulations to coordinate nitrogen (N) acquisition with the N status of the plant and with carbon (C) assimilation through photosynthesis. At the molecular level, C and N signaling pathways control gene expression of the NRT2 transporters. Although several regulators of these transporters have been identified in response to either N or C signals, the response of NRT2 gene expression to the interaction of these signals has never been specifically investigated, and the underlying molecular mechanisms remain largely unknown. To address this question we used an original systems biology approach to model a regulatory gene network targeting NRT2.1, NRT2.2, NRT2.4, and NRT2.5 in response to N/C signals. Our systems analysis of the data identified three transcription factors, TGA3, MYC1, and bHLH093. Functional analysis of mutants combined with yeast one-hybrid experiments confirmed that all three transcription factors are regulators of NRT2.4 or NRT2.5 in response to N or C signals. These results reveal a role for TGA3, MYC1, and bHLH093 in controlling the expression of root NRT2 transporter genes.
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Affiliation(s)
- Sandrine Ruffel
- BPMP, University of Montpellier, CNRS, INRAE, Institut Agro, Montpellier 34060, France
| | - Valentin Chaput
- BPMP, University of Montpellier, CNRS, INRAE, Institut Agro, Montpellier 34060, France
| | | | - Ian Fayos
- BPMP, University of Montpellier, CNRS, INRAE, Institut Agro, Montpellier 34060, France
| | - Catalina Ibarra
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Millennium Institute for Integrative Biology, FONDAP Center for Genome Regulation, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
| | - Tomas Moyano
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Millennium Institute for Integrative Biology, FONDAP Center for Genome Regulation, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
| | - Cécile Fizames
- BPMP, University of Montpellier, CNRS, INRAE, Institut Agro, Montpellier 34060, France
| | - Pascal Tillard
- BPMP, University of Montpellier, CNRS, INRAE, Institut Agro, Montpellier 34060, France
| | - Jose Antonio O’Brien
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Universidad Católica de Chile, Santiago 8331150, Chile
- Departamento de Fruticultura y Enología, Facultad de Agronomía e Ingeniería Forestal. Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
| | - Rodrigo A Gutiérrez
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Millennium Institute for Integrative Biology, FONDAP Center for Genome Regulation, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
| | - Alain Gojon
- BPMP, University of Montpellier, CNRS, INRAE, Institut Agro, Montpellier 34060, France
| | - Laurence Lejay
- BPMP, University of Montpellier, CNRS, INRAE, Institut Agro, Montpellier 34060, France
- Author for communication:
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19
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Ruffel S, Chaput V, Przybyla-Toscano J, Fayos I, Ibarra C, Moyano T, Fizames C, Tillard P, O'Brien JA, Gutiérrez RA, Gojon A, Lejay L. Genome-wide analysis in response to nitrogen and carbon identifies regulators for root AtNRT2 transporters. PLANT PHYSIOLOGY 2021; 186:696-714. [PMID: 33582801 DOI: 10.1101/822197] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 01/19/2021] [Indexed: 05/26/2023]
Abstract
In Arabidopsis (Arabidopsis thaliana), the High-Affinity Transport System (HATS) for root nitrate (NO3-) uptake depends mainly on four NRT2 NO3- transporters, namely NRT2.1, NRT2.2, NRT2.4, and NRT2.5. The HATS is the target of many regulations to coordinate nitrogen (N) acquisition with the N status of the plant and with carbon (C) assimilation through photosynthesis. At the molecular level, C and N signaling pathways control gene expression of the NRT2 transporters. Although several regulators of these transporters have been identified in response to either N or C signals, the response of NRT2 gene expression to the interaction of these signals has never been specifically investigated, and the underlying molecular mechanisms remain largely unknown. To address this question we used an original systems biology approach to model a regulatory gene network targeting NRT2.1, NRT2.2, NRT2.4, and NRT2.5 in response to N/C signals. Our systems analysis of the data identified three transcription factors, TGA3, MYC1, and bHLH093. Functional analysis of mutants combined with yeast one-hybrid experiments confirmed that all three transcription factors are regulators of NRT2.4 or NRT2.5 in response to N or C signals. These results reveal a role for TGA3, MYC1, and bHLH093 in controlling the expression of root NRT2 transporter genes.
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Affiliation(s)
- Sandrine Ruffel
- BPMP, University of Montpellier, CNRS, INRAE, Institut Agro, Montpellier 34060, France
| | - Valentin Chaput
- BPMP, University of Montpellier, CNRS, INRAE, Institut Agro, Montpellier 34060, France
| | | | - Ian Fayos
- BPMP, University of Montpellier, CNRS, INRAE, Institut Agro, Montpellier 34060, France
| | - Catalina Ibarra
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Millennium Institute for Integrative Biology, FONDAP Center for Genome Regulation, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
| | - Tomas Moyano
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Millennium Institute for Integrative Biology, FONDAP Center for Genome Regulation, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
| | - Cécile Fizames
- BPMP, University of Montpellier, CNRS, INRAE, Institut Agro, Montpellier 34060, France
| | - Pascal Tillard
- BPMP, University of Montpellier, CNRS, INRAE, Institut Agro, Montpellier 34060, France
| | - Jose Antonio O'Brien
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Universidad Católica de Chile, Santiago 8331150, Chile
- Departamento de Fruticultura y Enología, Facultad de Agronomía e Ingeniería Forestal. Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
| | - Rodrigo A Gutiérrez
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Millennium Institute for Integrative Biology, FONDAP Center for Genome Regulation, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
| | - Alain Gojon
- BPMP, University of Montpellier, CNRS, INRAE, Institut Agro, Montpellier 34060, France
| | - Laurence Lejay
- BPMP, University of Montpellier, CNRS, INRAE, Institut Agro, Montpellier 34060, France
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20
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Safi A, Medici A, Szponarski W, Martin F, Clément-Vidal A, Marshall-Colon A, Ruffel S, Gaymard F, Rouached H, Leclercq J, Coruzzi G, Lacombe B, Krouk G. GARP transcription factors repress Arabidopsis nitrogen starvation response via ROS-dependent and -independent pathways. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:3881-3901. [PMID: 33758916 PMCID: PMC8096604 DOI: 10.1093/jxb/erab114] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 03/22/2021] [Indexed: 05/04/2023]
Abstract
Plants need to cope with strong variations of nitrogen availability in the soil. Although many molecular players are being discovered concerning how plants perceive NO3- provision, it is less clear how plants recognize a lack of nitrogen. Following nitrogen removal, plants activate their nitrogen starvation response (NSR), which is characterized by the activation of very high-affinity nitrate transport systems (NRT2.4 and NRT2.5) and other sentinel genes involved in N remobilization such as GDH3. Using a combination of functional genomics via transcription factor perturbation and molecular physiology studies, we show that the transcription factors belonging to the HHO subfamily are important regulators of NSR through two potential mechanisms. First, HHOs directly repress the high-affinity nitrate transporters, NRT2.4 and NRT2.5. hho mutants display increased high-affinity nitrate transport activity, opening up promising perspectives for biotechnological applications. Second, we show that reactive oxygen species (ROS) are important to control NSR in wild-type plants and that HRS1 and HHO1 overexpressors and mutants are affected in their ROS content, defining a potential feed-forward branch of the signaling pathway. Taken together, our results define the relationships of two types of molecular players controlling the NSR, namely ROS and the HHO transcription factors. This work (i) up opens perspectives on a poorly understood nutrient-related signaling pathway and (ii) defines targets for molecular breeding of plants with enhanced NO3- uptake.
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Affiliation(s)
- Alaeddine Safi
- BPMP, Univ Montpellier, CNRS, INRA, SupAgro, Montpellier, France
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
- Correspondence: or
| | - Anna Medici
- BPMP, Univ Montpellier, CNRS, INRA, SupAgro, Montpellier, France
| | | | - Florence Martin
- CIRAD, AGAP Institut, Montpellier, France
- AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Anne Clément-Vidal
- CIRAD, AGAP Institut, Montpellier, France
- AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Amy Marshall-Colon
- New York University, Department of Biology, Center for Genomics & Systems Biology, New York, NY, USA
- Present address: Department of Plant Biology, University of Illinois at Urbana -Champaign, Urbana, IL, USA
| | - Sandrine Ruffel
- BPMP, Univ Montpellier, CNRS, INRA, SupAgro, Montpellier, France
| | - Frédéric Gaymard
- BPMP, Univ Montpellier, CNRS, INRA, SupAgro, Montpellier, France
| | - Hatem Rouached
- BPMP, Univ Montpellier, CNRS, INRA, SupAgro, Montpellier, France
- Department of Plant, Soil, and Microbial Sciences, and Plant Resilience Institute, Michigan State University, East Lansing, MI, USA
| | - Julie Leclercq
- CIRAD, AGAP Institut, Montpellier, France
- AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Gloria Coruzzi
- New York University, Department of Biology, Center for Genomics & Systems Biology, New York, NY, USA
| | - Benoît Lacombe
- BPMP, Univ Montpellier, CNRS, INRA, SupAgro, Montpellier, France
| | - Gabriel Krouk
- BPMP, Univ Montpellier, CNRS, INRA, SupAgro, Montpellier, France
- Correspondence: or
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21
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Zhang D, Yang K, Kan Z, Dang H, Feng S, Yang Y, Li L, Hou N, Xu L, Wang X, Malnoy M, Ma F, Hao Y, Guan Q. The regulatory module MdBT2-MdMYB88/MdMYB124-MdNRTs regulates nitrogen usage in apple. PLANT PHYSIOLOGY 2021; 185:1924-1942. [PMID: 33793944 PMCID: PMC8133671 DOI: 10.1093/plphys/kiaa118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 12/18/2020] [Indexed: 05/04/2023]
Abstract
Less than 40% of the nitrogen (N) fertilizer applied to soil is absorbed by crops. Thus, improving the N use efficiency of crops is critical for agricultural development. However, the underlying regulation of these processes remains largely unknown, particularly in woody plants. By conducting yeast two-hybrid assays, we identified one interacting protein of MdMYB88 and MdMYB124 in apple (Malus × domestica), namely BTB and TAZ domain protein 2 (MdBT2). Ubiquitination and protein stabilization analysis revealed that MdBT2 ubiquitinates and degrades MdMYB88 and MdMYB124 via the 26S proteasome pathway. MdBT2 negatively regulates nitrogen usage as revealed by the reduced fresh weight, dry weight, N concentration, and N usage index of MdBT2 overexpression calli under low-N conditions. In contrast, MdMYB88 and MdMYB124 increase nitrate absorption, allocation, and remobilization by regulating expression of MdNRT2.4, MdNRT1.8, MdNRT1.7, and MdNRT1.5 under N limitation, thereby regulating N usage. The results obtained illustrate the mechanism of a regulatory module comprising MdBT2-MdMYB88/MdMYB124-MdNRTs, through which plants modulate N usage. These data contribute to a molecular approach to improve the N usage of fruit crops under limited N acquisition.
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Affiliation(s)
- Dehui Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Kuo Yang
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong 271000, China
| | - Zhiyong Kan
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Huan Dang
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Shuxian Feng
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yusen Yang
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Lei Li
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Nan Hou
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Lingfei Xu
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiaofei Wang
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong 271000, China
| | - Mickael Malnoy
- Department of Biology and Genomics of Fruit Plants, Foundation Edmund Mach di San Michele all'Adige, Trento, Italy
| | - Fengwang Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yujin Hao
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong 271000, China
| | - Qingmei Guan
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
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Heerah S, Molinari R, Guerrier S, Marshall-Colon A. Granger-Causal Testing for Irregularly Sampled Time Series with Application to Nitrogen Signaling in Arabidopsis. Bioinformatics 2021; 37:2450-2460. [PMID: 33693548 PMCID: PMC8388030 DOI: 10.1093/bioinformatics/btab126] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 02/18/2021] [Accepted: 03/03/2021] [Indexed: 12/05/2022] Open
Abstract
Motivation Identification of system-wide causal relationships can contribute to our understanding of long-distance, intercellular signalling in biological organisms. Dynamic transcriptome analysis holds great potential to uncover coordinated biological processes between organs. However, many existing dynamic transcriptome studies are characterized by sparse and often unevenly spaced time points that make the identification of causal relationships across organs analytically challenging. Application of existing statistical models, designed for regular time series with abundant time points, to sparse data may fail to reveal biologically significant, causal relationships. With increasing research interest in biological time series data, there is a need for new statistical methods that are able to determine causality within and between time series data sets. Here, a statistical framework was developed to identify (Granger) causal gene-gene relationships of unevenly spaced, multivariate time series data from two different tissues of Arabidopsis thaliana in response to a nitrogen signal. Results This work delivers a statistical approach for modelling irregularly sampled bivariate signals which embeds functions from the domain of engineering that allow to adapt the model’s dependence structure to the specific sampling time. Using maximum-likelihood to estimate the parameters of this model for each bivariate time series, it is then possible to use bootstrap procedures for small samples (or asymptotics for large samples) in order to test for Granger-Causality. When applied to the A.thaliana data, the proposed approach produced 3078 significant interactions, in which 2012 interactions have root causal genes and 1066 interactions have shoot causal genes. Many of the predicted causal and target genes are known players in local and long-distance nitrogen signalling, including genes encoding transcription factors, hormones and signalling peptides. Of the 1007 total causal genes (either organ), 384 are either known or predicted mobile transcripts, suggesting that the identified causal genes may be directly involved in long-distance nitrogen signalling through intercellular interactions. The model predictions and subsequent network analysis identified nitrogen-responsive genes that can be further tested for their specific roles in long-distance nitrogen signalling. Availability and implementation The method was developed with the R statistical software and is made available through the R package ‘irg’ hosted on the GitHub repository https://github.com/SMAC-Group/irg where also a running example vignette can be found (https://smac-group.github.io/irg/articles/vignette.html). A few signals from the original data set are made available in the package as an example to apply the method and the complete A.thaliana data can be found at: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE97500. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Sachin Heerah
- Department of Plant Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Roberto Molinari
- Department of Mathematics and Statistics, Auburn University, Auburn, AL, USA
| | - Stéphane Guerrier
- Faculty of Science & Geneva School of Economics and Management, University of Geneva, Geneva, Switzerland
| | - Amy Marshall-Colon
- Department of Plant Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA
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23
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Santamaria ME, Garcia A, Arnaiz A, Rosa‐Diaz I, Romero‐Hernandez G, Diaz I, Martinez M. Comparative transcriptomics reveals hidden issues in the plant response to arthropod herbivores. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:312-326. [PMID: 33085192 PMCID: PMC7898633 DOI: 10.1111/jipb.13026] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 10/18/2020] [Indexed: 05/04/2023]
Abstract
Plants experience different abiotic/biotic stresses, which trigger their molecular machinery to cope with them. Besides general mechanisms prompted by many stresses, specific mechanisms have been introduced to optimize the response to individual threats. However, these key mechanisms are difficult to identify. Here, we introduce an in-depth species-specific transcriptomic analysis and conduct an extensive meta-analysis of the responses to related species to gain more knowledge about plant responses. The spider mite Tetranychus urticae was used as the individual species, several arthropod herbivores as the related species for meta-analysis, and Arabidopsis thaliana plants as the common host. The analysis of the transcriptomic data showed typical common responses to herbivory, such as jasmonate signaling or glucosinolate biosynthesis. Also, a specific set of genes likely involved in the particularities of the Arabidopsis-spider mite interaction was discovered. The new findings have determined a prominent role in this interaction of the jasmonate-induced pathways leading to the biosynthesis of anthocyanins and tocopherols. Therefore, tandem individual/general transcriptomic profiling has been revealed as an effective method to identify novel relevant processes and specificities in the plant response to environmental stresses.
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Affiliation(s)
- M. Estrella Santamaria
- Centro de Biotecnología y Genómica de Plantas, Instituto Nacional de Investigación y Tecnología Agraria y AlimentariaUniversidad Politécnica de MadridMadridSpain
| | - Alejandro Garcia
- Centro de Biotecnología y Genómica de Plantas, Instituto Nacional de Investigación y Tecnología Agraria y AlimentariaUniversidad Politécnica de MadridMadridSpain
| | - Ana Arnaiz
- Centro de Biotecnología y Genómica de Plantas, Instituto Nacional de Investigación y Tecnología Agraria y AlimentariaUniversidad Politécnica de MadridMadridSpain
| | - Irene Rosa‐Diaz
- Centro de Biotecnología y Genómica de Plantas, Instituto Nacional de Investigación y Tecnología Agraria y AlimentariaUniversidad Politécnica de MadridMadridSpain
| | - Gara Romero‐Hernandez
- Centro de Biotecnología y Genómica de Plantas, Instituto Nacional de Investigación y Tecnología Agraria y AlimentariaUniversidad Politécnica de MadridMadridSpain
| | - Isabel Diaz
- Centro de Biotecnología y Genómica de Plantas, Instituto Nacional de Investigación y Tecnología Agraria y AlimentariaUniversidad Politécnica de MadridMadridSpain
- Departamento de Biotecnología‐Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de BiosistemasUniversidad Politécnica de MadridMadridSpain
| | - Manuel Martinez
- Centro de Biotecnología y Genómica de Plantas, Instituto Nacional de Investigación y Tecnología Agraria y AlimentariaUniversidad Politécnica de MadridMadridSpain
- Departamento de Biotecnología‐Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de BiosistemasUniversidad Politécnica de MadridMadridSpain
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24
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Ren YR, Zhao Q, Yang YY, Zhang TE, Wang XF, You CX, Hao YJ. The apple 14-3-3 protein MdGRF11 interacts with the BTB protein MdBT2 to regulate nitrate deficiency-induced anthocyanin accumulation. HORTICULTURE RESEARCH 2021; 8:22. [PMID: 33518703 PMCID: PMC7848006 DOI: 10.1038/s41438-020-00457-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 11/16/2020] [Indexed: 05/08/2023]
Abstract
Nitrogen is an important factor that affects plant anthocyanin accumulation. In apple, the nitrate-responsive BTB/TAZ protein MdBT2 negatively regulates anthocyanin biosynthesis. In this study, we found that MdBT2 undergoes posttranslational modifications in response to nitrate deficiency. Yeast two-hybrid, protein pull-down, and bimolecular fluorescence complementation (BiFC) assays showed that MdBT2 interacts with MdGRF11, a 14-3-3 protein; 14-3-3 proteins compose a family of highly conserved phosphopeptide-binding proteins involved in multiple physiological and biological processes. The interaction of MdGRF11 negatively regulated the stability of the MdBT2 protein via a 26S proteasome-dependent pathway, which increased the abundance of MdMYB1 proteins to activate the expression of anthocyanin biosynthesis-related genes. Taken together, the results demonstrate the critical role of 14-3-3 proteins in the regulation of nitrate deficiency-induced anthocyanin accumulation. Our results provide a novel avenue to elucidate the mechanism underlying the induction of anthocyanin biosynthesis in response to nitrate deficiency.
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Affiliation(s)
- Yi-Ran Ren
- State Key Laboratory of Crop Biology, Shandong Collaborative Innovation Center for Fruit and Vegetable Production with High Quality and Efficiency, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong, 271018, China
| | - Qiang Zhao
- Qingdao Agricultural University, Qingdao, Shandong, 266109, China
| | - Yu-Ying Yang
- State Key Laboratory of Crop Biology, Shandong Collaborative Innovation Center for Fruit and Vegetable Production with High Quality and Efficiency, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong, 271018, China
| | - Tian-En Zhang
- State Key Laboratory of Crop Biology, Shandong Collaborative Innovation Center for Fruit and Vegetable Production with High Quality and Efficiency, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong, 271018, China
| | - Xiao-Fei Wang
- State Key Laboratory of Crop Biology, Shandong Collaborative Innovation Center for Fruit and Vegetable Production with High Quality and Efficiency, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong, 271018, China
| | - Chun-Xiang You
- State Key Laboratory of Crop Biology, Shandong Collaborative Innovation Center for Fruit and Vegetable Production with High Quality and Efficiency, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong, 271018, China
| | - Yu-Jin Hao
- State Key Laboratory of Crop Biology, Shandong Collaborative Innovation Center for Fruit and Vegetable Production with High Quality and Efficiency, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong, 271018, China.
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25
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Rossdeutsch L, Schreiner RP, Skinkis PA, Deluc L. Nitrate Uptake and Transport Properties of Two Grapevine Rootstocks With Varying Vigor. FRONTIERS IN PLANT SCIENCE 2021; 11:608813. [PMID: 33537044 PMCID: PMC7847936 DOI: 10.3389/fpls.2020.608813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 12/22/2020] [Indexed: 06/12/2023]
Abstract
In viticulture, rootstocks are essential to cope with edaphic constraints. They can also be used to modulate scion growth and development to help improve berry yield and quality. The rootstock contribution to scion growth is not fully understood. Since nitrogen (N) is a significant driver of grapevine growth, rootstock properties associated with N uptake and transport may play a key role in the growth potential of grafted grapevines. We evaluated N uptake and transport in a potted system using two grapevines rootstocks [Riparia Gloire (RG) and 1103 Paulsen (1103P)] grafted to Pinot noir (Pommard clone) scion. Combining results of nitrate induction and steady-state experiments at two N availability levels, we observed different responses in the uptake and utilization of N between the two rootstocks. The low vigor rootstock (RG) exhibited greater nitrate uptake capacity and nitrate assimilation in roots after nitrate resupply than the more vigorous 1103P rootstock. This behavior may be attributed to a greater root carbohydrate status observed in RG for both experiments. However, 1103P demonstrated a higher N translocation rate to shoots regardless of N availability. These distinct rootstock behaviors resulted in significant differences in biomass allocation between roots and shoots under N-limited conditions, although the overall vine biomass was not different. Under sufficient N supply, differences between rootstocks decreased but 1103P stored more N in roots, which may benefit growth in subsequent growing seasons. Overall, greater transpiration of vines grafted to 1103P rootstock causing higher N translocation to shoots could partially explain its known growth-promoting effect to scions under low and high N availability, whereas the low vigor typically conferred to scions by RG may result from the combination of lower N translocation to shoots and a greater allocation of biomass toward roots when N is low.
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Affiliation(s)
- Landry Rossdeutsch
- Department of Horticulture, Oregon Wine Research Institute, Oregon State University, Corvallis, OR, United States
| | - R. Paul Schreiner
- USDA-ARS Horticulture Crops Research Unit, Corvallis, OR, United States
- Oregon Wine Research Institute, Corvallis, OR, United States
| | - Patricia A. Skinkis
- Department of Horticulture, Oregon Wine Research Institute, Oregon State University, Corvallis, OR, United States
- Oregon Wine Research Institute, Corvallis, OR, United States
| | - Laurent Deluc
- Department of Horticulture, Oregon Wine Research Institute, Oregon State University, Corvallis, OR, United States
- Oregon Wine Research Institute, Corvallis, OR, United States
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26
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Sandhu N, Sethi M, Kumar A, Dang D, Singh J, Chhuneja P. Biochemical and Genetic Approaches Improving Nitrogen Use Efficiency in Cereal Crops: A Review. FRONTIERS IN PLANT SCIENCE 2021; 12:657629. [PMID: 34149755 PMCID: PMC8213353 DOI: 10.3389/fpls.2021.657629] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Accepted: 04/06/2021] [Indexed: 05/22/2023]
Abstract
Nitrogen is an essential nutrient required in large quantities for the proper growth and development of plants. Nitrogen is the most limiting macronutrient for crop production in most of the world's agricultural areas. The dynamic nature of nitrogen and its tendency to lose soil and environment systems create a unique and challenging environment for its proper management. Exploiting genetic diversity, developing nutrient efficient novel varieties with better agronomy and crop management practices combined with improved crop genetics have been significant factors behind increased crop production. In this review, we highlight the various biochemical, genetic factors and the regulatory mechanisms controlling the plant nitrogen economy necessary for reducing fertilizer cost and improving nitrogen use efficiency while maintaining an acceptable grain yield.
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27
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Tiwari JK, Buckseth T, Singh RK, Kumar M, Kant S. Prospects of Improving Nitrogen Use Efficiency in Potato: Lessons From Transgenics to Genome Editing Strategies in Plants. FRONTIERS IN PLANT SCIENCE 2020; 11:597481. [PMID: 33424892 PMCID: PMC7785987 DOI: 10.3389/fpls.2020.597481] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 12/10/2020] [Indexed: 05/27/2023]
Affiliation(s)
- Jagesh Kumar Tiwari
- Indian Council of Agricultural Research (ICAR)-Central Potato Research Institute, Shimla, India
| | - Tanuja Buckseth
- Indian Council of Agricultural Research (ICAR)-Central Potato Research Institute, Shimla, India
| | - Rajesh Kumar Singh
- Indian Council of Agricultural Research (ICAR)-Central Potato Research Institute, Shimla, India
| | - Manoj Kumar
- Indian Council of Agricultural Research (ICAR)-Central Potato Research Institute, Shimla, India
| | - Surya Kant
- Agriculture Victoria, Grains Innovation Park, Horsham, VIC, Australia
- Faculty of Veterinary and Agricultural Sciences, Centre for Agricultural Innovation, School of Agriculture and Food, The University of Melbourne, Melbourne, VIC, Australia
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28
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Anas M, Liao F, Verma KK, Sarwar MA, Mahmood A, Chen ZL, Li Q, Zeng XP, Liu Y, Li YR. Fate of nitrogen in agriculture and environment: agronomic, eco-physiological and molecular approaches to improve nitrogen use efficiency. Biol Res 2020; 53:47. [PMID: 33066819 PMCID: PMC7565752 DOI: 10.1186/s40659-020-00312-4] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 09/20/2020] [Indexed: 11/10/2022] Open
Abstract
Nitrogen is the main limiting nutrient after carbon, hydrogen and oxygen for photosynthetic process, phyto-hormonal, proteomic changes and growth-development of plants to complete its lifecycle. Excessive and inefficient use of N fertilizer results in enhanced crop production costs and atmospheric pollution. Atmospheric nitrogen (71%) in the molecular form is not available for the plants. For world's sustainable food production and atmospheric benefits, there is an urgent need to up-grade nitrogen use efficiency in agricultural farming system. The nitrogen use efficiency is the product of nitrogen uptake efficiency and nitrogen utilization efficiency, it varies from 30.2 to 53.2%. Nitrogen losses are too high, due to excess amount, low plant population, poor application methods etc., which can go up to 70% of total available nitrogen. These losses can be minimized up to 15-30% by adopting improved agronomic approaches such as optimal dosage of nitrogen, application of N by using canopy sensors, maintaining plant population, drip fertigation and legume based intercropping. A few transgenic studies have shown improvement in nitrogen uptake and even increase in biomass. Nitrate reductase, nitrite reductase, glutamine synthetase, glutamine oxoglutarate aminotransferase and asparagine synthetase enzyme have a great role in nitrogen metabolism. However, further studies on carbon-nitrogen metabolism and molecular changes at omic levels are required by using "whole genome sequencing technology" to improve nitrogen use efficiency. This review focus on nitrogen use efficiency that is the major concern of modern days to save economic resources without sacrificing farm yield as well as safety of global environment, i.e. greenhouse gas emissions, ammonium volatilization and nitrate leaching.
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Affiliation(s)
- Muhammad Anas
- College of Agriculture, Guangxi University, Nanning, 530005, China
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture/Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, Guangxi, China
| | - Fen Liao
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture/Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, Guangxi, China
| | - Krishan K Verma
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture/Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, Guangxi, China
| | | | - Aamir Mahmood
- College of Agriculture, Guangxi University, Nanning, 530005, China
| | - Zhong-Liang Chen
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture/Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, Guangxi, China
| | - Qiang Li
- College of Agriculture, Guangxi University, Nanning, 530005, China
| | - Xu-Peng Zeng
- College of Agriculture, Guangxi University, Nanning, 530005, China
| | - Yang Liu
- Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Nanning, 530007, China.
| | - Yang-Rui Li
- College of Agriculture, Guangxi University, Nanning, 530005, China.
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture/Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, Guangxi, China.
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Liu B, Wu J, Yang S, Schiefelbein J, Gan Y. Nitrate regulation of lateral root and root hair development in plants. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:4405-4414. [PMID: 31796961 PMCID: PMC7382377 DOI: 10.1093/jxb/erz536] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 12/03/2019] [Indexed: 05/16/2023]
Abstract
Nitrogen (N) is one of the most important macronutrients for plant growth and development. However, the concentration and distribution of N varies in soil due to a variety of environmental factors. In response, higher plants have evolved a developmentally flexible root system to efficiently take up N under N-limited conditions. Over the past decade, significant progress has been made in understanding this form of plant 'root-foraging' behavior, which is controlled by both a local and a long-distance systemic nitrate signaling pathway. In this review, we focus on the key components of nitrate perception, signaling, and transduction and its role in lateral root development. We also highlight recent findings on the molecular mechanisms of the nitrate systemic signaling pathway, including small signaling peptides involved in long-distance shoot-root communication. Furthermore, we summarize the transcription factor networks responsible for nitrate-dependent lateral root and root hair development.
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Affiliation(s)
- Bohan Liu
- Zhejiang Key Laboratory of Crop Germplasm, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Junyu Wu
- Zhejiang Key Laboratory of Crop Germplasm, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Shuaiqi Yang
- Zhejiang Key Laboratory of Crop Germplasm, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - John Schiefelbein
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
- Correspondence: or
| | - Yinbo Gan
- Zhejiang Key Laboratory of Crop Germplasm, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- Correspondence: or
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Vidal EA, Alvarez JM, Araus V, Riveras E, Brooks MD, Krouk G, Ruffel S, Lejay L, Crawford NM, Coruzzi GM, Gutiérrez RA. Nitrate in 2020: Thirty Years from Transport to Signaling Networks. THE PLANT CELL 2020; 32:2094-2119. [PMID: 32169959 PMCID: PMC7346567 DOI: 10.1105/tpc.19.00748] [Citation(s) in RCA: 154] [Impact Index Per Article: 38.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 02/05/2020] [Accepted: 03/10/2020] [Indexed: 05/18/2023]
Abstract
Nitrogen (N) is an essential macronutrient for plants and a major limiting factor for plant growth and crop production. Nitrate is the main source of N available to plants in agricultural soils and in many natural environments. Sustaining agricultural productivity is of paramount importance in the current scenario of increasing world population, diversification of crop uses, and climate change. Plant productivity for major crops around the world, however, is still supported by excess application of N-rich fertilizers with detrimental economic and environmental impacts. Thus, understanding how plants regulate nitrate uptake and metabolism is key for developing new crops with enhanced N use efficiency and to cope with future world food demands. The study of plant responses to nitrate has gained considerable interest over the last 30 years. This review provides an overview of key findings in nitrate research, spanning biochemistry, molecular genetics, genomics, and systems biology. We discuss how we have reached our current view of nitrate transport, local and systemic nitrate sensing/signaling, and the regulatory networks underlying nitrate-controlled outputs in plants. We hope this summary will serve not only as a timeline and information repository but also as a baseline to define outstanding questions for future research.
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Affiliation(s)
- Elena A Vidal
- Millennium Institute for Integrative Biology, Santiago, Chile, 7500565
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago, Chile, 8580745
- Escuela de Biotecnología, Facultad de Ciencias, Universidad Mayor, Santiago, Chile, 8580745
| | - José M Alvarez
- Millennium Institute for Integrative Biology, Santiago, Chile, 7500565
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago, Chile, 8580745
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York 10003
| | - Viviana Araus
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York 10003
| | - Eleodoro Riveras
- Millennium Institute for Integrative Biology, Santiago, Chile, 7500565
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile, 8331150
- FONDAP Center for Genome Regulation, Santiago, Chile, 8370415
| | - Matthew D Brooks
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York 10003
| | - Gabriel Krouk
- Biochemistry and Plant Molecular Physiology, CNRS, INRA, Montpellier SupAgro, Universite Montpellier, Montpellier, France, 34060
| | - Sandrine Ruffel
- Biochemistry and Plant Molecular Physiology, CNRS, INRA, Montpellier SupAgro, Universite Montpellier, Montpellier, France, 34060
| | - Laurence Lejay
- Biochemistry and Plant Molecular Physiology, CNRS, INRA, Montpellier SupAgro, Universite Montpellier, Montpellier, France, 34060
| | - Nigel M Crawford
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, California, 92093
| | - Gloria M Coruzzi
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York 10003
| | - Rodrigo A Gutiérrez
- Millennium Institute for Integrative Biology, Santiago, Chile, 7500565
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile, 8331150
- FONDAP Center for Genome Regulation, Santiago, Chile, 8370415
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Chardon F, Cueff G, Delannoy E, Aubé F, Lornac A, Bedu M, Gilard F, Pateyron S, Rogniaux H, Gargaros A, Mireau H, Rajjou L, Martin-Magniette ML, Budar F. The Consequences of a Disruption in Cyto-Nuclear Coadaptation on the Molecular Response to a Nitrate Starvation in Arabidopsis. PLANTS (BASEL, SWITZERLAND) 2020; 9:E573. [PMID: 32369924 PMCID: PMC7285260 DOI: 10.3390/plants9050573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 04/20/2020] [Accepted: 04/22/2020] [Indexed: 12/04/2022]
Abstract
Mitochondria and chloroplasts are important actors in the plant nutritional efficiency. So, it could be expected that a disruption of the coadaptation between nuclear and organellar genomes impact plant response to nutrient stresses. We addressed this issue using two Arabidopsis accessions, namely Ct1 and Jea, and their reciprocal cytolines possessing the nuclear genome from one parent and the organellar genomes of the other one. We measured gene expression, and quantified proteins and metabolites under N starvation and non-limiting conditions. We observed a typical response to N starvation at the phenotype and molecular levels. The phenotypical response to N starvation was similar in the cytolines compared to the parents. However, we observed an effect of the disruption of genomic coadaptation at the molecular levels, distinct from the previously described responses to organellar stresses. Strikingly, genes differentially expressed in cytolines compared to parents were mainly repressed in the cytolines. These genes encoded more mitochondrial and nuclear proteins than randomly expected, while N starvation responsive ones were enriched in genes for chloroplast and nuclear proteins. In cytolines, the non-coadapted cytonuclear genomic combination tends to modulate the response to N starvation observed in the parental lines on various biological processes.
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Affiliation(s)
- Fabien Chardon
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000 Versailles, France; (G.C.); (F.A.); (A.L.); (M.B.); (H.M.); (L.R.)
| | - Gwendal Cueff
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000 Versailles, France; (G.C.); (F.A.); (A.L.); (M.B.); (H.M.); (L.R.)
| | - Etienne Delannoy
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Univ Evry, 91405 Orsay, France; (E.D.); (F.G.); (S.P.); (M.-L.M.-M.)
- CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Université de Paris, 91405 Orsay, France
| | - Fabien Aubé
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000 Versailles, France; (G.C.); (F.A.); (A.L.); (M.B.); (H.M.); (L.R.)
| | - Aurélia Lornac
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000 Versailles, France; (G.C.); (F.A.); (A.L.); (M.B.); (H.M.); (L.R.)
| | - Magali Bedu
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000 Versailles, France; (G.C.); (F.A.); (A.L.); (M.B.); (H.M.); (L.R.)
| | - Françoise Gilard
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Univ Evry, 91405 Orsay, France; (E.D.); (F.G.); (S.P.); (M.-L.M.-M.)
- CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Université de Paris, 91405 Orsay, France
| | - Stéphanie Pateyron
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Univ Evry, 91405 Orsay, France; (E.D.); (F.G.); (S.P.); (M.-L.M.-M.)
- CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Université de Paris, 91405 Orsay, France
| | - Hélène Rogniaux
- INRAE, UR BIA, F-44316 Nantes, France; (H.R.); (A.G.)
- INRAE, BIBS Facility, F-44316 Nantes, France
| | - Audrey Gargaros
- INRAE, UR BIA, F-44316 Nantes, France; (H.R.); (A.G.)
- INRAE, BIBS Facility, F-44316 Nantes, France
| | - Hakim Mireau
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000 Versailles, France; (G.C.); (F.A.); (A.L.); (M.B.); (H.M.); (L.R.)
| | - Loïc Rajjou
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000 Versailles, France; (G.C.); (F.A.); (A.L.); (M.B.); (H.M.); (L.R.)
| | - Marie-Laure Martin-Magniette
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Univ Evry, 91405 Orsay, France; (E.D.); (F.G.); (S.P.); (M.-L.M.-M.)
- CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Université de Paris, 91405 Orsay, France
- UMR MIA-Paris, AgroParisTech, INRA, Université Paris-Saclay, 75005 Paris, France
| | - Françoise Budar
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000 Versailles, France; (G.C.); (F.A.); (A.L.); (M.B.); (H.M.); (L.R.)
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Fan H, Quan S, Qi S, Xu N, Wang Y. Novel Aspects of Nitrate Regulation in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2020; 11:574246. [PMID: 33362808 PMCID: PMC7758431 DOI: 10.3389/fpls.2020.574246] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 11/18/2020] [Indexed: 05/04/2023]
Abstract
Nitrogen (N) is one of the most essential macronutrients for plant growth and development. Nitrate (NO3 -), the major form of N that plants uptake from the soil, acts as an important signaling molecule in addition to its nutritional function. Over the past decade, significant progress has been made in identifying new components involved in NO3 - regulation and starting to unravel the NO3 - regulatory network. Great reviews have been made recently by scientists on the key regulators in NO3 - signaling, NO3 - effects on plant development, and its crosstalk with phosphorus (P), potassium (K), hormones, and calcium signaling. However, several novel aspects of NO3 - regulation have not been previously reviewed in detail. Here, we mainly focused on the recent advances of post-transcriptional regulation and non-coding RNA (ncRNAs) in NO3 - signaling, and NO3 - regulation on leaf senescence and the circadian clock. It will help us to extend the general picture of NO3 - regulation and provide a basis for further exploration of NO3 - regulatory network.
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Affiliation(s)
- Hongmei Fan
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai’an, China
| | - Shuxuan Quan
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai’an, China
| | - Shengdong Qi
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai’an, China
| | - Na Xu
- School of Biological Science, Jining Medical University, Rizhao, China
| | - Yong Wang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai’an, China
- *Correspondence: Yong Wang,
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Mu X, Luo J. Evolutionary analyses of NIN-like proteins in plants and their roles in nitrate signaling. Cell Mol Life Sci 2019; 76:3753-3764. [PMID: 31161283 PMCID: PMC11105697 DOI: 10.1007/s00018-019-03164-8] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 05/27/2019] [Accepted: 05/28/2019] [Indexed: 12/21/2022]
Abstract
Nitrogen (N) is one of the most important essential macro-elements for plant growth and development, and nitrate represents the most abundant inorganic form of N in soils. The nitrate uptake and assimilation processes are finely tuned according to the available nitrate in the surroundings as well as by the internal finely coordinated signaling pathways. The NIN-like proteins (NLPs) harbor both RWP-RK, and Phox and Bem1 (PB1) domains, and they belong to the well-characterized plant-specific RWP-RK transcription factor gene family. NLPs are known to be involved in the nitrate signaling pathway by activating downstream target genes, and thus they are implicated in the primary nitrate response in the nucleus via their RWP-RK domains. The PB1 domain is a ubiquitous protein-protein interaction domain and it comprises another regulatory layer for NLPs via the protein interactions within NLPs or with other essential components. Recently, Ca2+-Ca2+ sensor protein kinase-NLP signaling cascades have been identified and they allow NLPs to have central roles in mediating the nitrate signaling pathway. NLPs play essential roles in many aspects of plant growth and development via the finely tuned nitrate signaling pathway. Furthermore, recent studies have highlighted the emerging roles played by NLPs in the N starvation response, nodule formation in legumes, N and P interactions, and root cap release in higher plants. In this review, we consider recent advances in the identification, evolution, molecular characteristics, and functions of the NLP gene family in plant growth and development.
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Affiliation(s)
- Xiaohuan Mu
- State Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Jie Luo
- College of Horticulture and Forestry Sciences, Hubei Engineering Technology Research Center for Forestry Information, Huazhong Agricultural University, Wuhan, 430070, China.
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Zuluaga DL, Sonnante G. The Use of Nitrogen and Its Regulation in Cereals: Structural Genes, Transcription Factors, and the Role of miRNAs. PLANTS 2019; 8:plants8080294. [PMID: 31434274 PMCID: PMC6724420 DOI: 10.3390/plants8080294] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 08/15/2019] [Accepted: 08/16/2019] [Indexed: 01/31/2023]
Abstract
Cereals and, especially, rice, maize, and wheat, are essential commodities, on which human nutrition is based. Expanding population and food demand have required higher production which has been achieved by increasing fertilization, and especially nitrogen supply to cereal crops. In fact, nitrogen is a crucial nutrient for the plant, but excessive use poses serious environmental and health issues. Therefore, increasing nitrogen use efficiency in cereals is of pivotal importance for sustainable agriculture. The main steps in the use of nitrogen are uptake and transport, reduction and assimilation, and translocation and remobilization. Many studies have been carried out on the genes involved in these phases, and on transcription factors regulating these genes. Lately, increasing attention has been paid to miRNAs responding to abiotic stress, including nutrient deficiency. Many miRNAs have been found to regulate transcription factors acting on the expression of specific genes for nitrogen uptake or remobilization. Recent studies on gene regulatory networks have also demonstrated that miRNAs can interact with several nodes in the network, functioning as key regulators in nitrogen metabolism.
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Affiliation(s)
- Diana L Zuluaga
- Institute of Biosciences and Bioresources, National Research Council, Via Amendola 165/A, 70126 Bari, Italy.
| | - Gabriella Sonnante
- Institute of Biosciences and Bioresources, National Research Council, Via Amendola 165/A, 70126 Bari, Italy.
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Huang S, Liang Z, Chen S, Sun H, Fan X, Wang C, Xu G, Zhang Y. A Transcription Factor, OsMADS57, Regulates Long-Distance Nitrate Transport and Root Elongation. PLANT PHYSIOLOGY 2019; 180:882-895. [PMID: 30886113 PMCID: PMC6548263 DOI: 10.1104/pp.19.00142] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 02/25/2019] [Indexed: 05/19/2023]
Abstract
Root nitrate uptake adjusts to the plant's nitrogen demand for growth. Here, we report that OsMADS57, a MADS-box transcription factor, modulates nitrate translocation from rice (Oryza sativa) roots to shoots under low-nitrate conditions. OsMADS57 is abundantly expressed in xylem parenchyma cells of root stele and is induced by nitrate. Compared with wild-type rice plants supplied with 0.2 mM nitrate, osmads57 mutants had 31% less xylem loading of nitrate, while overexpression lines had 2-fold higher levels. Shoot-root 15N content ratios were 40% lower in the mutants and 76% higher in the overexpression lines. Rapid NO3 - root influx experiments showed that mutation of OsMADS57 did not affect root nitrate uptake. Reverse transcription quantitative PCR analysis of OsNRT2 nitrate transporter genes showed that after 5 min in 0.2 mM nitrate, only OsNRT2.3a (a vascular-specific high-affinity nitrate transporter) had reduced (by two-thirds) expression levels. At 60 min of nitrate treatment, lower expression levels were also observed for three additional NRT2 genes (OsNRT2.1/2.2/2.4). Conversely, in the overexpression lines, four NRT2 genes had much higher expression profiles at all time points tested. As previously reported, OsNRT2.3a functions in nitrate translocation, indicating the possible interaction between OsMADS57 and OsNRT2.3a Yeast one-hybrid and transient expression assays demonstrated that OsMADS57 binds to the CArG motif (CATTTTATAG) within the OsNRT2.3a promoter. Moreover, seminal root elongation was inhibited in osmads57 mutants, which may be associated with higher auxin levels in and auxin polar transport to root tips of mutant plants. Taken together, these results suggest that OsMADS57 has a role in regulating nitrate translocation from root to shoot via OsNRT2.3a.
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Affiliation(s)
- Shuangjie Huang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
- Henan Key Laboratory of Tea Plant Comprehensive Utilization in South Henan, Xinyang Agriculture and Forestry University, Xinyang 464000, China
| | - Zhihao Liang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Si Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Huwei Sun
- College of Agronomy, Collaborative Innovation Center of Henan Grain Crops, Key Laboratory of Rice Biology in Henan Province, Henan Agricultural University, Zhengzhou 450002, China
| | - Xiaorong Fan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Cailin Wang
- Institute of Food Crops of Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Guohua Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Yali Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
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Singh BN, Dwivedi P, Sarma BK, Singh GS, Singh HB. A novel function of N-signaling in plants with special reference to Trichoderma interaction influencing plant growth, nitrogen use efficiency, and cross talk with plant hormones. 3 Biotech 2019; 9:109. [PMID: 30863693 DOI: 10.1007/s13205-019-1638-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 02/16/2019] [Indexed: 10/27/2022] Open
Abstract
Trichoderma spp. is considered as a plant growth promoter and biocontrol fungal agents. They colonize on the surface of root in most of the agriculture crops. They secrete different secondary metabolites and enzymes which promote different physiological processes as well as protect plants from various environmental stresses. This is part of their vital functions. They are widely exploited as a biocontrol agent and plant growth promoter in agricultural fields. Colonization of Trichoderma with roots can enhance nutrient acquisition from surrounding soil to root and can substantially increase nitrogen use efficiency (NUE) in crops and linked with activation of plant signaling cascade. Among Trichoderma species, only some Trichoderma species were well characterized which help in the uptake of nitrogen-containing compound (especially nitrate form) and induced nitric oxide (NO) in plants. Both nitrate and NO are known as a signaling agent, involved in plant growth and development and disease resistance. Activation of these signaling molecules may crosstalk with other signaling molecule (Ca2+) and phytohormone (auxin, gibberellins, cytokinin and ethylene). This ability of Trichoderma is important to agriculture not only for increased plant growth but also to control plant diseases. Recently, Trichoderma strains have been shown to encompass the ability to regulate transcripts level of high-affinity nitrate transporters and probably it was positively regulated by NO. This review aims to focus the usage of Trichoderma strains on crops by their abilities to regulate transcript levels, probably through activation of plant N signaling transduction that improve plant health.
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Li J, Gao Z, Zhou L, Li L, Zhang J, Liu Y, Chen H. Comparative transcriptome analysis reveals K + transporter gene contributing to salt tolerance in eggplant. BMC PLANT BIOLOGY 2019; 19:67. [PMID: 30744551 PMCID: PMC6371450 DOI: 10.1186/s12870-019-1663-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 01/25/2019] [Indexed: 05/20/2023]
Abstract
BACKGROUND Soil salinization is one of the most crucial abiotic stresses that limit the growth and production of eggplant. The existing researches in eggplant were mostly focused on salt-induced morphological, biochemical and physiological changes, with only limited works centered on salt-response genes in eggplant at the transcriptomic level. RESULTS Our preliminary work found that Zhusiqie (No.118) is salt-tolerant and Hongqie (No.30) is salt-sensitive. Consequently, they were re-named as ST118 and SS30, respectively. ST118 showed less damaged on growth and higher K+/Na+ ratios in leaves than SS30. Comparative-transcriptome analysis was used as a powerful approach to understand the salt-response mechanisms in the leaves and roots of SS30 and ST118. And it revealed that genotype-specific and organ-specific manners exist in eggplant in response to salt stress. Strikingly, the genotype-specific differentially expressed genes (DEGs) in ST118 were considered crucial to its higher salt-tolerance, because the expression patterns of common DEGs in the leaves/roots of the two eggplant genotypes were almost the same. Among them, some transcription factors have been reported to be in response to elevated external salinity, including the members of C2C2-CO-like, WRKY, MYB and NAC family. In addition, the AKT1, KAT1 and SOS1 were up-regulated only in the leaves of ST118. Furthermore, the complementation assays demonstrated that the salt-tolerances of both yeast and Arabidopsis akt1 mutants were enhanced by heterologous expression of SmAKT1. CONCLUSION The comparative-transcriptome analysis indicated that the salt-tolerance can be increased by higher transcript level of some genotype-specific genes. This work revealed that eggplants seem to be more inclined to absorb K+ rather than to exclude Na+ under salt stress conditions because seven K+ transporters were significantly up-regulated, while only one Na+ transporter was similarly regulated. Finally, the complementation assays of SmAKT1, which is genotype-specific up-regulated in ST118, suggest that the other TFs and K+ transport genes were worthy of future investigation for their functions in salinity tolerance.
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Affiliation(s)
- Jing Li
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai, 200240 China
| | - Zhen Gao
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai, 200240 China
| | - Lu Zhou
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai, 200240 China
| | - Linzhi Li
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai, 200240 China
| | - Junhao Zhang
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai, 200240 China
| | - Yang Liu
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai, 200240 China
| | - Huoying Chen
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai, 200240 China
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38
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Gaudinier A, Rodriguez-Medina J, Zhang L, Olson A, Liseron-Monfils C, Bågman AM, Foret J, Abbitt S, Tang M, Li B, Runcie DE, Kliebenstein DJ, Shen B, Frank MJ, Ware D, Brady SM. Transcriptional regulation of nitrogen-associated metabolism and growth. Nature 2018; 563:259-264. [PMID: 30356219 DOI: 10.1038/s41586-018-0656-3] [Citation(s) in RCA: 148] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 08/22/2018] [Indexed: 11/09/2022]
Abstract
Nitrogen is an essential macronutrient for plant growth and basic metabolic processes. The application of nitrogen-containing fertilizer increases yield, which has been a substantial factor in the green revolution1. Ecologically, however, excessive application of fertilizer has disastrous effects such as eutrophication2. A better understanding of how plants regulate nitrogen metabolism is critical to increase plant yield and reduce fertilizer overuse. Here we present a transcriptional regulatory network and twenty-one transcription factors that regulate the architecture of root and shoot systems in response to changes in nitrogen availability. Genetic perturbation of a subset of these transcription factors revealed coordinate transcriptional regulation of enzymes involved in nitrogen metabolism. Transcriptional regulators in the network are transcriptionally modified by feedback via genetic perturbation of nitrogen metabolism. The network, genes and gene-regulatory modules identified here will prove critical to increasing agricultural productivity.
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Affiliation(s)
- Allison Gaudinier
- Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA, USA
| | - Joel Rodriguez-Medina
- Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA, USA
| | - Lifang Zhang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, Cold Spring Harbor, NY, USA
| | - Andrew Olson
- Cold Spring Harbor Laboratory, Cold Spring Harbor, Cold Spring Harbor, NY, USA
| | | | - Anne-Maarit Bågman
- Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA, USA
| | - Jessica Foret
- Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA, USA
| | | | - Michelle Tang
- Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA, USA.,Department of Plant Sciences, University of California, Davis, Davis, CA, USA
| | - Baohua Li
- Department of Plant Sciences, University of California, Davis, Davis, CA, USA
| | - Daniel E Runcie
- Department of Plant Sciences, University of California, Davis, Davis, CA, USA
| | - Daniel J Kliebenstein
- Department of Plant Sciences, University of California, Davis, Davis, CA, USA.,DynaMo Center of Excellence, University of Copenhagen, Frederiksberg C, Denmark
| | - Bo Shen
- DuPont Pioneer, Johnston, IA, USA
| | | | - Doreen Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, Cold Spring Harbor, NY, USA.,US Department of Agriculture, Agricultural Research Service, Ithaca, NY, USA
| | - Siobhan M Brady
- Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA, USA.
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39
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Wang XF, An JP, Liu X, Su L, You CX, Hao YJ. The Nitrate-Responsive Protein MdBT2 Regulates Anthocyanin Biosynthesis by Interacting with the MdMYB1 Transcription Factor. PLANT PHYSIOLOGY 2018; 178:890-906. [PMID: 29807931 PMCID: PMC6181044 DOI: 10.1104/pp.18.00244] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 05/17/2018] [Indexed: 05/19/2023]
Abstract
In addition to scavenging reactive oxygen species, anthocyanins are pigments that give organs their color. In apple (Malus domestica), R2R3-MYB transcription factor MdMYB1 is a master regulator of anthocyanin biosynthesis and fruit coloration. In this study, we found that MdMYB1 was degraded via a ubiquitin-dependent pathway in response to nitrate, an inhibitor of anthocyanin synthesis. Using a yeast two-hybrid (Y2H) approach, we found that the BTB-TAZ protein encoded by the nitrate-responsive gene MdBT2 interacts with MdMYB1. Pull-down and coimmunoprecipitation assays supported this conclusion. In vivo and in vitro experiments revealed that MdBT2 promoted the ubiquitination and degradation of MdMYB1 through a cullin protein MdCUL3-independent pathway. Expression analysis demonstrated that MdBT2 and MdMYB1 were inversely regulated by nitrate and other environmental signals. Furthermore, we used transgenic approaches in apple and Arabidopsis (Arabidopsis thaliana) to characterize the function of MdBT2 in regulating anthocyanin biosynthesis in response to nitrate. Our findings provide insight into a mechanism involving the MdBT2-MdMYB1 pathway that regulates anthocyanin accumulation in apple and possibly in other plant species.
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Affiliation(s)
- Xiao-Fei Wang
- National Key Laboratory of Crop Biology, Shandong Agricultural University, Tai-An 271018, Shandong, China
- National Research Center for Apple Engineering and Technology, Shandong Agricultural University, Tai-An 271018, Shandong, China
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An 271018, Shandong, China
| | - Jian-Ping An
- National Key Laboratory of Crop Biology, Shandong Agricultural University, Tai-An 271018, Shandong, China
- National Research Center for Apple Engineering and Technology, Shandong Agricultural University, Tai-An 271018, Shandong, China
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An 271018, Shandong, China
| | - Xin Liu
- National Key Laboratory of Crop Biology, Shandong Agricultural University, Tai-An 271018, Shandong, China
- National Research Center for Apple Engineering and Technology, Shandong Agricultural University, Tai-An 271018, Shandong, China
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An 271018, Shandong, China
| | - Ling Su
- National Key Laboratory of Crop Biology, Shandong Agricultural University, Tai-An 271018, Shandong, China
- National Research Center for Apple Engineering and Technology, Shandong Agricultural University, Tai-An 271018, Shandong, China
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An 271018, Shandong, China
| | - Chun-Xiang You
- National Key Laboratory of Crop Biology, Shandong Agricultural University, Tai-An 271018, Shandong, China
- National Research Center for Apple Engineering and Technology, Shandong Agricultural University, Tai-An 271018, Shandong, China
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An 271018, Shandong, China
| | - Yu-Jin Hao
- National Key Laboratory of Crop Biology, Shandong Agricultural University, Tai-An 271018, Shandong, China
- National Research Center for Apple Engineering and Technology, Shandong Agricultural University, Tai-An 271018, Shandong, China
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An 271018, Shandong, China
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40
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Liu C, Zeng L, Zhu S, Wu L, Wang Y, Tang S, Wang H, Zheng X, Zhao J, Chen X, Dai Q, Liu T. Draft genome analysis provides insights into the fiber yield, crude protein biosynthesis, and vegetative growth of domesticated ramie (Boehmeria nivea L. Gaud). DNA Res 2018; 25:173-181. [PMID: 29149285 PMCID: PMC5909428 DOI: 10.1093/dnares/dsx047] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 11/01/2017] [Indexed: 12/26/2022] Open
Abstract
Plentiful bast fiber, a high crude protein content, and vigorous vegetative growth make ramie a popular fiber and forage crop. Here, we report the draft genome of ramie, along with a genomic comparison and evolutionary analysis. The draft genome contained a sequence of approximately 335.6 Mb with 42,463 predicted genes. A high-density genetic map with 4,338 single nucleotide polymorphisms (SNPs) was developed and used to anchor the genome sequence, thus, creating an integrated genetic and physical map containing a 58.2-Mb genome sequence and 4,304 molecular markers. A genomic comparison identified 1,075 unique gene families in ramie, containing 4,082 genes. Among these unique genes, five were cellulose synthase genes that were specifically expressed in stem bark, and 3 encoded a WAT1-related protein, suggesting that they are probably related to high bast fiber yield. An evolutionary analysis detected 106 positively selected genes, 22 of which were related to nitrogen metabolism, indicating that they are probably responsible for the crude protein content and vegetative growth of domesticated varieties. This study is the first to characterize the genome and develop a high-density genetic map of ramie and provides a basis for the genetic and molecular study of this crop.
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Affiliation(s)
- Chan Liu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Liangbin Zeng
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Siyuan Zhu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Lingqing Wu
- Novogene Bioinformatics Institute, Beijing, China
| | - Yanzhou Wang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Shouwei Tang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Hongwu Wang
- Xianning Agriculture Academy of sciences, Hubei, China
| | - Xia Zheng
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Jian Zhao
- Novogene Bioinformatics Institute, Beijing, China
| | - Xiaorong Chen
- Yichun Institute of Agricultural Sciences, Jiangxi, China
| | - Qiuzhong Dai
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Touming Liu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
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41
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Perchlik M, Tegeder M. Leaf Amino Acid Supply Affects Photosynthetic and Plant Nitrogen Use Efficiency under Nitrogen Stress. PLANT PHYSIOLOGY 2018; 178:174-188. [PMID: 30082496 PMCID: PMC6130036 DOI: 10.1104/pp.18.00597] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 07/23/2018] [Indexed: 05/18/2023]
Abstract
The coordinated distribution of nitrogen to source leaves and sinks is essential for supporting leaf metabolism while also supplying sufficient nitrogen to seeds for development. This study aimed to understand how regulated amino acid allocation to leaves affects photosynthesis and overall plant nitrogen use efficiency in Arabidopsis (Arabidopsis thaliana) and how soil nitrogen availability influences these processes. Arabidopsis plants with a knockout of AAP2, encoding an amino acid permease involved in xylem-to-phloem transfer of root-derived amino acids, were grown in low-, moderate-, and high-nitrogen environments. We analyzed nitrogen allocation to shoot tissues, photosynthesis, and photosynthetic and plant nitrogen use efficiency in these knockout plants. Our results demonstrate that, independent of nitrogen conditions, aap2 plants allocate more nitrogen to leaves than wild-type plants. Increased leaf nitrogen supply positively affected chlorophyll and Rubisco levels, photosynthetic nitrogen use efficiency, and carbon assimilation and transport to sinks. The aap2 plants outperformed wild-type plants with respect to growth, seed yield and carbon storage pools, and nitrogen use efficiency in both high and deficient nitrogen environments. Overall, this study demonstrates that increasing nitrogen allocation to leaves represents an effective strategy for improving carbon fixation and photosynthetic nitrogen use efficiency. The results indicate that an optimized coordination of nitrogen and carbon partitioning processes is critical for high oilseed production in Arabidopsis, including in plants exposed to limiting nitrogen conditions.
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Affiliation(s)
- Molly Perchlik
- School of Biological Sciences, Washington State University, Pullman, Washington 99164
| | - Mechthild Tegeder
- School of Biological Sciences, Washington State University, Pullman, Washington 99164
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42
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Hsieh PH, Kan CC, Wu HY, Yang HC, Hsieh MH. Early molecular events associated with nitrogen deficiency in rice seedling roots. Sci Rep 2018; 8:12207. [PMID: 30111825 PMCID: PMC6093901 DOI: 10.1038/s41598-018-30632-1] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 07/31/2018] [Indexed: 11/16/2022] Open
Abstract
Nitrogen (N) deficiency is one of the most common problems in rice. The symptoms of N deficiency are well documented, but the underlying molecular mechanisms are largely unknown in rice. Here, we studied the early molecular events associated with N starvation (−N, 1 h), focusing on amino acid analysis and identification of −N-regulated genes in rice roots. Interestingly, levels of glutamine rapidly decreased within 15 min of −N treatment, indicating that part of the N-deficient signals could be mediated by glutamine. Transcriptome analysis revealed that genes involved in metabolism, plant hormone signal transduction (e.g. abscisic acid, auxin, and jasmonate), transporter activity, and oxidative stress responses were rapidly regulated by −N. Some of the −N-regulated genes encode transcription factors, protein kinases and protein phosphatases, which may be involved in the regulation of early −N responses in rice roots. Previously, we used similar approaches to identify glutamine-, glutamate-, and ammonium nitrate-responsive genes. Comparisons of the genes induced by different forms of N with the −N-regulated genes identified here have provided a catalog of potential N regulatory genes for further dissection of the N signaling pathwys in rice.
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Affiliation(s)
- Ping-Han Hsieh
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Chia-Cheng Kan
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Hsin-Yu Wu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Hsiu-Chun Yang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Ming-Hsiun Hsieh
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan.
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43
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Poitout A, Crabos A, Petřík I, Novák O, Krouk G, Lacombe B, Ruffel S. Responses to Systemic Nitrogen Signaling in Arabidopsis Roots Involve trans-Zeatin in Shoots. THE PLANT CELL 2018; 30:1243-1257. [PMID: 29764985 PMCID: PMC6048791 DOI: 10.1105/tpc.18.00011] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 03/19/2018] [Accepted: 05/14/2018] [Indexed: 05/18/2023]
Abstract
Plants face temporal and spatial variation in nitrogen (N) availability. This includes heterogeneity in soil nitrate (NO3-) content. To overcome these constraints, plants modify their gene expression and physiological processes to optimize N acquisition. This plasticity relies on a complex long-distance root-shoot-root signaling network that remains poorly understood. We previously showed that cytokinin (CK) biosynthesis is required to trigger systemic N signaling. Here, we performed split-root experiments and used a combination of CK-related mutant analyses, hormone profiling, transcriptomic analysis, NO3- uptake assays, and root growth measurements to gain insight into systemic N signaling in Arabidopsis thaliana By comparing wild-type plants and mutants affected in CK biosynthesis and ABCG14-dependent root-to-shoot translocation of CK, we revealed an important role for active trans-zeatin (tZ) in systemic N signaling. Both rapid sentinel gene regulation and long-term functional acclimation to heterogeneous NO3- supply, including NO3- transport and root growth regulation, are likely mediated by the integration of tZ content in shoots. Furthermore, shoot transcriptome profiling revealed that glutamate/glutamine metabolism is likely a target of tZ root-to-shoot translocation, prompting an interesting hypothesis regarding shoot-to-root communication. Finally, this study highlights tZ-independent pathways regulating gene expression in shoots as well as NO3- uptake activity in response to total N deprivation.
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Affiliation(s)
- Arthur Poitout
- BPMP, INRA, CNRS, Université de Montpellier, Montpellier SupAgro, 34090 Montpellier, France
| | - Amandine Crabos
- BPMP, INRA, CNRS, Université de Montpellier, Montpellier SupAgro, 34090 Montpellier, France
| | - Ivan Petřík
- Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany CAS and Faculty of Science of Palacký University, CZ-78371 Olomouc, Czech Republic
| | - Ondrej Novák
- Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany CAS and Faculty of Science of Palacký University, CZ-78371 Olomouc, Czech Republic
| | - Gabriel Krouk
- BPMP, INRA, CNRS, Université de Montpellier, Montpellier SupAgro, 34090 Montpellier, France
| | - Benoît Lacombe
- BPMP, INRA, CNRS, Université de Montpellier, Montpellier SupAgro, 34090 Montpellier, France
| | - Sandrine Ruffel
- BPMP, INRA, CNRS, Université de Montpellier, Montpellier SupAgro, 34090 Montpellier, France
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Misra A, McKnight TD, Mandadi KK. Bromodomain proteins GTE9 and GTE11 are essential for specific BT2-mediated sugar and ABA responses in Arabidopsis thaliana. PLANT MOLECULAR BIOLOGY 2018; 96:393-402. [PMID: 29363002 DOI: 10.1007/s11103-018-0704-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2017] [Accepted: 01/15/2018] [Indexed: 06/07/2023]
Abstract
Global Transcription Factor Group E proteins GTE9 and GTE11 interact with BT2 to mediate ABA and sugar responses in Arabidopsis thaliana. BT2 is a BTB-domain protein that regulates responses to various hormone, stress and metabolic conditions in Arabidopsis thaliana. Loss of BT2 results in plants that are hypersensitive to inhibition of germination by abscisic acid (ABA) and sugars. Conversely, overexpression of BT2 results in resistance to ABA and sugars. Here, we report the roles of BT2-interacting partners GTE9 and GTE11, bromodomain and extraterminal-domain proteins of Global Transcription Factor Group E, in BT2-mediated responses to sugars and hormones. Loss-of-function mutants, gte9-1 and gte11-1, mimicked the bt2-1-null mutant responses; germination of all three mutants was hypersensitive to inhibition by glucose and ABA. Loss of either GTE9 or GTE11 in a BT2 over-expressing line blocked resistance to sugars and ABA, indicating that both GTE9 and GTE11 were required for BT2 function. Co-immunoprecipitation of BT2 and GTE9 suggested that these proteins physically interact in vivo, and presumably function together to mediate responses to ABA and sugar signals.
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Affiliation(s)
- Anjali Misra
- Department of Biology, Texas A&M University, 3258 TAMU, College Station, TX, 77843-3258, USA
| | - Thomas D McKnight
- Department of Biology, Texas A&M University, 3258 TAMU, College Station, TX, 77843-3258, USA
| | - Kranthi K Mandadi
- Department of Plant Pathology and Microbiology, Texas A&M AgriLife Research & Extension Center, The Texas A&M University System, 2415 East Highway 83, Weslaco, TX, 78596-8344, USA.
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45
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Gras DE, Vidal EA, Undurraga SF, Riveras E, Moreno S, Dominguez-Figueroa J, Alabadi D, Blázquez MA, Medina J, Gutiérrez RA. SMZ/SNZ and gibberellin signaling are required for nitrate-elicited delay of flowering time in Arabidopsis thaliana. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:619-631. [PMID: 29309650 PMCID: PMC5853263 DOI: 10.1093/jxb/erx423] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 11/15/2017] [Indexed: 05/04/2023]
Abstract
The reproductive success of plants largely depends on the correct programming of developmental phase transitions, particularly the shift from vegetative to reproductive growth. The timing of this transition is finely regulated by the integration of an array of environmental and endogenous factors. Nitrogen is the mineral macronutrient that plants require in the largest amount, and as such its availability greatly impacts on many aspects of plant growth and development, including flowering time. We found that nitrate signaling interacts with the age-related and gibberellic acid pathways to control flowering time in Arabidopsis thaliana. We revealed that repressors of flowering time belonging to the AP2-type transcription factor family including SCHLAFMUTZE (SMZ) and SCHNARCHZAPFEN (SNZ) are important regulators of flowering time in response to nitrate. Our results support a model whereby nitrate activates SMZ and SNZ via the gibberellin pathway to repress flowering time in Arabidopsis thaliana.
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Affiliation(s)
- Diana E Gras
- FONDAP Center for Genome Regulation, Millennium Nucleus Center for Plant Systems and Synthetic Biology, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Paraje El Pozo, Santa Fe, Argentina
| | - Elena A Vidal
- FONDAP Center for Genome Regulation, Millennium Nucleus Center for Plant Systems and Synthetic Biology, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
- Centro de Genómica y Bioinformática, Universidad Mayor, Santiago, Chile
| | - Soledad F Undurraga
- FONDAP Center for Genome Regulation, Millennium Nucleus Center for Plant Systems and Synthetic Biology, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Eleodoro Riveras
- FONDAP Center for Genome Regulation, Millennium Nucleus Center for Plant Systems and Synthetic Biology, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Sebastián Moreno
- FONDAP Center for Genome Regulation, Millennium Nucleus Center for Plant Systems and Synthetic Biology, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - José Dominguez-Figueroa
- Centro de Biotecnología y Genómica de Plantas, (UPM-INIA) Campus de Montegancedo, Madrid, Spain
| | - David Alabadi
- Instituto de Biología Molecular y Celular de Plantas (CSIC-Universidad Politécnica de Valencia), Valencia, Spain
| | - Miguel A Blázquez
- Instituto de Biología Molecular y Celular de Plantas (CSIC-Universidad Politécnica de Valencia), Valencia, Spain
| | - Joaquín Medina
- Centro de Biotecnología y Genómica de Plantas, (UPM-INIA) Campus de Montegancedo, Madrid, Spain
| | - Rodrigo A Gutiérrez
- FONDAP Center for Genome Regulation, Millennium Nucleus Center for Plant Systems and Synthetic Biology, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
- Correspondence:
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Ibrahim A, Jin XL, Zhang YB, Cruz J, Vichyavichien P, Esiobu N, Zhang XH. Tobacco plants expressing the maize nitrate transporter ZmNrt2.1 exhibit altered responses of growth and gene expression to nitrate and calcium. BOTANICAL STUDIES 2017; 58:51. [PMID: 29143202 PMCID: PMC5688054 DOI: 10.1186/s40529-017-0203-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 11/09/2017] [Indexed: 05/30/2023]
Abstract
BACKGROUND Nitrate uptake is a highly regulated process. Understanding the intricate interactions between nitrate availability and genetically-controlled nitrate acquisition and metabolism is essential for improving nitrogen use efficiency and increasing nitrate uptake capacity for plants grown in both nitrate-poor and nitrate-enriched environments. In this report, we introduced into tobacco (Nicotiana tabacum) the constitutively expressed maize high-affinity transporter ZmNrt2.1 gene that would bypass the tight control for the endogenous nitrate-responsive genes. By using calcium inhibitors and varying levels of NO3-, Ca2+ and K+, we probed how the host plants were affected in their nitrate response. RESULTS We found that the ZmNrt2.1-expressing plants had better root growth than the wild type plants when Ca2+ was deficient regardless of the nitrate levels. The growth restriction associated with Ca2+-deficiency can be alleviated with a high level of K+. Furthermore, the transgenic plants exhibited altered expression patterns of several endogenous, nitrate-responsive genes, including the high- and low-affinity nitrate transporters, the Bric-a-Brac/Tramtrack/Broad protein BT2 and the transcription factor TGA-binding protein TGA1, in responding to treatments of NO3-, K+ or inhibitors for the calcium channel and the cytosolic Ca2+-regulating phospholipase C, as compared to the wild type plants under the same treatments. Their expression was not only responsive to nitrate, but also affected by Ca2+. There were also different patterns of gene expression between roots and shoots. CONCLUSION Our results demonstrate the ectopic effect of the maize nitrate transporter on the host plant's overall gene expression of nitrate sensing system, and further highlight the involvement of calcium in nitrate sensing in tobacco plants.
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Affiliation(s)
- Abubakar Ibrahim
- Department of Biological Sciences, Florida Atlantic University, Boca Raton, FL 33431 USA
- Department of Soil Sciences, Modibbo Adama University of Technology, Yola, Nigeria
| | - Xiao-Lu Jin
- Department of Biological Sciences, Florida Atlantic University, Boca Raton, FL 33431 USA
| | - Yu-Bin Zhang
- Department of Biological Sciences, Florida Atlantic University, Boca Raton, FL 33431 USA
- Monitoring Center for Marine Resources and Environments, Guangdong Ocean University, Zhanjiang, 524088 China
| | - Jessica Cruz
- Department of Biological Sciences, Florida Atlantic University, Boca Raton, FL 33431 USA
| | - Paveena Vichyavichien
- Department of Biological Sciences, Florida Atlantic University, Boca Raton, FL 33431 USA
| | - Nwadiuto Esiobu
- Department of Biological Sciences, Florida Atlantic University, Boca Raton, FL 33431 USA
| | - Xing-Hai Zhang
- Department of Biological Sciences, Florida Atlantic University, Boca Raton, FL 33431 USA
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Perchlik M, Tegeder M. Improving Plant Nitrogen Use Efficiency through Alteration of Amino Acid Transport Processes. PLANT PHYSIOLOGY 2017; 175:235-247. [PMID: 28733388 PMCID: PMC5580756 DOI: 10.1104/pp.17.00608] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 07/18/2017] [Indexed: 05/08/2023]
Abstract
Improving the efficiency of nitrogen (N) uptake and utilization in plants could potentially increase crop yields while reducing N fertilization and, subsequently, environmental pollution. Within most plants, N is transported primarily as amino acids. In this study, pea (Pisum sativum) plants overexpressing AMINO ACID PERMEASE1 (AAP1) were used to determine if and how genetic manipulation of amino acid transport from source to sink affects plant N use efficiency. The modified plants were grown under low, moderate, or high N fertilization regimes. The results showed that, independent of the N nutrition, the engineered plants allocate more N via the vasculature to the shoot and seeds and produce more biomass and higher seed yields than wild-type plants. Dependent on the amount of N supplied, the AAP1-overexpressing plants displayed improved N uptake or utilization efficiency, or a combination of the two. They also showed significantly increased N use efficiency in N-deficient as well as in N-rich soils and, impressively, required half the amount of N to produce as many fruits and seeds as control plants. Together, these data support that engineering N allocation from source to sink presents an effective strategy to produce crop plants with improved productivity as well as N use efficiency in a range of N environments.
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Affiliation(s)
- Molly Perchlik
- School of Biological Sciences, Washington State University, Pullman, Washington 99164
| | - Mechthild Tegeder
- School of Biological Sciences, Washington State University, Pullman, Washington 99164
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Li J, Su X, Wang Y, Yang W, Pan Y, Su C, Zhang X. Genome-wide identification and expression analysis of the BTB domain-containing protein gene family in tomato. Genes Genomics 2017; 40:1-15. [PMID: 29892895 DOI: 10.1007/s13258-017-0604-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 08/03/2017] [Indexed: 01/01/2023]
Abstract
BTB (broad-complex, tramtrack, and bric-a-brac) family proteins are characterized by the presence of a protein-protein interaction BTB domain. BTB proteins have diverse functions, including transcriptional regulation, protein degradation, chromatin remodeling, and cytoskeletal regulation. However, little is known about this gene family in tomato (Solanum lycopersicum), the most important model plant for crop species. In this study, 38 BTB genes were identified based on tomato whole-genome sequence. Phylogenetic analysis of BTB proteins in tomato revealed that SlBTB proteins could be divided into at least 4 subfamilies. The SlBTB proteins contains 1-3 BTB domains, and several other types of functional domains, including KCTD (Potassium channel tetramerization domain-containing), the MATH (meprin and TRAF homology), ANK (Ankyrin repeats), NPR1 (nonexpressor of pathogenesis-related proteins1), NPH3 (Nonphototropic Hypocotyl 3), TAZ zinc finger, C-terminal Kelch, Skp1 and Arm (Armadillo/beta-catenin-like repeat) domains are also found in some tomato BTB proteins. Moreover, their expression patterns in tissues/stages, in response to different abiotic stress treatments and hormones were also investigated. This study provides the first comprehensive analysis of BTB gene family in the tomato genome. The data will undoubtedly be useful for better understanding the potential functions of BTB genes, and their possible roles in mediating hormone cross-talk and abiotic stress in tomato as well as in some other relative species.
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Affiliation(s)
- Jinhua Li
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education; College of Horticulture and Landscape Architechture, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing, 400715, China
| | - Xiaoxing Su
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education; College of Horticulture and Landscape Architechture, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing, 400715, China
| | - Yinlei Wang
- Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Wei Yang
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education; College of Horticulture and Landscape Architechture, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing, 400715, China
| | - Yu Pan
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education; College of Horticulture and Landscape Architechture, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing, 400715, China
| | - Chenggang Su
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education; College of Horticulture and Landscape Architechture, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing, 400715, China
| | - Xingguo Zhang
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education; College of Horticulture and Landscape Architechture, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing, 400715, China.
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49
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Medici A, Lacombe B, Ruffel S. Nitrate supply to grapevine rootstocks - new genome-wide findings. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:3999-4001. [PMID: 28922777 PMCID: PMC5853248 DOI: 10.1093/jxb/erx273] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
This article comments on: Cochetel N, Escudié F, Cookson SJ, Dai Z, Vivin P, Bert P-F, Muñoz MS, Delrot S, Klopp C, Ollat N, Lauvergeat V. 2017. Root transcriptomic responses of grafted grapevine to heterogeneous N availability depend on rootstock genotype. Journal of Experimental Botany 68, 4339–4355.
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Affiliation(s)
- Anna Medici
- Laboratoire de Biochimie et Physiologie Moléculaire des Plantes, UMR CNRS/INRA/SupAgro/UM, Institut de Biologie Intégrative des Plantes ‘Claude Grignon’, Place Pierre Viala, Montpellier, France
| | - Benoit Lacombe
- Laboratoire de Biochimie et Physiologie Moléculaire des Plantes, UMR CNRS/INRA/SupAgro/UM, Institut de Biologie Intégrative des Plantes ‘Claude Grignon’, Place Pierre Viala, Montpellier, France
| | - Sandrine Ruffel
- Laboratoire de Biochimie et Physiologie Moléculaire des Plantes, UMR CNRS/INRA/SupAgro/UM, Institut de Biologie Intégrative des Plantes ‘Claude Grignon’, Place Pierre Viala, Montpellier, France
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50
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Cochetel N, Escudié F, Cookson SJ, Dai Z, Vivin P, Bert PF, Muñoz MS, Delrot S, Klopp C, Ollat N, Lauvergeat V. Root transcriptomic responses of grafted grapevines to heterogeneous nitrogen availability depend on rootstock genotype. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:4339-4355. [PMID: 28922755 PMCID: PMC5854021 DOI: 10.1093/jxb/erx224] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2017] [Accepted: 06/06/2017] [Indexed: 05/11/2023]
Abstract
In many fruit species, including grapevine, grafting is used to improve scion productivity and quality and to adapt the plant to environmental conditions. However, the mechanisms underlying the rootstock control of scion development are still poorly understood. The ability of rootstocks to regulate nitrogen uptake and assimilation may contribute to this control. A split-root system was used to grow heterografted grapevines and to investigate the molecular responses to changes in nitrate availability of two rootstocks known to affect scion growth differently. Transcriptome profiling by RNA sequencing was performed on root samples collected 3 and 24 h after nitrogen supply. The results demonstrated a common response involving nitrogen-related genes, as well as a more pronounced transcriptomic reprogramming in the genotype conferring the lower scion growth. A weighted gene co-expression network analysis allowed the identification of co-regulated gene modules, suggesting a role for nitrate transporter 2 family genes and some transcription factors as main actors controlling this genotype-dependent response to heterogeneous nitrogen supply. The relationship between nitrate, ethylene, and strigolactone hormonal pathways was found to differ between the two genotypes. These findings indicated that the genotypes responded differently to heterogeneous nitrogen availability, and this may contribute to their contrasting effect on scion growth.
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Affiliation(s)
- Noé Cochetel
- EGFV, Bordeaux Sciences Agro, INRA, Université de Bordeaux, Villenave d’Ornon, France
| | - Frédéric Escudié
- Genotoul Bioinformatics Platform, UR875 Mathematics and Applied Informatics of Toulouse, INRA, Castanet-Tolosan, France
| | - Sarah Jane Cookson
- EGFV, Bordeaux Sciences Agro, INRA, Université de Bordeaux, Villenave d’Ornon, France
| | - Zhanwu Dai
- EGFV, Bordeaux Sciences Agro, INRA, Université de Bordeaux, Villenave d’Ornon, France
| | - Philippe Vivin
- EGFV, Bordeaux Sciences Agro, INRA, Université de Bordeaux, Villenave d’Ornon, France
| | - Pierre-François Bert
- EGFV, Bordeaux Sciences Agro, INRA, Université de Bordeaux, Villenave d’Ornon, France
| | - Mindy Stephania Muñoz
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Alameda, Santiago, Chile
| | - Serge Delrot
- EGFV, Bordeaux Sciences Agro, INRA, Université de Bordeaux, Villenave d’Ornon, France
| | - Christophe Klopp
- Genotoul Bioinformatics Platform, UR875 Mathematics and Applied Informatics of Toulouse, INRA, Castanet-Tolosan, France
| | - Nathalie Ollat
- EGFV, Bordeaux Sciences Agro, INRA, Université de Bordeaux, Villenave d’Ornon, France
| | - Virginie Lauvergeat
- EGFV, Bordeaux Sciences Agro, INRA, Université de Bordeaux, Villenave d’Ornon, France
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