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Sun S, Su W, Gao L, Bi J, Wang Q, Xu Q. Genome-wide identification and examination of the wheat glycosyltransferase family 43 regulation during Fusarium graminearum infection. Int J Biol Macromol 2024; 271:132475. [PMID: 38772456 DOI: 10.1016/j.ijbiomac.2024.132475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Revised: 04/11/2024] [Accepted: 05/15/2024] [Indexed: 05/23/2024]
Abstract
In Arabidopsis and rice, the glycosyltransferase (GT) 43 family is involved in xylan synthesis. However, there have been limited reports on the study of the TaGT43 family in wheat. In this study, 28 TaGT43 family members were identified in wheat (Triticum aestivum L.) and clustered into three major groups based on the similarity of amino acid sequences. The results of the TaGT43 family's conserved motif and gene structure analyses agree with this result. Collinearity analysis revealed segmental duplications mainly promoted TaGT43 family expansion. cis-Acting element analysis revealed that the TaGT43 genes were involved in the light response, phytohormone response, abiotic/biotic stress response, and growth and development. The TaGT43 family showed a tissue-specific expression pattern, primarily expressed in roots and stems. Besides, the transcriptional and expression levels of multiple TaGT43 genes were upregulated during the infection of F. graminearum. According to metabolomics studies, F. graminearum infection affected the phenylpropanoid biosynthesis pathway in wheat, a critical factor in cell wall construction. Furthermore, GO enrichment analysis indicated that the TaGT43 genes play a significant role in cell wall organization. Based on these results, it may be concluded that the TaGT43 family mediates cell wall organization in response to F. graminearum infection.
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Affiliation(s)
- Shufang Sun
- National Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Taian 271018, China
| | - Wenli Su
- National Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Taian 271018, China
| | - Liwei Gao
- National Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Taian 271018, China
| | - Jianjie Bi
- National Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Taian 271018, China
| | - Qunqing Wang
- National Key Laboratory of Wheat Improvement, College of Plant Protection, Shandong Agricultural University, Taian 271018, China
| | - Qian Xu
- National Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Taian 271018, China
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Sivabharathi RC, Rajagopalan VR, Suresh R, Sudha M, Karthikeyan G, Jayakanthan M, Raveendran M. Haplotype-based breeding: A new insight in crop improvement. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 346:112129. [PMID: 38763472 DOI: 10.1016/j.plantsci.2024.112129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 05/09/2024] [Accepted: 05/15/2024] [Indexed: 05/21/2024]
Abstract
Haplotype-based breeding (HBB) is one of the cutting-edge technologies in the realm of crop improvement due to the increasing availability of Single Nucleotide Polymorphisms identified by Next Generation Sequencing technologies. The complexity of the data can be decreased with fewer statistical tests and a lower probability of spurious associations by combining thousands of SNPs into a few hundred haplotype blocks. The presence of strong genomic regions in breeding lines of most crop species facilitates the use of haplotypes to improve the efficiency of genomic and marker-assisted selection. Haplotype-based breeding as a Genomic Assisted Breeding (GAB) approach harnesses the genome sequence data to pinpoint the allelic variation used to hasten the breeding cycle and circumvent the challenges associated with linkage drag. This review article demonstrates ways to identify candidate genes, superior haplotype identification, haplo-pheno analysis, and haplotype-based marker-assisted selection. The crop improvement strategies that utilize superior haplotypes will hasten the breeding progress to safeguard global food security.
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Affiliation(s)
- R C Sivabharathi
- Department of Genetics and Plant breeding, CPBG, Tamil Nadu Agricultural University, Coimbatore 641003, India
| | - Veera Ranjani Rajagopalan
- Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, 641003, India
| | - R Suresh
- Department of Rice, CPBG, Tamil Nadu Agricultural University, Coimbatore 641003, India
| | - M Sudha
- Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, 641003, India.
| | - G Karthikeyan
- Department of Plant Pathology, CPPS, Tamil Nadu Agricultural University, Coimbatore 641003, India
| | - M Jayakanthan
- Department of Plant Molecular Biology and Bioinformatics, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore 641003, India
| | - M Raveendran
- Directorate of research, Tamil Nadu Agricultural University, Coimbatore 641003, India.
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Kaur A, Madhu, Sharma A, Singh K, Upadhyay SK. Investigation of two-pore K + (TPK) channels in Triticum aestivum L. suggests their role in stress response. Heliyon 2024; 10:e27814. [PMID: 38533012 PMCID: PMC10963239 DOI: 10.1016/j.heliyon.2024.e27814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 02/28/2024] [Accepted: 03/07/2024] [Indexed: 03/28/2024] Open
Abstract
Two-pore K+ (TPK) channels are voltage-independent and involved in stress response in plants. Herein, we identified 12 TaTPK genes located on nine chromosomes in the Triticum aestivum genome. The majority of TaTPK genes comprised two exons. Each TaTPK channel comprised four transmembrane (TM) helices, N- and C-terminal ion-channel domains, two EF-hand domains and one 14-3-3 binding site. Additionally, highly conserved 'GYGD' motif responsible for K+ ion specificity, was found in between the TMs in both the ion-channel domains. Nine TaTPK channels were predicted to be localised at the plasma membrane, while three were vacuolar. The protein-protein and protein-chemical interactions indicated the coordinated functioning of the TaTPK channels with the other K+ transporters and their possible interaction with the Ca2+-signaling pathway. Expression studies suggested their importance in both vegetative and reproductive tissues development. Significantly modulated expression of various TaTPK genes during heat, drought, combined heat and drought and salt stresses, and after fungal infestation, depicted their function in stress responses. The miRNAs and transcription factors interaction analyses suggested their role in the hormone, light, growth and development-related, and stress-responsive signaling cascades. The current study suggested vital functions of various TaTPK genes, especially in stress response, and would provide an opportunity for their detailed characterization in future studies.
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Affiliation(s)
- Amandeep Kaur
- Department of Botany, Panjab University, Chandigarh, India, 160014
| | - Madhu
- Department of Botany, Panjab University, Chandigarh, India, 160014
| | - Alok Sharma
- Department of Botany, Panjab University, Chandigarh, India, 160014
- Regional Ayurveda Research Institute, Gwalior, Madhya Pradesh, 474001, India
| | - Kashmir Singh
- Department of Biotechnology, Panjab University, Chandigarh, India
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Mallikarjuna MG, Tomar R, Lohithaswa HC, Sahu S, Mishra DC, Rao AR, Chinnusamy V. Genome-wide identification of potassium channels in maize showed evolutionary patterns and variable functional responses to abiotic stresses. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 206:108235. [PMID: 38039585 DOI: 10.1016/j.plaphy.2023.108235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 11/08/2023] [Accepted: 11/22/2023] [Indexed: 12/03/2023]
Abstract
Potassium (K) channels are essential components of plant biology, mediating not only K ion (K+) homeostasis but also regulating several physiological processes and stress tolerance. In the current investigation, we identified 27 K+ channels in maize and deciphered the evolution and divergence pattern with four monocots and five dicot species. Chromosomal localization and expansion of K+ channel genes showed uneven distribution and were independent of genome size. The dispersed duplication is the major force in expanding K+ channels in the target genomes. The mean Ka/Ks ratio of <0.5 in paralogs and orthologs indicates horizontal and vertical expansions of K+ channel genes under strong purifying selection. The one-to-one K+ channel orthologs were prominent among the closely related species, with higher synteny between maize and the rest of the monocots. Comprehensive K+ channels promoter analysis revealed various cis-regulatory elements mediating stress tolerance with the predominance of MYB and STRE binding sites. The regulatory network showed AP2-EREBP TFs, miR164 and miR399 are prominent regulatory elements of K+ channels. The qRT-PCR analysis of K+ channels and regulatory miRNAs showed significant expressions in response to drought and waterlogging stresses. The present study expanded the knowledge on K+ channels in maize and will serve as a basis for an in-depth functional analysis.
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Affiliation(s)
| | - Rakhi Tomar
- Division of Genetics, ICAR- Indian Agricultural Research Institute, New Delhi, 110012, India
| | | | - Sarika Sahu
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India
| | - Dwijesh Chandra Mishra
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India
| | - Atmakuri Ramakrishna Rao
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India
| | - Viswanathan Chinnusamy
- Division of Plant Physiology, ICAR- Indian Agricultural Research Institute, New Delhi, 110012, India
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Degon Z, Dixon S, Rahmatallah Y, Galloway M, Gulutzo S, Price H, Cook J, Glazko G, Mukherjee A. Azospirillum brasilense improves rice growth under salt stress by regulating the expression of key genes involved in salt stress response, abscisic acid signaling, and nutrient transport, among others. FRONTIERS IN AGRONOMY 2023; 5:1216503. [PMID: 38223701 PMCID: PMC10785826 DOI: 10.3389/fagro.2023.1216503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/16/2024]
Abstract
Major food crops, such as rice and maize, display severe yield losses (30-50%) under salt stress. Furthermore, problems associated with soil salinity are anticipated to worsen due to climate change. Therefore, it is necessary to implement sustainable agricultural strategies, such as exploiting beneficial plant-microbe associations, for increased crop yields. Plants can develop associations with beneficial microbes, including arbuscular mycorrhiza and plant growth-promoting bacteria (PGPB). PGPB improve plant growth via multiple mechanisms, including protection against biotic and abiotic stresses. Azospirillum brasilense, one of the most studied PGPB, can mitigate salt stress in different crops. However, little is known about the molecular mechanisms by which A. brasilense mitigates salt stress. This study shows that total and root plant mass is improved in A. brasilense-inoculated rice plants compared to the uninoculated plants grown under high salt concentrations (100 mM and 200 mM NaCl). We observed this growth improvement at seven- and fourteen days post-treatment (dpt). Next, we used transcriptomic approaches and identified differentially expressed genes (DEGs) in rice roots when exposed to three treatments: 1) A. brasilense, 2) salt (200 mM NaCl), and 3) A. brasilense and salt (200 mM NaCl), at seven dpt. We identified 786 DEGs in the A. brasilense-treated plants, 4061 DEGs in the salt-stressed plants, and 1387 DEGs in the salt-stressed A. brasilense-treated plants. In the A. brasilense-treated plants, we identified DEGs involved in defense, hormone, and nutrient transport, among others. In the salt-stressed plants, we identified DEGs involved in abscisic acid and jasmonic acid signaling, antioxidant enzymes, sodium and potassium transport, and calcium signaling, among others. In the salt-stressed A. brasilense-treated plants, we identified some genes involved in salt stress response and tolerance (e.g., abscisic acid and jasmonic acid signaling, antioxidant enzymes, calcium signaling), and sodium and potassium transport differentially expressed, among others. We also identified some A. brasilense-specific plant DEGs, such as nitrate transporters and defense genes. Furthermore, our results suggest genes involved in auxin and ethylene signaling are likely to play an important role during these interactions. Overall, our transcriptomic data indicate that A. brasilense improves rice growth under salt stress by regulating the expression of key genes involved in defense and stress response, abscisic acid and jasmonic acid signaling, and ion and nutrient transport, among others. Our findings will provide essential insights into salt stress mitigation in rice by A. brasilense.
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Affiliation(s)
- Zachariah Degon
- Department of Biology, University of Central Arkansas, Conway, AR, United States
| | - Seth Dixon
- Department of Biology, University of Central Arkansas, Conway, AR, United States
| | - Yasir Rahmatallah
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Mary Galloway
- Department of Biology, University of Central Arkansas, Conway, AR, United States
| | - Sophia Gulutzo
- Department of Biology, University of Central Arkansas, Conway, AR, United States
| | - Hunter Price
- Department of Biology, University of Central Arkansas, Conway, AR, United States
| | - John Cook
- Department of Biology, University of Central Arkansas, Conway, AR, United States
| | - Galina Glazko
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Arijit Mukherjee
- Department of Biology, University of Central Arkansas, Conway, AR, United States
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Lin G, Ma L, He X, Tang J, Wang L. Gene regulation and ionome homeostasis in rice plants in response to arsenite stress: potential connection between transcriptomics and ionomics. Biometals 2023; 36:1157-1169. [PMID: 37198524 DOI: 10.1007/s10534-023-00510-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 05/11/2023] [Indexed: 05/19/2023]
Abstract
Ionomics and transcriptomics were applied to demonstrate response of rice to arsenite [As(III)] stress in the current study. Rice plants were cultured in nutrient solutions treated with 0, 100 and 500 μg/L As(III) coded as CK, As1 and As5, respectively. The rice ionomes exhibited discriminatory response to environmental disturbances. Solid evidence of the effects of As(III) stress on binding, transport or metabolism of P, K, Ca, Zn and Cu was obtained in this work. Differentially expressed genes (DEGs) in the shoots were identified in three datasets: As1 vs CK, As5 vs CK and As5 vs As1. DEGs identified simultaneously in two or three datasets were selected for subsequent interaction and enrichment analyses. Upregulation of genes involved in protein kinase activity, phosphorus metabolic process and phosphorylation were detected in the rice treated with As(III), resulting in the maintenance of P homeostasis in the shoots. Zn and Ca binding genes were up-regulated since excess As inhibited the translocation of Zn and Ca from roots to shoots. Increased expression of responsive genes including HMA, WRKY, NAC and PUB genes conferred As tolerance in the rice plants to cope with external As(III) stress. The results suggested that As(III) stress could disturb the uptake and translocation of macro and essential elements by rice. Plants could regulate the expression of corresponding genes to maintain mineral nutrient homeostasis for essential metabolic processes.
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Affiliation(s)
- Guobing Lin
- College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083, China
| | - Li Ma
- College of Forestry, Henan Agriculture University, Zhengzhou, 450002, China
| | - Xiaoman He
- College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083, China
| | - Jie Tang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410008, China.
| | - Lin Wang
- College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083, China.
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Paul A, Chumbale SS, Lakra A, Kumar V, Alhat DS, Singh S. Insights into Leishmania donovani potassium channel family and their biological functions. 3 Biotech 2023; 13:266. [PMID: 37425093 PMCID: PMC10326225 DOI: 10.1007/s13205-023-03692-y] [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: 09/27/2022] [Accepted: 06/26/2023] [Indexed: 07/11/2023] Open
Abstract
Leishmania donovani is the causative organism for visceral leishmaniasis. Although this parasite was discovered over a century ago, nothing is known about role of potassium channels in L. donovani. Potassium channels are known for their crucial roles in cellular functions in other organisms. Recently the presence of a calcium-activated potassium channel in L. donovani was reported which prompted us to look for other proteins which could be potassium channels and to investigate their possible physiological roles. Twenty sequences were identified in L. donovani genome and subjected to estimation of physio-chemical properties, motif analysis, localization prediction and transmembrane domain analysis. Structural predictions were also done. The channels were majorly α-helical and predominantly localized in cell membrane and lysosomes. The signature selectivity filter of potassium channel was present in all the sequences. In addition to the conventional potassium channel activity, they were associated with gene ontology terms for mitotic cell cycle, cell death, modulation by virus of host process, cell motility etc. The entire study indicates the presence of potassium channel families in L. donovani which may have involvement in several cellular pathways. Further investigations on these putative potassium channels are needed to elucidate their roles in Leishmania. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03692-y.
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Affiliation(s)
- Anindita Paul
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, SAS Nagar, Mohali, 160062 Punjab India
| | - Shubham Sunil Chumbale
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, SAS Nagar, Mohali, 160062 Punjab India
| | - Anjana Lakra
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, SAS Nagar, Mohali, 160062 Punjab India
| | - Vijay Kumar
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, SAS Nagar, Mohali, 160062 Punjab India
| | - Dhanashri Sudam Alhat
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, SAS Nagar, Mohali, 160062 Punjab India
| | - Sushma Singh
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, SAS Nagar, Mohali, 160062 Punjab India
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Shirazi Z, Khakdan F, Rafiei F, Balalami MY, Ranjbar M. Genome-wide identification and expression profile analysis of metal tolerance protein gene family in Eucalyptus grandis under metal stresses. BMC PLANT BIOLOGY 2023; 23:240. [PMID: 37149585 PMCID: PMC10163719 DOI: 10.1186/s12870-023-04240-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 04/21/2023] [Indexed: 05/08/2023]
Abstract
Metal tolerance proteins (MTPs) as Me2+/H+(K+) antiporters participate in the transport of divalent cations, leading to heavy metal stress resistance and mineral utilization in plants. In the present study, to obtain better knowledge of the biological functions of the MTPs family, 20 potential EgMTPs genes were identified in Eucalyptus grandis and classified into seven groups belonging to three cation diffusion facilitator groups (Mn-CDFs, Zn/Fe-CDFs, and Zn-CDFs) and seven groups. EgMTP-encoded amino acids ranged from 315 to 884, and most of them contained 4-6 recognized transmembrane domains and were clearly prognosticated to localize into the cell vacuole. Almost all EgMTP genes experienced gene duplication events, in which some might be uniformly distributed in the genome. The numbers of cation efflux and the zinc transporter dimerization domain were highest in EgMTP proteins. The promoter regions of EgMTP genes have different cis-regulatory elements, indicating that the transcription rate of EgMTP genes can be a controlled response to different stimuli in multiple pathways. Our findings provide accurate perception on the role of the predicted miRNAs and the presence of SSR marker in the Eucalyptus genome and clarify their functions in metal tolerance regulation and marker-assisted selection, respectively. Gene expression profiling based on previous RNA-seq data indicates a probable function for EgMTP genes during development and responses to biotic stress. Additionally, the upregulation of EgMTP6, EgMTP5, and EgMTP11.1 to excess Cd2+ and Cu2+ exposure might be responsible for metal translocation from roots to leaves.
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Affiliation(s)
- Zahra Shirazi
- Department of Biotechnology Research, Research Institute of Forests and Rangelands, Agricultural Research, Education and Extension Organization (AREEO), National Botanical Garden, Tehran Karaj Freeway, P.O. Box 13185-116, Tehran, Iran.
| | | | - Fariba Rafiei
- Department of Agronomy, Purdue University, West Lafayette, IN, 47907, USA
| | - Mahdi Yahyazadeh Balalami
- Department of Medicinal Plant Research, Research Institute of Forests and Rangelands, Agricultural Research, Education and Extension Organization (AREEO), National Botanical Garden, Tehran Karaj Freeway, P.O. Box 13185-116, Tehran, Iran
| | - Mojtaba Ranjbar
- Microbial Biotechnology Department, College of Biotechnology, University of Special Modern Technologies, Amol, Iran
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Salvatierra A, Mateluna P, Toro G, Solís S, Pimentel P. Genome-Wide Identification and Gene Expression Analysis of Sweet Cherry Aquaporins ( Prunus avium L.) under Abiotic Stresses. Genes (Basel) 2023; 14:genes14040940. [PMID: 37107698 PMCID: PMC10138167 DOI: 10.3390/genes14040940] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 04/13/2023] [Accepted: 04/14/2023] [Indexed: 04/29/2023] Open
Abstract
Aquaporins (AQPs) are integral transmembrane proteins well known as channels involved in the mobilization of water, small uncharged molecules and gases. In this work, the main objective was to carry out a comprehensive study of AQP encoding genes in Prunus avium (cv. Mazzard F12/1) on a genome-wide scale and describe their transcriptional behaviors in organs and in response to different abiotic stresses. A total of 28 non-redundant AQP genes were identified in Prunus spp. Genomes, which were phylogenetically grouped into five subfamilies (seven PIPs, eight NIPs, eight TIPs, three SIPs and two XIPs). Bioinformatic analyses revealed a high synteny and remarkable conservation of structural features among orthologs of different Prunus genomes. Several cis-acting regulatory elements (CREs) related to stress regulation were detected (ARE, WRE3, WUN, STRE, LTR, MBS, DRE, AT-rich and TC-rich). The above could be accounting for the expression variations associated with plant organs and, especially, each abiotic stress analyzed. Gene expressions of different PruavAQPs were shown to be preferentially associated with different stresses. PruavXIP2;1 and PruavXIP1;1 were up-regulated in roots at 6 h and 72 h of hypoxia, and in PruavXIP2;1 a slight induction of expression was also detected in leaves. Drought treatment strongly down-regulated PruavTIP4;1 but only in roots. Salt stress exhibited little or no variation in roots, except for PruavNIP4;1 and PruavNIP7;1, which showed remarkable gene repression and induction, respectively. Interestingly, PruavNIP4;1, the AQP most expressed in cherry roots subjected to cold temperatures, also showed this pattern in roots under high salinity. Similarly, PruavNIP4;2 consistently was up-regulated at 72 h of heat and drought treatments. From our evidence is possible to propose candidate genes for the development of molecular markers for selection processes in breeding programs for rootstocks and/or varieties of cherry.
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Affiliation(s)
- Ariel Salvatierra
- Centro de Estudios Avanzados en Fruticultura (CEAF), Camino Las Parcelas 882, km 105 Ruta 5 Sur, Sector Los Choapinos, Rengo 2940000, Chile
| | - Patricio Mateluna
- Centro de Estudios Avanzados en Fruticultura (CEAF), Camino Las Parcelas 882, km 105 Ruta 5 Sur, Sector Los Choapinos, Rengo 2940000, Chile
| | - Guillermo Toro
- Centro de Estudios Avanzados en Fruticultura (CEAF), Camino Las Parcelas 882, km 105 Ruta 5 Sur, Sector Los Choapinos, Rengo 2940000, Chile
| | - Simón Solís
- Centro de Estudios Avanzados en Fruticultura (CEAF), Camino Las Parcelas 882, km 105 Ruta 5 Sur, Sector Los Choapinos, Rengo 2940000, Chile
| | - Paula Pimentel
- Centro de Estudios Avanzados en Fruticultura (CEAF), Camino Las Parcelas 882, km 105 Ruta 5 Sur, Sector Los Choapinos, Rengo 2940000, Chile
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10
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Gao Q, Yin X, Wang F, Hu S, Liu W, Chen L, Dai X, Liang M. OsJRL40, a Jacalin-Related Lectin Gene, Promotes Salt Stress Tolerance in Rice. Int J Mol Sci 2023; 24:ijms24087441. [PMID: 37108614 PMCID: PMC10138497 DOI: 10.3390/ijms24087441] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 04/12/2023] [Accepted: 04/13/2023] [Indexed: 04/29/2023] Open
Abstract
High salinity is a major stress factor affecting the quality and productivity of rice (Oryza sativa L.). Although numerous salt tolerance-related genes have been identified in rice, their molecular mechanisms remain unknown. Here, we report that OsJRL40, a jacalin-related lectin gene, confers remarkable salt tolerance in rice. The loss of function of OsJRL40 increased sensitivity to salt stress in rice, whereas its overexpression enhanced salt tolerance at the seedling stage and during reproductive growth. β-glucuronidase (GUS) reporter assays indicated that OsJRL40 is expressed to higher levels in roots and internodes than in other tissues, and subcellular localization analysis revealed that the OsJRL40 protein localizes to the cytoplasm. Further molecular analyses showed that OsJRL40 enhances antioxidant enzyme activities and regulates Na+-K+ homeostasis under salt stress. RNA-seq analysis revealed that OsJRL40 regulates salt tolerance in rice by controlling the expression of genes encoding Na+/K+ transporters, salt-responsive transcription factors, and other salt response-related proteins. Overall, this study provides a scientific basis for an in-depth investigation of the salt tolerance mechanism in rice and could guide the breeding of salt-tolerant rice cultivars.
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Affiliation(s)
- Qinmei Gao
- Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, Hunan Normal University, Changsha 410081, China
| | - Xiaolin Yin
- Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, Hunan Normal University, Changsha 410081, China
| | - Feng Wang
- Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, Hunan Normal University, Changsha 410081, China
| | - Shuchang Hu
- Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, Hunan Normal University, Changsha 410081, China
| | - Weihao Liu
- Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, Hunan Normal University, Changsha 410081, China
| | - Liangbi Chen
- Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, Hunan Normal University, Changsha 410081, China
| | - Xiaojun Dai
- Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, Hunan Normal University, Changsha 410081, China
| | - Manzhong Liang
- Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, Hunan Normal University, Changsha 410081, China
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11
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Hashemipetroudi SH, Arab M, Heidari P, Kuhlmann M. Genome-wide analysis of the laccase (LAC) gene family in Aeluropus littoralis: A focus on identification, evolution and expression patterns in response to abiotic stresses and ABA treatment. FRONTIERS IN PLANT SCIENCE 2023; 14:1112354. [PMID: 36938021 PMCID: PMC10014554 DOI: 10.3389/fpls.2023.1112354] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 01/23/2023] [Indexed: 05/27/2023]
Abstract
Laccases are plant enzymes with essential functions during growth and development. These monophenoloxidases are involved in lignin polymerization, and their expression respond to environmental stress. However, studies of laccases in some plants and fungi have highlighted that many structural and functional aspects of these genes are still unknown. Here, the laccase gene family in Aeluropus littoralis (AlLAC) is described based on sequence structure and expression patterns under abiotic stresses and ABA treatment. Fifteen non-redundant AlLACs were identified from the A. littoralis genome, which showed differences in physicochemical characteristics and gene structure. Based on phylogenetic analysis, AlLACs and their orthologues were classified into five groups. A close evolutionary relationship was observed between LAC gene family members in rice and A. littoralis. According to the interaction network, AlLACs interact more with proteins involved in biological processes such as iron incorporation into the metallo-sulfur cluster, lignin catabolism, regulation of the symbiotic process and plant-type primary cell wall biogenesis. Gene expression analysis of selected AlLACs using real-time RT (reverse transcription)-PCR revealed that AlLACs are induced in response to abiotic stresses such as cold, salt, and osmotic stress, as well as ABA treatment. Moreover, AlLACs showed differential expression patterns in shoot and root tissues. Our findings indicate that AlLACs are preferentially involved in the late response of A. littoralis to abiotic stress.
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Affiliation(s)
- Seyyed Hamidreza Hashemipetroudi
- Department of Genetic Engineering and Biology, Genetics and Agricultural Biotechnology Institute of Tabarestan (GABIT), Sari Agricultural Sciences and Natural Resources University (SANRU), Sari, Iran
- RG Heterosis, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Mozhdeh Arab
- Department of Genetic Engineering and Biology, Genetics and Agricultural Biotechnology Institute of Tabarestan (GABIT), Sari Agricultural Sciences and Natural Resources University (SANRU), Sari, Iran
- National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Parviz Heidari
- Faculty of Agriculture, Shahrood University of Technology, Shahrood, Iran
| | - Markus Kuhlmann
- RG Heterosis, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
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12
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Negi Y, Kumar K. Cloning, homology modelling and expression analysis of Oryza sativa WNK gene family. Int J Biol Macromol 2023; 229:994-1008. [PMID: 36608863 DOI: 10.1016/j.ijbiomac.2022.12.328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 12/17/2022] [Accepted: 12/26/2022] [Indexed: 01/06/2023]
Abstract
With No Lysine kinases (WNKs) represents a gene family that encodes Ser/Thr kinases, with anomalous disposition of catalytic lysine residue in subdomain I. In plants, WNKs had been linked to circadian rhythm, photoperiodic response and abiotic stress tolerance with mechanism yet undeciphered. In the present study, full-length CDS sequences of rice WNKs (OsWNK1 to 8) were cloned from indica cultivar IR64. A total of six highly conserved kinase subdomains were identified. Comparative analysis of protein sequences from six different species of rice showed varying magnitudes of substitution (76.2 %), deletion (15.4 %), and addition (8.4 %) events. ConSurf analysis coupled with CASTp results identified functional residues that were clustered together in modelled 3-D structures. Among post-translational modifications (PTMs) studied, 87.7 % of phosphorylation sites were predicted. Mined protein-protein interactions (PPIs) depicted OsWNKs to interact notably with other OsWNK members and with key proteins like PRR95 involved in photoperiodic response and protein phosphatase like PP2C involved in ABA signalling. Gene duplication analysis revealed two paralogous duplicated gene pairs: WNK6-WNK9 and WNK7-WNK8. Oryza sativa showed maximum syntenic relationship with Sorghum bicolor among the compared species. OsWNKs showed differential transcript expression profiles on treatment with plant growth regulators indicating its versatile role in plant growth and development.
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Affiliation(s)
- Yogesh Negi
- Department of Biological Sciences, Birla Institute of Technology & Science Pilani, K. K. Birla Goa Campus, Goa 403726, India
| | - Kundan Kumar
- Department of Biological Sciences, Birla Institute of Technology & Science Pilani, K. K. Birla Goa Campus, Goa 403726, India.
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13
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Yang Y, Zhao L, Wang J, Lu N, Ma W, Ma J, Zhang Y, Fu P, Yao C, Hu J, Wang N. Genome-wide identification of DnaJ gene family in Catalpa bungei and functional analysis of CbuDnaJ49 in leaf color formation. FRONTIERS IN PLANT SCIENCE 2023; 14:1116063. [PMID: 36968394 PMCID: PMC10038198 DOI: 10.3389/fpls.2023.1116063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 02/06/2023] [Indexed: 06/18/2023]
Abstract
DnaJs are the common molecular chaperone proteins with strong structural and functional diversity. In recent years, only several DnaJ family members have been found to be able to regulate leaf color, and it remains to be explored whether there are other potential members that also regulate this character. Here, we identified 88 putative DnaJ proteins from Catalpa bungei, and classified them into four types according to their domain. Gene-structure analysis revealed that each member of CbuDnaJ family had same or similar exon-intron structure. Chromosome mapping and collinearity analysis showed that tandem and fragment duplication occurred in the process of evolution. Promoter analyses suggested that CbuDnaJs might be involved in a variety of biological processes. The expression levels of DnaJ family members in different color leaves of Maiyuanjinqiu were respectively extracted from the differential transcriptome. Among these, CbuDnaJ49 was the largest differentially expressed gene between the green and yellow sectors. Ectopic overexpression of CbuDnaJ49 in tobacco showed that the positive transgenic seedlings exhibited albino leaves, and the contents of chlorophyll and carotenoid were significantly reduced compared with those of wild type. The results suggested that CbuDnaJ49 played an important role in regulating leaf color. This study not only identified a novel gene of DnaJ family members regulating leaf color, but also provided new germplasm for landscaping.
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Affiliation(s)
- Yingying Yang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, National Innovation Alliance of Catalpa bungei, Beijing, China
- Biotechnology Research Center of China Three Gorges University, Yichang, China
| | - Linjiao Zhao
- Hekou Yao Autonomous County Forestry and Grassland Bureau, Hekou, China
| | - Junhui Wang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, National Innovation Alliance of Catalpa bungei, Beijing, China
| | - Nan Lu
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, National Innovation Alliance of Catalpa bungei, Beijing, China
| | - Wenjun Ma
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, National Innovation Alliance of Catalpa bungei, Beijing, China
| | - Jiang Ma
- Biotechnology Research Center of China Three Gorges University, Yichang, China
| | - Yu Zhang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, National Innovation Alliance of Catalpa bungei, Beijing, China
| | - Pengyue Fu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Chengcheng Yao
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, National Innovation Alliance of Catalpa bungei, Beijing, China
| | - Jiwen Hu
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, National Innovation Alliance of Catalpa bungei, Beijing, China
| | - Nan Wang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, National Innovation Alliance of Catalpa bungei, Beijing, China
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14
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Heidari P, Hasanzadeh S, Faraji S, Ercisli S, Mora-Poblete F. Genome-Wide Characterization of the Sulfate Transporter Gene Family in Oilseed Crops: Camelina sativa and Brassica napus. PLANTS (BASEL, SWITZERLAND) 2023; 12:628. [PMID: 36771712 PMCID: PMC9919929 DOI: 10.3390/plants12030628] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 01/23/2023] [Accepted: 01/28/2023] [Indexed: 06/18/2023]
Abstract
Sulfate transporters (SULTRs) are responsible for the uptake of sulfate (SO42-) ions in the rhizosphere by roots and their distribution to plant organs. In this study, SULTR family members in the genomes of two oilseed crops (Camelina sativa and Brassica napus) were identified and characterized based on their sequence structures, duplication events, phylogenetic relationships, phosphorylation sites, and expression levels. In total, 36 and 45 putative SULTR genes were recognized in the genomes of C. sativa and B. napus, respectively. SULTR proteins were predicted to be basophilic proteins with low hydrophilicity in both studied species. According to the observed phylogenetic relationships, we divided the SULTRs into five groups, out of which the SULTR 3 group showed the highest variation. Additionally, several duplication events were observed between the SULTRs. The first duplication event occurred approximately five million years ago between three SULTR 3.1 genes in C. sativa. Furthermore, two subunits were identified in the 3D structures of the SULTRs, which demonstrated that the active binding sites differed between C. sativa and B. napus. According to the available RNA-seq data, the SULTRs showed diverse expression levels in tissues and diverse responses to stimuli. SULTR 3 was expressed in all tissues. SULTR 3.1 was more upregulated in response to abiotic stresses in C. sativa, while SULTR 3.3 and SULTR 2.1 were upregulated in B. napus. Furthermore, SULTR 3 and SULTR 4.1 were upregulated in response to biotic stresses in B. napus. Additionally, the qPCR data showed that the SULTRs in C. sativa were involved in the plant's response to salinity. Based on the distribution of cis-regulatory elements in the promoter region, we speculated that SULTRs might be controlled by phytohormones, such as ABA and MeJA. Therefore, it seems likely that SULTR genes in C. sativa have been more heavily influenced by evolutionary processes and have acquired further diversity. The results reveal new insights of the structures and functions of SULTRs in oilseed crops. However, further analyses, related to functional studies, are needed to uncover the role of SULTRs in the plants' development and growth processes, as well as in their response to stimuli.
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Affiliation(s)
- Parviz Heidari
- Faculty of Agriculture, Shahrood University of Technology, Shahrood 3619995161, Iran
| | - Soosan Hasanzadeh
- Faculty of Agriculture, Shahrood University of Technology, Shahrood 3619995161, Iran
| | - Sahar Faraji
- Department of Plant Breeding, Faculty of Crop Sciences, Sari Agricultural Sciences and Natural Resources University (SANRU), Sari 4818168984, Iran
| | - Sezai Ercisli
- Department of Horticulture, Faculty of Agriculture, Ataturk University, 25240 Erzurum, Turkey
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15
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Puresmaeli F, Heidari P, Lawson S. Insights into the Sulfate Transporter Gene Family and Its Expression Patterns in Durum Wheat Seedlings under Salinity. Genes (Basel) 2023; 14:genes14020333. [PMID: 36833260 PMCID: PMC9956213 DOI: 10.3390/genes14020333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Revised: 01/23/2023] [Accepted: 01/24/2023] [Indexed: 02/03/2023] Open
Abstract
Sulfate transporters (SULTRs) are an essential plant transporter class responsible for the absorption and distribution of sulfur, an essential plant growth element. SULTRs are also involved in processes related to growth and development and in response to environmental stimuli. In the present study, 22 TdSULTR family members were identified and characterized in the genome of Triticum turgidum L. ssp. durum (Desf.) using available bioinformatics tools. The expression levels of candidate TdSULTR genes were investigated under salt treatments of 150 and 250 mM NaCl after several different exposure times. TdSULTRs showed diversity in terms of physiochemical properties, gene structure, and pocket sites. TdSULTRs and their orthologues were classified into the known five main plant groups of highly diverse subfamilies. In addition, it was noted that segmental duplication events could lengthen TdSULTR family members under evolutionary processes. Based on pocket site analysis, the amino acids leucine (L), valine (V), and serine (S) were most often detected in TdSULTR protein binding sites. Moreover, it was predicted that TdSULTRs have a high potential to be targeted by phosphorylation modifications. According to promoter site analysis, the plant bioregulators ABA and MeJA were predicted to affect TdSULTR expression patterns. Real-time PCR analysis revealed TdSULTR genes are differentially expressed at 150 mM NaCl but show similar expression in response to 250 mM NaCl. TdSULTR reached a maximum level of expression 72 h after the 250 mM salt treatment. Overall, we conclude that TdSULTR genes are involved in the response to salinity in durum wheat. However, additional studies of functionality are needed to determine their precise function and linked-interaction pathways.
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Affiliation(s)
- Fatemeh Puresmaeli
- Faculty of Agriculture, Shahrood University of Technology, Shahrood 3619995161, Iran
| | - Parviz Heidari
- Faculty of Agriculture, Shahrood University of Technology, Shahrood 3619995161, Iran
- Correspondence:
| | - Shaneka Lawson
- USDA Forest Service, Northern Research Station, Hardwood Tree Improvement and Regeneration Center (HTIRC), Department of Forestry and Natural Resources, Purdue University, 715 West State Street, West Lafayette, IN 47906, USA
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16
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Yaghobi M, Heidari P. Genome-Wide Analysis of Aquaporin Gene Family in Triticum turgidum and Its Expression Profile in Response to Salt Stress. Genes (Basel) 2023; 14:genes14010202. [PMID: 36672943 PMCID: PMC9859376 DOI: 10.3390/genes14010202] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 01/07/2023] [Accepted: 01/10/2023] [Indexed: 01/13/2023] Open
Abstract
During the response of plants to water stresses, aquaporin (AQP) plays a prominent role in membrane water transport based on the received upstream signals. Due to the importance of the AQP gene family, studies have been conducted that investigate the function and regulatory system of these genes. However, many of their molecular aspects are still unknown. This study aims to carry out a genome-wide investigation of the AQP gene family in Triticum turgidum using bioinformatics tools and to investigate the expression patterns of some members in response to salt stress. Our results show that there are 80 TtAQP genes in T. turgidum, which are classified into four main groups based on phylogenetic analysis. Several duplications were observed between the members of the TtAQP gene family, and high diversity in response to post-translational modifications was observed between TtAQP family members. The expression pattern of TtAQP genes disclosed that these genes are primarily upregulated in response to salt stress. Additionally, the qPCR data revealed that TtAQPs are more induced in delayed responses to salinity stress. Overall, our findings illustrate that TtAQP members are diverse in terms of their structure, regulatory systems, and expression levels.
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17
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Parakkunnel R, Naik K B, Vanishree G, C S, Purru S, Bhaskar K U, Bhat KV, Kumar S. Gene fusions, micro-exons and splice variants define stress signaling by AP2/ERF and WRKY transcription factors in the sesame pan-genome. FRONTIERS IN PLANT SCIENCE 2022; 13:1076229. [PMID: 36618639 PMCID: PMC9817154 DOI: 10.3389/fpls.2022.1076229] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 12/02/2022] [Indexed: 06/17/2023]
Abstract
Evolutionary dynamics of AP2/ERF and WRKY genes, the major components of defense response were studied extensively in the sesame pan-genome. Massive variation was observed for gene copy numbers, genome location, domain structure, exon-intron structure and protein parameters. In the pan-genome, 63% of AP2/ERF members were devoid of introns whereas >99% of WRKY genes contained multiple introns. AP2 subfamily was found to be micro-exon rich with the adjoining intronic sequences sharing sequence similarity to many stress-responsive and fatty acid metabolism genes. WRKY family included extensive multi-domain gene fusions where the additional domains significantly enhanced gene and exonic sizes as well as gene copy numbers. The fusion genes were found to have roles in acquired immunity, stress response, cell and membrane integrity as well as ROS signaling. The individual genomes shared extensive synteny and collinearity although ecological adaptation was evident among the Chinese and Indian accessions. Significant positive selection effects were noticed for both micro-exon and multi-domain genes. Splice variants with changes in acceptor, donor and branch sites were common and 6-7 splice variants were detected per gene. The study ascertained vital roles of lipid metabolism and chlorophyll biosynthesis in the defense response and stress signaling pathways. 60% of the studied genes localized in the nucleus while 20% preferred chloroplast. Unique cis-element distribution was noticed in the upstream promoter region with MYB and STRE in WRKY genes while MYC was present in the AP2/ERF genes. Intron-less genes exhibited great diversity in the promoter sequences wherein the predominance of dosage effect indicated variable gene expression levels. Mimicking the NBS-LRR genes, a chloroplast localized WRKY gene, Swetha_24868, with additional domains of chorismate mutase, cAMP and voltage-dependent potassium channel was found to act as a master regulator of defense signaling, triggering immunity and reducing ROS levels.
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Affiliation(s)
- Ramya Parakkunnel
- ICAR- Indian Institute of Seed Science, Regional Station, Gandhi Krishi Vigyana Kendra (GKVK) Campus, Bengaluru, India
| | - Bhojaraja Naik K
- ICAR- Indian Institute of Seed Science, Regional Station, Gandhi Krishi Vigyana Kendra (GKVK) Campus, Bengaluru, India
| | - Girimalla Vanishree
- ICAR- Indian Institute of Seed Science, Regional Station, Gandhi Krishi Vigyana Kendra (GKVK) Campus, Bengaluru, India
| | - Susmita C
- ICAR- Indian Institute of Seed Science, Mau, Uttar Pradesh, India
| | - Supriya Purru
- ICAR- National Academy of Agricultural Research Management, Hyderabad, Telengana, India
| | - Udaya Bhaskar K
- ICAR- Indian Institute of Seed Science, Regional Station, Gandhi Krishi Vigyana Kendra (GKVK) Campus, Bengaluru, India
| | - KV. Bhat
- Division of Genomic Resources, ICAR- National Bureau of Plant Genetic Resources, New Delhi, India
| | - Sanjay Kumar
- ICAR- Indian Institute of Seed Science, Mau, Uttar Pradesh, India
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18
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Yao Y, Yang R, Liao W, Wang Y, Liu W, Huang X, Wang X, Zhang P. Is Oxalic Acid Secretion A Detoxification Strategy for Rice Exposed to Tl(I) or Tl(III)? BULLETIN OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2022; 109:920-926. [PMID: 36129516 DOI: 10.1007/s00128-022-03613-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 08/23/2022] [Indexed: 06/15/2023]
Abstract
Thallium (Tl) is a highly toxic element with two species, Tl(I) and Tl(III). We discovered the Tl uptake in rice exposed to Tl(III) hydroponic treatment was significantly lower than that to Tl(I) treatment, but the content of oxalic acid secreted from roots in Tl(III) treatment was higher than that in Tl(I). The physiological and molecular mechanisms underlying the difference between the two Tl species were studied using a hydroponic system. The results showed the reduction of oxalic acid content had no effect on the amount of Tl on the root surface, indicating oxalic acid might not immobilize Tl to affect the Tl uptake. Therefore, the secretion of oxalic acid from roots may not be a strategy for detoxifying Tl in rice. Notably, Tl(III) increased the expression of Oryza sativa H+-ATPase genes OsAs and the activity of H+-ATPase, and decreased potassium transport gene expression of OsKAT1.1 and OsHKT2;4, which indicated that the difference in Tl uptake of rice between the two Tl species mainly cause by the potassium transport system rather than oxalic acid.
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Affiliation(s)
- Yan Yao
- School of Life Science, Guangzhou University, 510006, Guangzhou, China.
| | - Ruiqi Yang
- School of Life Science, Guangzhou University, 510006, Guangzhou, China
| | - Wenqin Liao
- School of Life Science, Guangzhou University, 510006, Guangzhou, China
| | - Yuqi Wang
- School of Life Science, Guangzhou University, 510006, Guangzhou, China.
- School of Environmental Science and Engineering, Guangzhou University, 510006, Guangzhou, China.
| | - Wei Liu
- School of Environmental Science and Engineering, Guangzhou University, 510006, Guangzhou, China
| | - Xuexia Huang
- School of Environmental Science and Engineering, Guangzhou University, 510006, Guangzhou, China
| | - Xiaolan Wang
- School of Life Science, Guangzhou University, 510006, Guangzhou, China.
- School of Chemistry and Chemical Engineering, Guangzhou University, 510006, Guangzhou, China.
| | - Ping Zhang
- School of Chemistry and Chemical Engineering, Guangzhou University, 510006, Guangzhou, China.
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Zhu H, Yang X, Li Q, Guo J, Ma T, Liu S, Lin S, Zhou Y, Zhao C, Wang J, Sui J. The Sweetpotato Voltage-Gated K + Channel β Subunit, KIbB1, Positively Regulates Low-K + and High-Salinity Tolerance by Maintaining Ion Homeostasis. Genes (Basel) 2022; 13:genes13061100. [PMID: 35741862 PMCID: PMC9222298 DOI: 10.3390/genes13061100] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 06/17/2022] [Accepted: 06/17/2022] [Indexed: 12/26/2022] Open
Abstract
Voltage-gated K+ channel β subunits act as a structural component of Kin channels in different species. The β subunits are not essential to the channel activity but confer different properties through binding the T1 domain or the C-terminal of α subunits. Here, we studied the physiological function of a novel gene, KIbB1, encoding a voltage-gated K+ channel β subunit in sweetpotato. The transcriptional level of this gene was significantly higher in the low-K+-tolerant line than that in the low-K+-sensitive line under K+ deficiency conditions. In Arabidopsis, KIbB1 positively regulated low-K+ tolerance through regulating K+ uptake and translocation. Under high-salinity stress, the growth conditions of transgenic lines were obviously better than wild typr (WT). Enzymatic and non-enzymatic reactive oxygen species (ROS) scavenging were activated in transgenic plants. Accordingly, the malondialdehyde (MDA) content and the accumulation of ROS such as H2O2 and O2− were lower in transgenic lines under salt stress. It was also found that the overexpression of KIbB1 enhanced K+ uptake, but the translocation from root to shoot was not affected under salt stress. This demonstrates that KIbB1 acted as a positive regulator in high-salinity stress resistance through regulating Na+ and K+ uptake to maintain K+/Na+ homeostasis. These results collectively suggest that the mechanisms of KIbB1 in regulating K+ were somewhat different between low-K+ and high-salinity conditions.
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Affiliation(s)
- Hong Zhu
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China; (H.Z.); (X.Y.); (Q.L.); (J.G.); (T.M.); (S.L.); (S.L.); (C.Z.); (J.W.)
| | - Xue Yang
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China; (H.Z.); (X.Y.); (Q.L.); (J.G.); (T.M.); (S.L.); (S.L.); (C.Z.); (J.W.)
- Laboratory of Microbiology, Institute of Biology, Hebei Academy of Sciences, Shijiazhuang 050081, China
| | - Qiyan Li
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China; (H.Z.); (X.Y.); (Q.L.); (J.G.); (T.M.); (S.L.); (S.L.); (C.Z.); (J.W.)
| | - Jiayu Guo
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China; (H.Z.); (X.Y.); (Q.L.); (J.G.); (T.M.); (S.L.); (S.L.); (C.Z.); (J.W.)
| | - Tao Ma
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China; (H.Z.); (X.Y.); (Q.L.); (J.G.); (T.M.); (S.L.); (S.L.); (C.Z.); (J.W.)
| | - Shuyan Liu
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China; (H.Z.); (X.Y.); (Q.L.); (J.G.); (T.M.); (S.L.); (S.L.); (C.Z.); (J.W.)
| | - Shunyu Lin
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China; (H.Z.); (X.Y.); (Q.L.); (J.G.); (T.M.); (S.L.); (S.L.); (C.Z.); (J.W.)
| | - Yuanyuan Zhou
- Crop Research Institute, Shandong Academy of Agricultural Sciences/Scientific Observing and Experimental Station of Tuber and Root Crops in Huang-Huai-Hai Region, Ministry of Agriculture and Rural Affairs, Jinan 250100, China;
| | - Chunmei Zhao
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China; (H.Z.); (X.Y.); (Q.L.); (J.G.); (T.M.); (S.L.); (S.L.); (C.Z.); (J.W.)
| | - Jingshan Wang
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China; (H.Z.); (X.Y.); (Q.L.); (J.G.); (T.M.); (S.L.); (S.L.); (C.Z.); (J.W.)
| | - Jiongming Sui
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China; (H.Z.); (X.Y.); (Q.L.); (J.G.); (T.M.); (S.L.); (S.L.); (C.Z.); (J.W.)
- Correspondence:
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20
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Xiao-Lin Z, Bao-Qiang W, Xiao-Hong W. Identification and expression analysis of the CqSnRK2 gene family and a functional study of the CqSnRK2.12 gene in quinoa (Chenopodium quinoa Willd.). BMC Genomics 2022; 23:397. [PMID: 35610576 PMCID: PMC9131629 DOI: 10.1186/s12864-022-08626-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 05/09/2022] [Indexed: 11/10/2022] Open
Abstract
Background Sucrose non-fermenting 1 (SNF1)-associated protein kinase 2 (SnRK2) proteins belong to a relatively small family of plant-specific serine/threonine (Ser/Thr) protein kinases. SnRK2s participate in the abscisic acid (ABA) signaling pathway and play important roles in many biotic and abiotic stresses. At present, no SnRK2 gene has been reported in quinoa, and the recently published genome for this species provides an opportunity to identify and characterize the SnRK2 gene family. Results We identified 13 SnRK2 genes in the C. quinoa genome by bioinformatics analysis. Based on their phylogenetic relationships, these genes were divided into three subfamilies, similar to the situation in other plant species. Gene duplication analysis showed that there were seven pairs of homologous genes in the CqSnRK2 family, and that purifying selection played an important role in the evolution of SnRK2 genes. Gene structure analysis showed that the first exon in the SnRK2 family genes has the same length as the last exon, and that CqSnRK2 genes in the same subfamily have similar gene structures. Sequence analysis showed that the N-terminal region contains three highly conserved motifs. In addition, many kinds of cis-elements were identified in the promoter region of CqSnRK2, including those for hormone responses, stress responses, and tissue-specific expression. Transcription data analysis and qRT-PCR results showed that CqSnRK2 has different expression patterns in roots, stems, and leaves, and responded to biotic and abiotic stresses such as low temperature, salt, drought, and abscisic acid (ABA). In addition, we found that the protein encoded by CqSnRK2.12 was localized to the cytoplasm and nucleus, and there was no self-activation. The results of CqSnRK2.12 overexpression showed that transgenic Arabidopsis thaliana lines had increased drought tolerance compared to the controls. Conclusion The results of our study provide references for further studies on the evolution, function, and expression of the SnRK2 gene family in quinoa. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08626-1.
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Affiliation(s)
- Zhu Xiao-Lin
- College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China.,College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China.,Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070, China
| | - Wang Bao-Qiang
- College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China.,College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China.,Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070, China
| | - Wei Xiao-Hong
- College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China. .,College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China. .,Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070, China.
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Dai J, Sun J, Peng W, Liao W, Zhou Y, Zhou XR, Qin Y, Cheng Y, Cao S. FAR1/FHY3 Transcription Factors Positively Regulate the Salt and Temperature Stress Responses in Eucalyptus grandis. FRONTIERS IN PLANT SCIENCE 2022; 13:883654. [PMID: 35599891 PMCID: PMC9115564 DOI: 10.3389/fpls.2022.883654] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 04/05/2022] [Indexed: 06/15/2023]
Abstract
FAR-RED ELONGATED HYPOCOTYLS3 (FHY3) and its homolog FAR-RED IMPAIRED RESPONSE1 (FAR1), which play pivotal roles in plant growth and development, are essential for the photo-induced phyA nuclear accumulation and subsequent photoreaction. The FAR1/FHY3 family has been systematically characterized in some plants, but not in Eucalyptus grandis. In this study, genome-wide identification of FAR1/FHY3 genes in E. grandis was performed using bioinformatic methods. The gene structures, chromosomal locations, the encoded protein characteristics, 3D models, phylogenetic relationships, and promoter cis-elements were analyzed with this gene family. A total of 33 FAR1/FHY3 genes were identified in E. grandis, which were divided into three groups based on their phylogenetic relationships. A total of 21 pairs of duplicated repeats were identified by homology analysis. Gene expression analysis showed that most FAR1/FHY3 genes were differentially expressed in a spatial-specific manner. Gene expression analysis also showed that FAR1/FHY3 genes responded to salt and temperature stresses. These results and observation will enhance our understanding of the evolution and function of the FAR1/FHY3 genes in E. grandis and facilitate further studies on the molecular mechanism of the FAR1/FHY3 gene family in growth and development regulations, especially in response to salt and temperature.
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Affiliation(s)
- Jiahao Dai
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
- University Key Laboratory of Forest Stress Physiology, Ecology and Molecular Biology of Fujian Province, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jin Sun
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Wenjing Peng
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Wenhai Liao
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
- University Key Laboratory of Forest Stress Physiology, Ecology and Molecular Biology of Fujian Province, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yuhan Zhou
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xue-Rong Zhou
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Canberra, ACT, Australia
| | - Yuan Qin
- Fujian Agriculture and Forestry University and University of Illinois at Urbana-Champaign School of Integrative Biology Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Science, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Corps, College of Life Science, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
- Guangxi Key Lab of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, China
| | - Yan Cheng
- Fujian Agriculture and Forestry University and University of Illinois at Urbana-Champaign School of Integrative Biology Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Science, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Corps, College of Life Science, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shijiang Cao
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
- University Key Laboratory of Forest Stress Physiology, Ecology and Molecular Biology of Fujian Province, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
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Tang R, Dong H, He L, Li P, Shi Y, Yang Q, Jia X, Li XQ. Genome-wide identification, evolutionary and functional analyses of KFB family members in potato. BMC PLANT BIOLOGY 2022; 22:226. [PMID: 35501691 PMCID: PMC9063267 DOI: 10.1186/s12870-022-03611-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 04/18/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Kelch repeat F-box (KFB) proteins play vital roles in the regulation of multitudinous biochemical and physiological processes in plants, including growth and development, stress response and secondary metabolism. Multiple KFBs have been characterized in various plant species, but the family members and functions have not been systematically identified and analyzed in potato. RESULTS Genome and transcriptome analyses of StKFB gene family were conducted to dissect the structure, evolution and function of the StKFBs in Solanum tuberosum L. Totally, 44 StKFB members were identified and were classified into 5 groups. The chromosomal localization analysis showed that the 44 StKFB genes were located on 12 chromosomes of potato. Among these genes, two pairs of genes (StKFB15/16 and StKFB40/41) were predicted to be tandemly duplicated genes, and one pair of genes (StKFB15/29) was segmentally duplicated genes. The syntenic analysis showed that the KFBs in potato were closely related to the KFBs in tomato and pepper. Expression profiles of the StKFBs in 13 different tissues and in potato plants with different treatments uncovered distinct spatial expression patterns of these genes and their potential roles in response to various stresses, respectively. Multiple StKFB genes were differentially expressed in yellow- (cultivar 'Jin-16'), red- (cultivar 'Red rose-2') and purple-fleshed (cultivar 'Xisen-8') potato tubers, suggesting that they may play important roles in the regulation of anthocyanin biosynthesis in potato. CONCLUSIONS This study reports the structure, evolution and expression characteristics of the KFB family in potato. These findings pave the way for further investigation of functional mechanisms of StKFBs, and also provide candidate genes for potato genetic improvement.
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Affiliation(s)
- Ruimin Tang
- College of life sciences, Shanxi Agricultural University, Taigu, 030801 Shanxi China
| | - Haitao Dong
- College of life sciences, Shanxi Agricultural University, Taigu, 030801 Shanxi China
| | - Liheng He
- College of Agriculture, Shanxi Agricultural University, Taigu, 030801 Shanxi China
| | - Peng Li
- College of life sciences, Shanxi Agricultural University, Taigu, 030801 Shanxi China
| | - Yuanrui Shi
- College of life sciences, Shanxi Agricultural University, Taigu, 030801 Shanxi China
| | - Qing Yang
- College of life sciences, Nanjing Agricultural University, Nanjing, 210095 Jiangsu China
| | - Xiaoyun Jia
- College of life sciences, Shanxi Agricultural University, Taigu, 030801 Shanxi China
| | - Xiu-Qing Li
- Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, Fredericton, New Brunswick E3B 4Z7 Canada
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Joshi S, Nath J, Singh AK, Pareek A, Joshi R. Ion transporters and their regulatory signal transduction mechanisms for salinity tolerance in plants. PHYSIOLOGIA PLANTARUM 2022; 174:e13702. [PMID: 35524987 DOI: 10.1111/ppl.13702] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 05/03/2022] [Accepted: 05/06/2022] [Indexed: 06/14/2023]
Abstract
Soil salinity is one of the most serious threats to plant growth and productivity. Due to global climate change, burgeoning population and shrinking arable land, there is an urgent need to develop crops with minimum reduction in yield when cultivated in salt-affected areas. Salinity stress imposes osmotic stress as well as ion toxicity, which impairs major plant processes such as photosynthesis, cellular metabolism, and plant nutrition. One of the major effects of salinity stress in plants includes the disturbance of ion homeostasis in various tissues. In the present study, we aimed to review the regulation of uptake, transport, storage, efflux, influx, and accumulation of various ions in plants under salinity stress. We have summarized major research advancements towards understanding the ion homeostasis at both cellular and whole-plant level under salinity stress. We have also discussed various factors regulating the function of ion transporters and channels in maintaining ion homeostasis and ionic interactions under salt stress, including plant antioxidative defense, osmo-protection, and osmoregulation. We further elaborated on stress perception at extracellular and intracellular levels, which triggers downstream intracellular-signaling cascade, including secondary messenger molecules generation. Various signaling and signal transduction mechanisms under salinity stress and their role in improving ion homeostasis in plants are also discussed. Taken together, the present review focuses on recent advancements in understanding the regulation and function of different ion channels and transporters under salt stress, which may pave the way for crop improvement.
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Affiliation(s)
- Shubham Joshi
- Division of Biotechnology, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC Campus, Ghaziabad, Uttar Pradesh, India
| | - Jhilmil Nath
- Division of Biotechnology, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC Campus, Ghaziabad, Uttar Pradesh, India
| | - Anil Kumar Singh
- ICAR-National Institute for Plant Biotechnology, LBS Centre, New Delhi, India
| | - Ashwani Pareek
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
- National Agri-Food Biotechnology Institute, Mohali, India
| | - Rohit Joshi
- Division of Biotechnology, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC Campus, Ghaziabad, Uttar Pradesh, India
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Genome-Wide Identification of Cotton (Gossypium spp.) Trehalose-6-Phosphate Phosphatase (TPP) Gene Family Members and the Role of GhTPP22 in the Response to Drought Stress. PLANTS 2022; 11:plants11081079. [PMID: 35448808 PMCID: PMC9024796 DOI: 10.3390/plants11081079] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 04/11/2022] [Accepted: 04/12/2022] [Indexed: 01/10/2023]
Abstract
Trehalose-6-phosphate phosphatase (TPP) is a key enzyme involved in trehalose synthesis in higher plants. Previous studies have shown that TPP family genes increase yields without affecting plant growth under drought conditions, but their functions in cotton have not been reported. In this study, 17, 12, 26 and 24 TPP family genes were identified in Gossypium arboreum, Gossypium raimondii, Gossypium barbadense and Gossypium hirsutum, respectively. The 79 TPP family genes were divided into three subgroups by phylogenetic analysis. Virus-induced gene silencing (VIGS) of GhTPP22 produced TRV::GhTPP22 plants that were more sensitive to drought stress than the control plants, and the relative expression of GhTPP22 was decreased, as shown by qRT–PCR. Moreover, we analysed the gene structure, targeted small RNAs, and gene expression patterns of TPP family members and the physicochemical properties of their encoded proteins. Overall, members of the TPP gene family in cotton were systematically identified, and the function of GhTPP22 under drought stress conditions was preliminarily verified. These findings provide new information for improving drought resistance for cotton breeding in the future.
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Hao Z, Ma S, Liang L, Feng T, Xiong M, Lian S, Zhu J, Chen Y, Meng L, Li M. Candidate Genes and Pathways in Rice Co-Responding to Drought and Salt Identified by gcHap Network. Int J Mol Sci 2022; 23:ijms23074016. [PMID: 35409377 PMCID: PMC8999833 DOI: 10.3390/ijms23074016] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 03/26/2022] [Accepted: 04/01/2022] [Indexed: 01/24/2023] Open
Abstract
Drought and salinity stresses are significant abiotic factors that limit rice yield. Exploring the co-response mechanism to drought and salt stress will be conducive to future rice breeding. A total of 1748 drought and salt co-responsive genes were screened, most of which are enriched in plant hormone signal transduction, protein processing in the endoplasmic reticulum, and the MAPK signaling pathways. We performed gene-coding sequence haplotype (gcHap) network analysis on nine important genes out of the total amount, which showed significant differences between the Xian/indica and Geng/japonica population. These genes were combined with related pathways, resulting in an interesting mechanistic draft called the ‘gcHap-network pathway’. Meanwhile, we collected a lot of drought and salt breeding varieties, especially the introgression lines (ILs) with HHZ as the parent, which contained the above-mentioned nine genes. This might imply that these ILs have the potential to improve the tolerance to drought and salt. In this paper, we focus on the relationship of drought and salt co-response gene gcHaps and their related pathways using a novel angle. The haplotype network will be helpful to explore the desired haplotypes that can be implemented in haplotype-based breeding programs.
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Affiliation(s)
- Zhiqi Hao
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China; (Z.H.); (S.M.); (L.L.); (T.F.); (M.X.); (S.L.); (J.Z.); (Y.C.)
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Sai Ma
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China; (Z.H.); (S.M.); (L.L.); (T.F.); (M.X.); (S.L.); (J.Z.); (Y.C.)
| | - Lunping Liang
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China; (Z.H.); (S.M.); (L.L.); (T.F.); (M.X.); (S.L.); (J.Z.); (Y.C.)
| | - Ting Feng
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China; (Z.H.); (S.M.); (L.L.); (T.F.); (M.X.); (S.L.); (J.Z.); (Y.C.)
| | - Mengyuan Xiong
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China; (Z.H.); (S.M.); (L.L.); (T.F.); (M.X.); (S.L.); (J.Z.); (Y.C.)
| | - Shangshu Lian
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China; (Z.H.); (S.M.); (L.L.); (T.F.); (M.X.); (S.L.); (J.Z.); (Y.C.)
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Jingyan Zhu
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China; (Z.H.); (S.M.); (L.L.); (T.F.); (M.X.); (S.L.); (J.Z.); (Y.C.)
| | - Yanjun Chen
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China; (Z.H.); (S.M.); (L.L.); (T.F.); (M.X.); (S.L.); (J.Z.); (Y.C.)
| | - Lijun Meng
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- Correspondence: (L.M.); (M.L.)
| | - Min Li
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China; (Z.H.); (S.M.); (L.L.); (T.F.); (M.X.); (S.L.); (J.Z.); (Y.C.)
- Correspondence: (L.M.); (M.L.)
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Wang S, Zhang X, Li B, Zhao X, Shen Y, Yuan Z. Genome-wide identification and characterization of bZIP gene family and cloning of candidate genes for anthocyanin biosynthesis in pomegranate (Punica granatum). BMC PLANT BIOLOGY 2022; 22:170. [PMID: 35379169 PMCID: PMC8978422 DOI: 10.1186/s12870-022-03560-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 03/23/2022] [Indexed: 05/02/2023]
Abstract
BACKGROUND The basic leucine zipper (bZIP) transcription factor is one of the most abundant and conserved gene families in eukaryotes. In addition to participating in plant development and growth, bZIP transcription factors play crucial roles in various abiotic stress responses and anthocyanin accumulation. Up to now, analysis of bZIP gene family members in pomegranate (Punica granatum) has not been reported. Three published pomegranate genome sequences provide valuable resources for further gene function analysis. RESULTS Using bioinformatics analysis, 65 PgbZIPs were identified and analyzed from the 'Taishanhong' pomegranate genome. We divided them into 13 groups (A, B, C, D, E, F, G, H, I, J, K, M, and S) according to the phylogenetic relationship with those of Arabidopsis, each containing a different number of genes. The regularity of exon/intron number and distribution was consistent with the classification of groups in the evolutionary tree. Transcriptome analysis of different tissues showed that members of the PgbZIP gene family were differentially expressed in different developmental stages and tissues of pomegranate. Among them, we selected PgbZIP16 and PgbZIP34 as candidate genes which affect anthocyanin accumulation. The full-length CDS region of PgbZIP16 and PgbZIP34 were cloned from pomegranate petals by homologous cloning technique, encoding 170 and 174 amino acids, which were 510 bp and 522 bp, respectively. Subcellular localization assays suggested that both PgbZIP16 and PgbZIP34 were nucleus-localized. Real-time quantitative PCR (qPCR) was used to explore the expression of PgbZIP16 and PgbZIP34 in the petals of three kinds of ornamental pomegranates at the full flowering stage. The results demonstrated that the expression of PgbZIP16 in red petals was 5.83 times of that in white petals, while PgbZIP34 was 3.9 times. The results of transient expression in tobacco showed that consistent trends were observed in anthocyanin concentration and expression levels of related genes, which both increased and then decreased. Both PgbZIP16 and PgbZIP34 could promote anthocyanin accumulation in tobacco leaves. We obtained transgenic strains overexpressing PgbZIP16, and the histochemical staining for GUS activity showed that overexpressed PgbZIP16 seedlings were expressed in the stem. Transgenic experiments indicated that overexpression of PgbZIP16 significantly upregulated UF3GT, ANS and DFR genes in Arabidopsis and enhanced anthocyanin accumulation. CONCLUSIONS The whole genome identification, gene structure, phylogeny, gene cloning, subcellular location and functional verification of the pomegranate bZIP gene family provide a theoretical foundation for the functional study of the PgbZIP gene family and candidate genes for anthocyanin biosynthesis.
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Affiliation(s)
- Sha Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
- College of Forestry, Nanjing Forestry University, Nanjing, 210037, China
| | - Xinhui Zhang
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
- College of Forestry, Nanjing Forestry University, Nanjing, 210037, China
| | - Bianbian Li
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
- College of Forestry, Nanjing Forestry University, Nanjing, 210037, China
| | - Xueqing Zhao
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
- College of Forestry, Nanjing Forestry University, Nanjing, 210037, China
| | - Yu Shen
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
- College of Forestry, Nanjing Forestry University, Nanjing, 210037, China
| | - Zhaohe Yuan
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China.
- College of Forestry, Nanjing Forestry University, Nanjing, 210037, China.
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Yuan Y, Yu J, Kong L, Zhang W, Hou X, Cui G. Genome-wide investigation of the PLD gene family in alfalfa (Medicago sativa L.): identification, analysis and expression. BMC Genomics 2022; 23:243. [PMID: 35350974 PMCID: PMC8962232 DOI: 10.1186/s12864-022-08424-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 02/22/2022] [Indexed: 11/16/2022] Open
Abstract
Background External environmental factors, such as salt, alkali and drought, severely limit the acreage and yield of alfalfa. The mining of tolerance-related genes in alfalfa and improving the stress resistance of this plant are essential for increasing alfalfa yield. PLD is the main phospholipid hydrolase in plants and plays an important role in plant growth, development, signaling, and resistance to adverse stress. With the availability of whole genome sequences, the annotation and expression of PLDs in alfalfa can now be achieved. At present, few studies have investigated PLDs in alfalfa. Here, we conducted a study of PLDs in alfalfa and identified and analyzed the expression pattern of PLDs under different treatments. Results Fifty-nine MsPLDs were identified in alfalfa and classified into six subtypes: MsPLDα, β, γ, δ and ε belong to the C2-PLD subfamily, and MsPLDζ belongs to the PXPH-PLD subfamily. Members of the same PLD subtype have similar physicochemical properties, sequence structure and domains, but their cis-acting elements are different. A qRT-PCR analysis revealed that MsPLDs are expressed in multiple tissues. MsPLDs can respond to alkali, drought, ABA, IAA, and GA3 treatments and particularly to salt stress. Different expression patterns were found for the same gene under different treatments and different genes under the same treatment. Expression of MsPLD05 improved salt tolerance in yeast. Conclusion This study represents the first genome-wide characterization of MsPLDs in alfalfa. Most MsPLDs are expressed mainly in mature leaves and respond positively to abiotic stresses and hormonal treatments. This study further expands the resistance gene pool in legume forage grasses and provides a reference for further in-depth study of MsPLDs in alfalfa. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08424-9.
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Wang H, Ni D, Shen J, Deng S, Xuan H, Wang C, Xu J, Zhou L, Guo N, Zhao J, Xing H. Genome-Wide Identification of the AP2/ERF Gene Family and Functional Analysis of GmAP2/ERF144 for Drought Tolerance in Soybean. FRONTIERS IN PLANT SCIENCE 2022; 13:848766. [PMID: 35419020 PMCID: PMC8996232 DOI: 10.3389/fpls.2022.848766] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 02/08/2022] [Indexed: 05/31/2023]
Abstract
Drought is a major environmental constraint that causes substantial reductions in plant growth and yield. Expression of stress-related genes is largely regulated by transcription factors (TFs), including in soybean [Glycine max (L.) Merr.]. In this study, 301 GmAP2/ERF genes that encode TFs were identified in the soybean genome. The TFs were divided into five categories according to their homology. Results of previous studies were then used to select the target gene GmAP2/ERF144 from among those up-regulated by drought and salt stress in the transcriptome. According to respective tissue expression analysis and subcellular determination, the gene was highly expressed in leaves and encoded a nuclear-localized protein. To validate the function of GmAP2/ERF144, the gene was overexpressed in soybean using Agrobacterium-mediated transformation. Compared with wild-type soybean, drought resistance of overexpression lines increased significantly. Under drought treatment, leaf relative water content was significantly higher in overexpressed lines than in the wild-type genotype, whereas malondialdehyde content and electrical conductivity were significantly lower than those in the wild type. Thus, drought resistance of transgenic soybean increased with overexpression of GmAP2/ERF144. To understand overall function of the gene, network analysis was used to predict the genes that interacted with GmAP2/ERF144. Reverse-transcription quantitative PCR showed that expression of those interacting genes in two transgenic lines was 3 to 30 times higher than that in the wild type. Therefore, GmAP2/ERF144 likely interacted with those genes; however, that conclusion needs to be verified in further specific experiments.
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Mao P, Run Y, Wang H, Han C, Zhang L, Zhan K, Xu H, Cheng X. Genome-Wide Identification and Functional Characterization of the Chloride Channel TaCLC Gene Family in Wheat (Triticum aestivum L.). Front Genet 2022; 13:846795. [PMID: 35368658 PMCID: PMC8966409 DOI: 10.3389/fgene.2022.846795] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 02/11/2022] [Indexed: 12/27/2022] Open
Abstract
In plants, chloride channels (CLC) are involved in a series of specific functions, such as regulation of nutrient transport and stress tolerance. Members of the wheat Triticum aestivum L. CLC (TaCLC) gene family have been proposed to encode anion channels/transporters that may be related to nitrogen transportation. To better understand their roles, TaCLC family was screened and 23 TaCLC gene sequences were identified using a Hidden Markov Model in conjunction with wheat genome database. Gene structure, chromosome location, conserved motif, and expression pattern of the resulting family members were then analyzed. Phylogenetic analysis showed that the TaCLC family can be divided into two subclasses (I and II) and seven clusters (-a, -c1, -c2, -e, -f1, -f2, and -g2). Using a wheat RNA-seq database, the expression pattern of TaCLC family members was determined to be an inducible expression type. In addition, seven genes from seven different clusters were selected for quantitative real-time PCR (qRT-PCR) analysis under low nitrogen stress or salt stress conditions, respectively. The results indicated that the gene expression levels of this family were up-regulated under low nitrogen stress and salt stress, except the genes of TaCLC-c2 cluster which were from subfamily -c. The yeast complementary experiments illustrated that TaCLC-a-6AS-1, TaCLC-c1-3AS, and TaCLC-e-3AL all had anion transport functions for NO3− or Cl−, and compensated the hypersensitivity of yeast GEF1 mutant strain YJR040w (Δgef1) in restoring anion-sensitive phenotype. This study establishes a theoretical foundation for further functional characterization of TaCLC genes and provides an initial reference for better understanding nitrate nitrogen transportation in wheat.
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Affiliation(s)
| | | | | | | | | | | | - Haixia Xu
- *Correspondence: Haixia Xu, ; Xiyong Cheng,
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Tao J, Jia H, Wu M, Zhong W, Jia D, Wang Z, Huang C. Genome-wide identification and characterization of the TIFY gene family in kiwifruit. BMC Genomics 2022; 23:179. [PMID: 35247966 PMCID: PMC8897921 DOI: 10.1186/s12864-022-08398-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 02/17/2022] [Indexed: 12/25/2022] Open
Abstract
Background The TIFY gene family is a group of plant-specific transcription factors involved in regulation of plant growth and development and a variety of stress responses. However, the TIFY family has not yet been well characterized in kiwifruit, a popular fruit with important nutritional and economic value. Results A total of 27 and 21 TIFY genes were identified in the genomes of Actinidia eriantha and A. chinensis, respectively. Phylogenetic analyses showed that kiwifruit TIFY genes could be classified into four major groups, JAZ, ZML, TIFY and PPD, and the JAZ group could be further clustered into six subgroups (JAZ I to JAZ VI). Members within the same group or subgroup have similar exon-intron structures and conserved motif compositions. The kiwifruit TIFY genes are unevenly distributed on the chromosomes, and the segmental duplication events played a vital role in the expansion of the TIFY genes in kiwifruit. Syntenic analyses of TIFY genes between kiwifruit and other five plant species (including Arabidopsis thaliana, Camellia sinensis, Oryza sativa, Solanum lycopersicum and Vitis vinifera) and between the two kiwifruit species provided valuable clues for understanding the potential evolution of the kiwifruit TIFY family. Molecular evolutionary analysis showed that the evolution of kiwifruit TIFY genes was primarily constrained by intense purifying selection. Promoter cis-element analysis showed that most kiwifruit TIFY genes possess multiple cis-elements related to stress-response, phytohormone signal transduction and plant growth and development. The expression pattern analyses indicated that TIFY genes might play a role in different kiwifruit tissues, including fruit at specific development stages. In addition, several TIFY genes with high expression levels during Psa (Pseudomonas syringae pv. actinidiae) infection were identified, suggesting a role in the process of Pas infection. Conclusions In this study, the kiwifruit TIFY genes were identified from two assembled kiwifruit genomes. In addition, their basic physiochemical properties, chromosomal localization, phylogeny, gene structures and conserved motifs, synteny analyses, promoter cis-elements and expression patters were systematically examined. The results laid a foundation for further understanding the function of TIFY genes in kiwifruit, and provided a new potential approach for the prevention and treatment of Psa infection. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08398-8.
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Cao Y, Shan T, Fang H, Sun K, Shi W, Tang B, Wu J, Wang K, Li P, Wang B. Genome-wide analysis reveals the spatiotemporal expression patterns of SOS3 genes in the maize B73 genome in response to salt stress. BMC Genomics 2022; 23:60. [PMID: 35034642 PMCID: PMC8761280 DOI: 10.1186/s12864-021-08287-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 12/29/2021] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Salt damage is an important abiotic stress that affects the growth and yield of maize worldwide. As an important member of the salt overly sensitive (SOS) signal transduction pathway, the SOS3 gene family participates in the transmission of stress signals and plays a vital role in improving the salt tolerance of plants. RESULTS In this study, we identified 59 SOS3 genes in the maize B73 genome using bioinformatics methods and genome-wide analyses. SOS3 proteins were divided into 5 different subfamilies according to the phylogenetic relationships. A close relationship between the phylogenetic classification and intron mode was observed, with most SOS3 genes in the same group sharing common motifs and similar exon-intron structures in the corresponding genes. These genes were unequally distributed on five chromosomes of B73. A total of six SOS3 genes were identified as repeated genes, and 12 pairs of genes were proven to be segmentally duplicated genes, indicating that gene duplication may play an important role in the expansion of the SOS3 gene family. The expression analysis of 10 genes that were randomly selected from different subgroups suggested that all 10 genes were significantly differentially expressed within 48 h after salt treatment, of which eight SOS3 genes showed a significant decline while Zm00001d025938 and Zm00001d049665 did not. By observing the subcellular localization results, we found that most genes were expressed in chloroplasts while some genes were expressed in the cell membrane and nucleus. CONCLUSIONS Our study provides valuable information for elucidating the evolutionary relationship and functional characteristics of the SOS3 gene family and lays the foundation for further study of the SOS3 gene family in the maize B73 genome.
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Affiliation(s)
- Yunying Cao
- Ministry of Agricultural Scientific Observing and Experimental Station of Maize in Plain Area of Southern Region, School of Life Sciences, Nantong University, Nantong, 226019, Jiangsu, China
| | - Tingyu Shan
- Ministry of Agricultural Scientific Observing and Experimental Station of Maize in Plain Area of Southern Region, School of Life Sciences, Nantong University, Nantong, 226019, Jiangsu, China
| | - Hui Fang
- Ministry of Agricultural Scientific Observing and Experimental Station of Maize in Plain Area of Southern Region, School of Life Sciences, Nantong University, Nantong, 226019, Jiangsu, China
| | - Kangtai Sun
- Ministry of Agricultural Scientific Observing and Experimental Station of Maize in Plain Area of Southern Region, School of Life Sciences, Nantong University, Nantong, 226019, Jiangsu, China
| | - Wen Shi
- Ministry of Agricultural Scientific Observing and Experimental Station of Maize in Plain Area of Southern Region, School of Life Sciences, Nantong University, Nantong, 226019, Jiangsu, China
| | - Bei Tang
- Ministry of Agricultural Scientific Observing and Experimental Station of Maize in Plain Area of Southern Region, School of Life Sciences, Nantong University, Nantong, 226019, Jiangsu, China
| | - Junping Wu
- Nantong Changjiang Seed Co., Ltd, Nantong, 226368, Jiangsu, China
| | - Kai Wang
- Ministry of Agricultural Scientific Observing and Experimental Station of Maize in Plain Area of Southern Region, School of Life Sciences, Nantong University, Nantong, 226019, Jiangsu, China.
| | - Ping Li
- Ministry of Agricultural Scientific Observing and Experimental Station of Maize in Plain Area of Southern Region, School of Life Sciences, Nantong University, Nantong, 226019, Jiangsu, China.
| | - Baohua Wang
- Ministry of Agricultural Scientific Observing and Experimental Station of Maize in Plain Area of Southern Region, School of Life Sciences, Nantong University, Nantong, 226019, Jiangsu, China.
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Wu W, Zhu S, Xu L, Zhu L, Wang D, Liu Y, Liu S, Hao Z, Lu Y, Yang L, Shi J, Chen J. Genome-wide identification of the Liriodendron chinense WRKY gene family and its diverse roles in response to multiple abiotic stress. BMC PLANT BIOLOGY 2022; 22:25. [PMID: 35012508 PMCID: PMC8744262 DOI: 10.1186/s12870-021-03371-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 11/29/2021] [Indexed: 05/27/2023]
Abstract
BACKGROUND Liriodendron chinense (Lchi) is a tree species within the Magnoliaceae family and is considered a basal angiosperm. The too low or high temperature or soil drought will restrict its growth as the adverse environmental conditions, thus improving L. chinense abiotic tolerance was the key issues to study. WRKYs are a major family of plant transcription factors known to often be involved in biotic and abiotic stress responses. So far, it is still largely unknown if and how the LchiWRKY gene family is tied to regulating L. chinense stress responses. Therefore, studying the involvement of the WRKY gene family in abiotic stress regulation in L. chinense could be very informative in showing how this tree deals with such stressful conditions. RESULTS In this research, we performed a genome-wide analysis of the Liriodendron chinense (Lchi) WRKY gene family, studying their classification relationships, gene structure, chromosomal locations, gene duplication, cis-element, and response to abiotic stress. The 44 members of the LchiWRKY gene family contain a significant amount of sequence diversity, with their lengths ranging from 525 bp to 40,981 bp. Using classification analysis, we divided the 44 LchiWRKY genes into three phylogenetic groups (I, II, II), with group II then being further divided into five subgroups (IIa, IIb, IIc, IId, IIe). Comparative phylogenetic analysis including the WRKY families from 17 plant species suggested that LchiWRKYs are closely related to the Magnolia Cinnamomum kanehirae WRKY family, and has fewer family members than higher plants. We found the LchiWRKYs to be evenly distributed across 15 chromosomes, with their duplication events suggesting that tandem duplication may have played a major role in LchiWRKY gene expansion model. A Ka/Ks analysis indicated that they mainly underwent purifying selection and distributed in the group IId. Motif analysis showed that LchiWRKYs contained 20 motifs, and different phylogenetic groups contained conserved motif. Gene ontology (GO) analysis showed that LchiWRKYs were mainly enriched in two categories, i.e., biological process and molecular function. Two group IIc members (LchiWRKY10 and LchiWRKY37) contain unique WRKY element sequence variants (WRKYGKK and WRKYGKS). Gene structure analysis showed that most LchiWRKYs possess 3 exons and two different types of introns: the R- and V-type which are both contained within the WRKY domain (WD). Additional promoter cis-element analysis indicated that 12 cis-elements that play different functions in environmental adaptability occur across all LchiWRKY groups. Heat, cold, and drought stress mainly induced the expression of group II and I LchiWRKYs, some of which had undergone gene duplication during evolution, and more than half of which had three exons. LchiWRKY33 mainly responded to cold stress and LchiWRKY25 mainly responded to heat stress, and LchiWRKY18 mainly responded to drought stress, which was almost 4-fold highly expressed, while 5 LchiWRKYs (LchiWRKY5, LchiWRKY23, LchiWRKY14, LchiWRKY27, and LchiWRKY36) responded equally three stresses with more than 6-fold expression. Subcellular localization analysis showed that all LchiWRKYs were localized in the nucleus, and subcellular localization experiments of LchiWRKY18 and 36 also showed that these two transcription factors were expressed in the nucleus. CONCLUSIONS This study shows that in Liriodendron chinense, several WRKY genes like LchiWRKY33, LchiWRKY25, and LchiWRKY18, respond to cold or heat or drought stress, suggesting that they may indeed play a role in regulating the tree's response to such conditions. This information will prove a pivotal role in directing further studies on the function of the LchiWRKY gene family in abiotic stress response and provides a theoretical basis for popularizing afforestation in different regions of China.
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Affiliation(s)
- Weihuang Wu
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education of China, Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Sheng Zhu
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Lin Xu
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education of China, Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Liming Zhu
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education of China, Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Dandan Wang
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education of China, Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Yang Liu
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education of China, Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Siqin Liu
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education of China, Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Zhaodong Hao
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education of China, Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Ye Lu
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education of China, Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Liming Yang
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Jisen Shi
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education of China, Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Jinhui Chen
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education of China, Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China.
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Ma X, Liu JN, Yan L, Liang Q, Fang H, Wang C, Dong Y, Chai Z, Zhou R, Bao Y, Hou W, Yang KQ, Wu D. Comparative Transcriptome Analysis Unravels Defense Pathways of Fraxinus velutina Torr Against Salt Stress. FRONTIERS IN PLANT SCIENCE 2022; 13:842726. [PMID: 35310642 PMCID: PMC8931533 DOI: 10.3389/fpls.2022.842726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 01/17/2022] [Indexed: 05/03/2023]
Abstract
Fraxinus velutina Torr with high salt tolerance has been widely grown in saline lands in the Yellow River Delta, China. However, the salt-tolerant mechanisms of F. velutina remain largely elusive. Here, we identified two contrasting cutting clones of F. velutina, R7 (salt-tolerant), and S4 (salt-sensitive) by measuring chlorophyll fluorescence characteristics (Fv/Fm ratio) in the excised leaves and physiological indexes in roots or leaves under salt treatment. To further explore the salt resistance mechanisms, we compared the transcriptomes of R7 and S4 from leaf and root tissues exposed to salt stress. The results showed that when the excised leaves of S4 and R7 were, respectively, exposed to 250 mM NaCl for 48 h, Fv/Fm ratio decreased significantly in S4 compared with R7, confirming that R7 is more tolerant to salt stress. Comparative transcriptome analysis showed that salt stress induced the significant upregulation of stress-responsive genes in R7, making important contributions to the high salt tolerance. Specifically, in the R7 leaves, salt stress markedly upregulated key genes involved in plant hormone signaling and mitogen-activated protein kinase signaling pathways; in the R7 roots, salt stress induced the upregulation of main genes involved in proline biosynthesis and starch and sucrose metabolism. In addition, 12 genes encoding antioxidant enzyme peroxidase were all significantly upregulated in both leaves and roots. Collectively, our findings revealed the crucial defense pathways underlying high salt tolerance of R7 through significant upregulation of some key genes involving metabolism and hub signaling pathways, thus providing novel insights into salt-tolerant F. velutina breeding.
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Affiliation(s)
- Xinmei Ma
- College of Forestry, Shandong Agricultural University, Tai’an, China
| | - Jian Ning Liu
- College of Forestry, Shandong Agricultural University, Tai’an, China
| | - Liping Yan
- Shandong Provincial Academy of Forestry, Jinan, China
| | - Qiang Liang
- College of Forestry, Shandong Agricultural University, Tai’an, China
- State Forestry and Grassland Administration Key Laboratory of Silviculture in the Downstream Areas of the Yellow River, Shandong Agricultural University, Tai’an, China
- Shandong Taishan Forest Ecosystem Research Station, Shandong Agricultural University, Tai’an, China
| | - Hongcheng Fang
- College of Forestry, Shandong Agricultural University, Tai’an, China
- State Forestry and Grassland Administration Key Laboratory of Silviculture in the Downstream Areas of the Yellow River, Shandong Agricultural University, Tai’an, China
- Shandong Taishan Forest Ecosystem Research Station, Shandong Agricultural University, Tai’an, China
| | - Changxi Wang
- College of Forestry, Shandong Agricultural University, Tai’an, China
| | - Yuhui Dong
- College of Forestry, Shandong Agricultural University, Tai’an, China
- State Forestry and Grassland Administration Key Laboratory of Silviculture in the Downstream Areas of the Yellow River, Shandong Agricultural University, Tai’an, China
- Shandong Taishan Forest Ecosystem Research Station, Shandong Agricultural University, Tai’an, China
| | - Zejia Chai
- College of Forestry, Shandong Agricultural University, Tai’an, China
| | - Rui Zhou
- College of Forestry, Shandong Agricultural University, Tai’an, China
| | - Yan Bao
- College of Forestry, Shandong Agricultural University, Tai’an, China
| | - Wenrui Hou
- College of Forestry, Shandong Agricultural University, Tai’an, China
| | - Ke Qiang Yang
- College of Forestry, Shandong Agricultural University, Tai’an, China
- State Forestry and Grassland Administration Key Laboratory of Silviculture in the Downstream Areas of the Yellow River, Shandong Agricultural University, Tai’an, China
- Shandong Taishan Forest Ecosystem Research Station, Shandong Agricultural University, Tai’an, China
- *Correspondence: Ke Qiang Yang,
| | - Dejun Wu
- Shandong Provincial Academy of Forestry, Jinan, China
- Dejun Wu,
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Li Q, Zhang L, Chen P, Wu C, Zhang H, Yuan J, Zhou J, Li X. Genome-Wide Identification of APETALA2/ETHYLENE RESPONSIVE FACTOR Transcription Factors in Cucurbita moschata and Their Involvement in Ethylene Response. FRONTIERS IN PLANT SCIENCE 2022; 13:847754. [PMID: 35371131 PMCID: PMC8965380 DOI: 10.3389/fpls.2022.847754] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 02/11/2022] [Indexed: 05/03/2023]
Abstract
APETALA2/ETHYLENE RESPONSIVE FACTOR (AP2/ERF), a plant-specific transcription factor (TF) family, plays an essential role in the growth and development of plants, and in their response to biotic and abiotic stresses. However, information on AP2/ERF in Cucurbita moschata (pumpkin), an edible and medicinal vegetable used worldwide, is scarce. A total of 212 AP2/ERF genes were identified in the C. moschata genome (CmoAP2/ERFs). Based on phylogenetic analysis, they were divided into four groups-28 AP2s, 92 ERFs, 86 dehydration-responsive element-binding (DREB) factors, and 6 ABI3/VPs (RAV). The 212 AP2/ERF genes were unevenly distributed on the 20 chromosomes of C. moschata. The results of structural analysis showed the absence of introns on 132 CmoAP2/ERFs. Four pairs of tandem duplication and 155 pairs of segmental duplication events were identified, which indicated that segmental duplications might be the main reason for the expansion of the CmoAP2/ERF family. The analysis of cis-regulatory elements (CREs) showed that most of the CmoAP2/ERFs contained hormone response elements (ABREs, EREs) in their promoters, suggesting that AP2/ERFs could contribute to the processes regulated by ethylene and abscisic acid. By comparing the transcriptome of ethephon-treated and control plants, we found that 16 CmoAP2/ERFs were significantly upregulated after ethephon treatment. Furthermore, we determined the expression patterns of these genes at different developmental stages of female and male flowers. This study provides insights into the identification, classification, physicochemical property, phylogenetic analysis, chromosomal location, gene structure, motif identification, and CRE prediction of the AP2/ERF superfamily in C. moschata. Sixteen CmoAP2/ERF genes were identified as ethylene-inducible genes. The results of this study will be valuable for understanding the roles of CmoAP2/ERFs in ethylene response and should provide a foundation for elucidating the function of AP2/ERF TFs in C. moschata.
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Affiliation(s)
- Qingfei Li
- College of Horticulture and Landscape, Henan Institute of Science and Technology, Xinxiang, China
- Henan Province Engineering Research Center of Horticultural Plant Resource Utilization and Germplasm Enhancement, Xinxiang, China
| | - Li Zhang
- College of Horticulture and Landscape, Henan Institute of Science and Technology, Xinxiang, China
- Henan Province Engineering Research Center of Horticultural Plant Resource Utilization and Germplasm Enhancement, Xinxiang, China
| | - Peiwen Chen
- College of Horticulture and Landscape, Henan Institute of Science and Technology, Xinxiang, China
- Henan Province Engineering Research Center of Horticultural Plant Resource Utilization and Germplasm Enhancement, Xinxiang, China
| | - Chunhui Wu
- College of Horticulture and Landscape, Henan Institute of Science and Technology, Xinxiang, China
- Henan Province Engineering Research Center of Horticultural Plant Resource Utilization and Germplasm Enhancement, Xinxiang, China
| | - Huaixia Zhang
- College of Horticulture and Landscape, Henan Institute of Science and Technology, Xinxiang, China
- Henan Province Engineering Research Center of Horticultural Plant Resource Utilization and Germplasm Enhancement, Xinxiang, China
| | - Jingping Yuan
- College of Horticulture and Landscape, Henan Institute of Science and Technology, Xinxiang, China
- Henan Province Engineering Research Center of Horticultural Plant Resource Utilization and Germplasm Enhancement, Xinxiang, China
| | - Junguo Zhou
- College of Horticulture and Landscape, Henan Institute of Science and Technology, Xinxiang, China
- Henan Province Engineering Research Center of Horticultural Plant Resource Utilization and Germplasm Enhancement, Xinxiang, China
| | - Xinzheng Li
- College of Horticulture and Landscape, Henan Institute of Science and Technology, Xinxiang, China
- Henan Province Engineering Research Center of Horticultural Plant Resource Utilization and Germplasm Enhancement, Xinxiang, China
- *Correspondence: Xinzheng Li,
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Azeem F, Zameer R, Rehman Rashid MA, Rasul I, Ul-Allah S, Siddique MH, Fiaz S, Raza A, Younas A, Rasool A, Ali MA, Anwar S, Siddiqui MH. Genome-wide analysis of potassium transport genes in Gossypium raimondii suggest a role of GrHAK/KUP/KT8, GrAKT2.1 and GrAKT1.1 in response to abiotic stress. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 170:110-122. [PMID: 34864561 DOI: 10.1016/j.plaphy.2021.11.038] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/22/2021] [Accepted: 11/23/2021] [Indexed: 06/13/2023]
Abstract
Potassium (K+) is an important macro-nutrient for plants, which comprises almost 10% of plant's dry mass. It plays a crucial role in the growth of plants as well as other important processes related to metabolism and stress tolerance. Plants have a complex and well-organized potassium distribution system (channels and transporters). Cotton is the most important economic crop, which is the primary source of natural fiber. Soil deficiency in K+ can negatively affect yield and fiber quality of cotton. However, potassium transport system in cotton is poorly studied. Current study identified 43 Potassium Transport System (PTS) genes in Gossypium raimondii genome. Based on conserved domains, transmembrane domains, and motif structures, these genes were classified as K+ transporters (2 HKTs, 7 KEAs, and 16 KUP/HAK/KTs) and K+ channels (11 Shakers and 7 TPKs/KCO). The phylogenetic comparison of GrPTS genes from Arabidopsis thaliana, Glycine max, Oryza sativa, Medicago truncatula and Cicer arietinum revealed variations in PTS gene conservation. Evolutionary analysis predicted that most GrPTS genes were segmentally duplicated. Gene structure analysis showed that the intron/exon organization of these genes was conserved in specific-family. Chromosomal localization demonstrated a random distribution of PTS genes across all the thirteen chromosomes except chromosome six. Many stress responsive cis-regulatory elements were predicted in promoter regions of GrPTS genes. The RNA-seq data analysis followed by qRT-PCR validation demonstrated that PTS genes potentially work in groups against environmental factors. Moreover, a transporter gene (GrHAK/KUP/KT8) and two channel genes (GrAKT2.1 and GrAKT1.1) are important candidate genes for plant stress response. These results provide useful information for further functional characterization of PTS genes with the breeding aim of stress-resistant cultivars.
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Affiliation(s)
- Farrukh Azeem
- Department of Bioinformatics and Biotechnology, Govt. College University, Faisalabad, Pakistan
| | - Roshan Zameer
- Department of Bioinformatics and Biotechnology, Govt. College University, Faisalabad, Pakistan
| | | | - Ijaz Rasul
- Department of Bioinformatics and Biotechnology, Govt. College University, Faisalabad, Pakistan
| | - Sami Ul-Allah
- College of Agriculture, Bahauddin Zakariya University, Bahadur Sub-Campus, Layyah, Pakistan
| | | | - Sajid Fiaz
- Department of Plant Breeding and Genetics, The University of Haripur, 22620, Haripir, Pakistan.
| | - Ali Raza
- Fujian Provincial Key Laboratory of Crop Molecular and Cell Biology, Oil Crops Research Institute, Center of Legume Crop Genetics and Systems Biology/College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, Fujian, 350002, China
| | - Afifa Younas
- Department of Botany, Lahore College for Women University, Lahore, Pakistan
| | - Asima Rasool
- Department of Bioinformatics and Biotechnology, Govt. College University, Faisalabad, Pakistan
| | - Muhammad Amjad Ali
- Department of Plant Pathology, University of Agriculture, Faisalabad, Pakistan
| | - Sultana Anwar
- Department of Agronomy, University of Florida, Gainesville, USA
| | - Manzer H Siddiqui
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
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Wei YL, Jin JP, Liang D, Gao J, Li J, Xie Q, Lu CQ, Yang FX, Zhu GF. Genome-wide identification of Cymbidium sinense WRKY gene family and the importance of its Group III members in response to abiotic stress. FRONTIERS IN PLANT SCIENCE 2022; 13:969010. [PMID: 35968117 PMCID: PMC9365948 DOI: 10.3389/fpls.2022.969010] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 07/07/2022] [Indexed: 05/13/2023]
Abstract
Transcription factors (TFs) of the WRKY family play pivotal roles in defense responses and secondary metabolism of plants. Although WRKY TFs are well documented in numerous plant species, no study has performed a genome-wide investigation of the WRKY gene family in Cymbidium sinense. In the present work, we found 64 C. sinense WRKY (CsWRKY) TFs, and they were further divided into eight subgroups. Chromosomal distribution of CsWRKYs revealed that the majority of these genes were localized on 16 chromosomes, especially on Chromosome 2. Syntenic analysis implied that 13 (20.31%) genes were derived from segmental duplication events, and 17 orthologous gene pairs were identified between Arabidopsis thaliana WRKY (AtWRKY) and CsWRKY genes. Moreover, 55 of the 64 CsWRKYs were detectable in different plant tissues in response to exposure to plant hormones. Among them, Group III members were strongly induced in response to various hormone treatments, indicating their potential essential roles in hormone signaling. We subsequently analyzed the function of CsWRKY18 in Group III. The CsWRKY18 was localized in the nucleus. The constitutive expression of CsWRKY18 in Arabidopsis led to enhanced sensitivity to ABA-mediated seed germination and root growth and elevated plant tolerance to abiotic stress within the ABA-dependent pathway. Overall, our study represented the first genome-wide characterization and functional analysis of WRKY TFs in C. sinense, which could provide useful clues about the evolution and functional description of CsWRKY genes.
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Awan SA, Khan I, Tariq R, Rizwan M, Wang X, Zhang X, Huang L. Genome-Wide Expression and Physiological Profiling of Pearl Millet Genotype Reveal the Biological Pathways and Various Gene Clusters Underlying Salt Resistance. FRONTIERS IN PLANT SCIENCE 2022; 13:849618. [PMID: 35419021 PMCID: PMC8996197 DOI: 10.3389/fpls.2022.849618] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 02/07/2022] [Indexed: 05/04/2023]
Abstract
Pearl millet (Pennisetum glaucum L.) is a vital staple food and an important cereal crop used as food, feed, and forage. It can withstand heat and drought due to the presence of some unique genes; however, the mechanism of salt stress has been missing in pearl millet until now. Therefore, we conducted a comparative transcriptome profiling to reveal the differentially expressed transcripts (DETs) associated with salt stress in pearl millet at different time points, such as 1, 3, and 7 h, of salt treatment. The physiological results suggested that salt stress significantly increased proline, malondialdehyde (MDA) content, and hydrogen peroxide (H2O2) in pearl millet at 1, 3, and 7 h of salt treatment. In addition, pearl millet plants regulated the activities of superoxide dismutase, catalase, and peroxidase to lessen the impact of salinity. The transcriptomic results depicted that salt stress upregulated and downregulated the expression of various transcripts involved in different metabolic functions. At 1 and 7 h of salt treatment, most of the transcripts were highly upregulated as compared to the 3 h treatment. Moreover, among commonly enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, the mitogen-activated protein kinase (MAPK) signaling pathway and peroxisome pathway were significantly enriched. The DETs related to hormone signaling (auxins, ethylene, gibberellin, and abscisic acid), kinases, protein modifications, and degradation were also identified, depicting the possible role of hormones and kinases to enhance plant tolerance against salt stress. Furthermore, the transcription factors, such as ethylene-responsive element binding factors (ERF), basic helix-loop-helix (bHLH), HMG box-containing protein (HBP), MADS, myeloblastosis (MYB), and WRKY, were predicted to significantly regulate different transcripts involved in salt stress responses at three different time points. Overall, this study will provide new insights to better understand the salt stress regulation mechanisms in pearl millet to improve its resistance against salinity and to identify new transcripts that control these mechanisms in other cereals.
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Affiliation(s)
- Samrah Afzal Awan
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Imran Khan
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Rezwan Tariq
- Department of Plant Protection, Akdeniz University, Antalya, Turkey
| | - Muhammad Rizwan
- Department of Environmental Sciences and Engineering, Government College University Faisalabad, Faisalabad, Pakistan
| | - Xiaoshan Wang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Xinquan Zhang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Linkai Huang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
- *Correspondence: Linkai Huang,
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Faraji S, Heidari P, Amouei H, Filiz E, Abdullah, Poczai P. Investigation and Computational Analysis of the Sulfotransferase (SOT) Gene Family in Potato ( Solanum tuberosum): Insights into Sulfur Adjustment for Proper Development and Stimuli Responses. PLANTS (BASEL, SWITZERLAND) 2021; 10:2597. [PMID: 34961068 PMCID: PMC8707064 DOI: 10.3390/plants10122597] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 11/22/2021] [Accepted: 11/24/2021] [Indexed: 07/20/2023]
Abstract
Various kinds of primary metabolisms in plants are modulated through sulfate metabolism, and sulfotransferases (SOTs), which are engaged in sulfur metabolism, catalyze sulfonation reactions. In this study, a genome-wide approach was utilized for the recognition and characterization of SOT family genes in the significant nutritional crop potato (Solanum tuberosum L.). Twenty-nine putative StSOT genes were identified in the potato genome and were mapped onto the nine S. tuberosum chromosomes. The protein motifs structure revealed two highly conserved 5'-phosphosulfate-binding (5' PSB) regions and a 3'-phosphate-binding (3' PB) motif that are essential for sulfotransferase activities. The protein-protein interaction networks also revealed an interesting interaction between SOTs and other proteins, such as PRTase, APS-kinase, protein phosphatase, and APRs, involved in sulfur compound biosynthesis and the regulation of flavonoid and brassinosteroid metabolic processes. This suggests the importance of sulfotransferases for proper potato growth and development and stress responses. Notably, homology modeling of StSOT proteins and docking analysis of their ligand-binding sites revealed the presence of proline, glycine, serine, and lysine in their active sites. An expression essay of StSOT genes via potato RNA-Seq data suggested engagement of these gene family members in plants' growth and extension and responses to various hormones and biotic or abiotic stimuli. Our predictions may be informative for the functional characterization of the SOT genes in potato and other nutritional crops.
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Affiliation(s)
- Sahar Faraji
- Department of Plant Breeding, Faculty of Crop Science, Sari Agricultural Sciences and Natural Resources University (SANRU), Sari 4818166996, Iran; (S.F.); (H.A.)
| | - Parviz Heidari
- Faculty of Agriculture, Shahrood University of Technology, Shahrood 3619995161, Iran
| | - Hoorieh Amouei
- Department of Plant Breeding, Faculty of Crop Science, Sari Agricultural Sciences and Natural Resources University (SANRU), Sari 4818166996, Iran; (S.F.); (H.A.)
| | - Ertugrul Filiz
- Department of Crop and Animal Production, Cilimli Vocational School, Duzce University, 81750 Duzce, Turkey;
| | - Abdullah
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan;
| | - Peter Poczai
- Finnish Museum of Natural History, University of Helsinki, P.O. Box 7, 00014 Helsinki, Finland
- Faculty of Biological and Environmental Sciences, University of Helsinki, P.O. Box 65, 00065 Helsinki, Finland
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Abdullah, Faraji S, Heidari P, Poczai P. The BAHD Gene Family in Cacao (Theobroma cacao, Malvaceae): Genome-Wide Identification and Expression Analysis. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.707708] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The benzyl alcohol O-acetyl transferase, anthocyanin O-hydroxycinnamoyl transferase, N-hydroxycinnamoyl anthranilate benzoyl transferase, and deacetylvindoline 4-O-acetyltransferase (BAHD) enzymes play a critical role in regulating plant metabolites and affecting cell stability. In the present study, members of the BAHD gene family were recognized in the genome of Theobroma cacao and characterized using various bioinformatics tools. We found 27 non-redundant putative tcBAHD genes in cacao for the first time. Our findings indicate that tcBAHD genes are diverse based on sequence structure, physiochemical properties, and function. When analyzed with BAHDs of Gossypium raimondii and Corchorus capsularis clustered into four main groups. According to phylogenetic analysis, BAHD genes probably evolved drastically after their divergence. The divergence time of duplication events with purifying selection pressure was predicted to range from 1.82 to 15.50 MYA. Pocket analysis revealed that serine amino acid is more common in the binding site than other residuals, reflecting its key role in regulating the activity of tcBAHDs. Furthermore, cis-acting elements related to the responsiveness of stress and hormone, particularly ABA and MeJA, were frequently observed in the promoter region of tcBAHD genes. RNA-seq analysis further illustrated that tcBAHD13 and tcBAHD26 are involved in response to Phytophthora megakarya fungi. In conclusion, it is likely that evolutionary processes, such as duplication events, have caused high diversity in the structure and function of tcBAHD genes.
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El-Sappah AH, Elbaiomy RG, Elrys AS, Wang Y, Zhu Y, Huang Q, Yan K, Xianming Z, Abbas M, El-Tarabily KA, Li J. Genome-Wide Identification and Expression Analysis of Metal Tolerance Protein Gene Family in Medicago truncatula Under a Broad Range of Heavy Metal Stress. Front Genet 2021; 12:713224. [PMID: 34603378 PMCID: PMC8482800 DOI: 10.3389/fgene.2021.713224] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 06/30/2021] [Indexed: 01/02/2023] Open
Abstract
Metal tolerance proteins (MTPs) encompass plant membrane divalent cation transporters to specifically participate in heavy metal stress resistance and mineral acquisition. However, the molecular behaviors and biological functions of this family in Medicago truncatula are scarcely known. A total of 12 potential MTP candidate genes in the M. truncatula genome were successfully identified and analyzed for a phylogenetic relationship, chromosomal distributions, gene structures, docking analysis, gene ontology, and previous gene expression. M. truncatula MTPs (MtMTPs) were further classified into three major cation diffusion facilitator (CDFs) groups: Mn-CDFs, Zn-CDFs, and Fe/Zn-CDFs. The structural analysis of MtMTPs displayed high gene similarity within the same group where all of them have cation_efflux domain or ZT_dimer. Cis-acting element analysis suggested that various abiotic stresses and phytohormones could induce the most MtMTP gene transcripts. Among all MTPs, PF16916 is the specific domain, whereas GLY, ILE, LEU, MET, ALA, SER, THR, VAL, ASN, and PHE amino acids were predicted to be the binding residues in the ligand-binding site of all these proteins. RNA-seq and gene ontology analysis revealed the significant role of MTP genes in the growth and development of M. truncatula. MtMTP genes displayed differential responses in plant leaves, stems, and roots under five divalent heavy metals (Cd2+, Co2+, Mn2+, Zn2+, and Fe2+). Ten, seven, and nine MtMTPs responded to at least one metal ion treatment in the leaves, stems, and roots, respectively. Additionally, MtMTP1.1, MtMTP1.2, and MtMTP4 exhibited the highest expression responses in most heavy metal treatments. Our results presented a standpoint on the evolution of MTPs in M. truncatula. Overall, our study provides a novel insight into the evolution of the MTP gene family in M. truncatula and paves the way for additional functional characterization of this gene family.
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Affiliation(s)
- Ahmed H El-Sappah
- School of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China.,Genetics Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
| | | | - Ahmed S Elrys
- Soil Science Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
| | - Yu Wang
- School of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
| | - Yumin Zhu
- School of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
| | - Qiulan Huang
- College of Tea Science, Yibin University, Yibin, China
| | - Kuan Yan
- School of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
| | - Zhao Xianming
- School of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
| | - Manzar Abbas
- School of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
| | - Khaled A El-Tarabily
- Department of Biology, College of Science, United Arab Emirates University, Al Ain, United Arab Emirates.,Harry Butler Institute, Murdoch University, Murdoch, WA, Australia
| | - Jia Li
- School of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
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Abdullah, Faraji S, Mehmood F, Malik HMT, Ahmed I, Heidari P, Poczai P. The GASA Gene Family in Cacao (Theobroma cacao, Malvaceae): Genome Wide Identification and Expression Analysis. AGRONOMY 2021; 11:1425. [DOI: 10.3390/agronomy11071425] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
The gibberellic acid-stimulated Arabidopsis (GASA/GAST) gene family is widely distributed in plants and involved in various physiological and biological processes. These genes also provide resistance to abiotic and biotic stresses, including antimicrobial, antiviral, and antifungal. We are interested in characterizing the GASA gene family and determining its role in various physiological and biological process in Theobroma cacao. Here, we report 17 tcGASA genes distributed on six chromosomes in T. cacao. The gene structure, promoter region, protein structure and biochemical properties, expression, and phylogenetics of all tcGASAs were analyzed. Phylogenetic analyses divided tcGASA proteins into five groups. Among 17 tcGASA genes, nine segmentally duplicating genes were identified which formed four pairs and cluster together in phylogenetic tree. Differential expression analyses revealed that most of the tcGASA genes showed elevated expression in the seeds (cacao food), implying their role in seed development. The differential expression of tcGASAs was recorded between the tolerant and susceptible cultivars of cacao, which indicating their possible role as fungal resistant. Our findings provide new insight into the function, evolution, and regulatory system of the GASA family genes in T.cacao and may suggest new target genes for development of fungi-resistant cacao varieties in breeding programs.
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Wang X, Li J, Li F, Pan Y, Cai D, Mao D, Chen L, Luan S. Rice Potassium Transporter OsHAK8 Mediates K + Uptake and Translocation in Response to Low K + Stress. FRONTIERS IN PLANT SCIENCE 2021; 12:730002. [PMID: 34413871 PMCID: PMC8369890 DOI: 10.3389/fpls.2021.730002] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 07/13/2021] [Indexed: 05/13/2023]
Abstract
Potassium (K+) levels in the soil often limit plant growth and development. As a result, crop production largely relies on the heavy use of chemical fertilizers, presenting a challenging problem in sustainable agriculture. To breed crops with higher K+-use efficiency (KUE), we must learn how K+ is acquired from the soil by the root system and transported to the rest of the plant through K+ transporters. In this study, we identified the function of the rice K+ transporter OsHAK8, whose expression level is downregulated in response to low-K+ stress. When OsHAK8 was disrupted by CRISPR/Cas9-mediated mutagenesis, Oshak8 mutant plants showed stunted growth, especially under low-K+ conditions. Ion content analyses indicated that K+ uptake and root-to-shoot K+ transport were significantly impaired in Oshak8 mutants under low-K+ conditions. As the OsHAK8 gene was broadly expressed in different cell types in the roots and its protein was targeted to the plasma membrane, we propose that OsHAK8 serves as a major transporter for both uptake and root-to-shoot translocation in rice plants.
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Affiliation(s)
- Xiaohui Wang
- Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Junfeng Li
- Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Fei Li
- Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Yu Pan
- Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Dan Cai
- Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Dandan Mao
- Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, College of Life Sciences, Hunan Normal University, Changsha, China
- *Correspondence: Dandan Mao,
| | - Liangbi Chen
- Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, College of Life Sciences, Hunan Normal University, Changsha, China
- Liangbi Chen,
| | - Sheng Luan
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
- Sheng Luan,
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