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Saeed SH, Shah GM, Mahmood Q, Shaheen S, Zeb BS, Nawazish S, Almutairi KF, Avila-Quezada GD, Abd Allah EF. Phytoremediation ability and selected genetic transcription in Hydrocotyle umbellata-under cadmium stress. INTERNATIONAL JOURNAL OF PHYTOREMEDIATION 2024; 26:1144-1153. [PMID: 38143325 DOI: 10.1080/15226514.2023.2295354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2023]
Abstract
Cadmium (Cd) is the most toxic element which may cause serious consequences to microbial communities, animals, and plants. The use of green technologies like phytoremediation employs plants with high biomass and metal tolerance to extract toxic metals from their rooting zones. In the present work, Hydrocotyle umbellata was exposed to five Cd concentrations (2, 4, 6, 8, and 10 µmol) in triplicates to judge its phytoextraction ability. Effects of metal exposure on chlorophyll (Chl), bio-concentration factor (BCF), translocation factor (TF), and electrolyte leakage (EL) were analyzed after 10 days of treatment. Metal-responding genes were also observed through transcriptomic analysis. Roots were the primary organs for cadmium accumulation followed by stolon and leaves. There was an increase in EL. Plants showed various symptoms under increasing metal stress namely, chlorosis, browning of the leaf margins, burn-like areas on the leaves, and stunted growth, suggesting a positive relationship between EL, and programmed cell death (PCD). Metal-responsive genes, including glutathione, expansin, and cystatin were equally expressed. The phytoextraction capacity and adaptability of H. umbellata L. against Cd metal stress was also demonstrated by BCF more than 1 and TF less than 1.
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Affiliation(s)
- Sidra H Saeed
- Department of Botany, Hazara University Garden Campus, Mansehra, Pakistan
| | - Ghulam M Shah
- Department of Botany, Hazara University Garden Campus, Mansehra, Pakistan
| | - Qaisar Mahmood
- Department of Environmental Sciences, COMSATS University Islamabad, Abbottabad Campus, Abbottabad, Pakistan
- Department of Environmental Sciences, Kohsar University, Murree, Pakistan
| | - Shahida Shaheen
- Department of Biology, College of Science, University of Bahrain, Sakhir, Bahrain
| | - Bibi S Zeb
- Department of Environmental Sciences, COMSATS University Islamabad, Abbottabad Campus, Abbottabad, Pakistan
| | - Shamyla Nawazish
- Department of Environmental Sciences, COMSATS University Islamabad, Abbottabad Campus, Abbottabad, Pakistan
| | - Khalid F Almutairi
- Plant Production Department, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
| | | | - Elsayed Fathi Abd Allah
- Plant Production Department, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
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2
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Transcriptome analysis of Kentucky bluegrass subject to drought and ethephon treatment. PLoS One 2021; 16:e0261472. [PMID: 34914788 PMCID: PMC8675742 DOI: 10.1371/journal.pone.0261472] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 12/03/2021] [Indexed: 11/19/2022] Open
Abstract
Kentucky bluegrass (Poa pratensis L.) is an excellent cool-season turfgrass utilized widely in Northern China. However, turf quality of Kentucky bluegrass declines significantly due to drought. Ethephon seeds-soaking treatment has been proved to effectively improve the drought tolerance of Kentucky bluegrass seedlings. In order to investigate the effect of ethephon leaf-spraying method on drought tolerance of Kentucky bluegrass and understand the underlying mechanism, Kentucky bluegrass plants sprayed with and without ethephon are subjected to either drought or well watered treatments. The relative water content and malondialdehyde conent were measured. Meanwhile, samples were sequenced through Illumina. Results showed that ethephon could improve the drought tolerance of Kentucky bluegrass by elevating relative water content and decreasing malondialdehyde content under drought. Transcriptome analysis showed that 58.43% transcripts (254,331 out of 435,250) were detected as unigenes. A total of 9.69% (24,643 out of 254,331) unigenes were identified as differentially expressed genes in one or more of the pairwise comparisons. Differentially expressed genes due to drought stress with or without ethephon pre-treatment showed that ethephon application affected genes associated with plant hormone, signal transduction pathway and plant defense, protein degradation and stabilization, transportation and osmosis, antioxidant system and the glyoxalase pathway, cell wall and cuticular wax, fatty acid unsaturation and photosynthesis. This study provides a theoretical basis for revealing the mechanism for how ethephon regulates drought response and improves drought tolerance of Kentucky bluegrass.
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Muhammad A, Li J, Hu W, Yu J, Khan SU, Khan MHU, Xie G, Wang J, Wang L. Uncovering genomic regions controlling plant architectural traits in hexaploid wheat using different GWAS models. Sci Rep 2021; 11:6767. [PMID: 33762669 PMCID: PMC7990932 DOI: 10.1038/s41598-021-86127-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Accepted: 03/10/2021] [Indexed: 01/31/2023] Open
Abstract
Wheat is a major food crop worldwide. The plant architecture is a complex trait mostly influenced by plant height, tiller number, and leaf morphology. Plant height plays a crucial role in lodging and thus affects yield and grain quality. In this study, a wheat population was genotyped by using Illumina iSelect 90K single nucleotide polymorphism (SNP) assay and finally 22,905 high-quality SNPs were used to perform a genome-wide association study (GWAS) for plant architectural traits employing four multi-locus GWAS (ML-GWAS) and three single-locus GWAS (SL-GWAS) models. As a result, 174 and 97 significant SNPs controlling plant architectural traits were detected by ML-GWAS and SL-GWAS methods, respectively. Among these SNP makers, 43 SNPs were consistently detected, including seven across multiple environments and 36 across multiple methods. Interestingly, five SNPs (Kukri_c34553_89, RAC875_c8121_1490, wsnp_Ex_rep_c66315_64480362, Ku_c5191_340, and tplb0049a09_1302) consistently detected across multiple environments and methods, played a role in modulating both plant height and flag leaf length. Furthermore, candidate SNPs (BS00068592_51, Kukri_c4750_452 and BS00022127_51) constantly repeated in different years and methods associated with flag leaf width and number of tillers. We also detected several SNPs (Jagger_c6772_80, RAC875_c8121_1490, BS00089954_51, Excalibur_01167_1207, and Ku_c5191_340) having common associations with more than one trait across multiple environments. By further appraising these GWAS methods, the pLARmEB and FarmCPU models outperformed in SNP detection compared to the other ML-GWAS and SL-GWAS methods, respectively. Totally, 152 candidate genes were found to be likely involved in plant growth and development. These finding will be helpful for better understanding of the genetic mechanism of architectural traits in wheat.
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Affiliation(s)
- Ali Muhammad
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, 100 Daxue Rd., Nanning, Guangxi, China
- College of Plant Science and Technology & Biomass and Bioenergy Research Center, Huazhong Agricultural University, Wuhan, 430070, China
- Department of Agriculture, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Jianguo Li
- College of Plant Science and Technology & Biomass and Bioenergy Research Center, Huazhong Agricultural University, Wuhan, 430070, China
| | - Weichen Hu
- College of Plant Science and Technology & Biomass and Bioenergy Research Center, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jinsheng Yu
- College of Agriculture and Food Science, Zhejiang A&F University, Lin'an, 311300, China
| | - Shahid Ullah Khan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Muhammad Hafeez Ullah Khan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Guosheng Xie
- College of Plant Science and Technology & Biomass and Bioenergy Research Center, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jibin Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, 100 Daxue Rd., Nanning, Guangxi, China
| | - Lingqiang Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, 100 Daxue Rd., Nanning, Guangxi, China.
- College of Plant Science and Technology & Biomass and Bioenergy Research Center, Huazhong Agricultural University, Wuhan, 430070, China.
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Chen H, Li J, He Y. Overexpression of a novel E3 ubiquitin ligase gene from Coptis chinensis Franch enhances drought tolerance in transgenic tobacco. Z NATURFORSCH C 2020; 75:417-424. [PMID: 32589609 DOI: 10.1515/znc-2019-0211] [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: 11/27/2019] [Accepted: 05/31/2020] [Indexed: 11/15/2022]
Abstract
Drought stress has a significant effect on the growth, physiology and biochemistry of medicinal plants. SDIR1 (Salt- and Drought-Induced Ring Finger1), a C3H2C3-type RING-finger E3 ubiquitin ligase gene plays an important role in the stress response of various plants. However, the role of this gene is not clear in Coptis chinensis. In this study, the CcSDIR1 gene was cloned from C. chinensis using RACE and RT-PCR. Sequence analysis revealed that CcSDIR1 had an open reading frame of 840 bp that encodes 279 amino acids with a theoretical molecular weight about 31 kDa and pI value of 5.65 and shared conserved domains with other plants. On comparison with the wild-type plants, overexpression of CcSDIR1 in transgenic tobaccos increased drought tolerance and showed better growth performance. However, lower malondialdehyde contents and high antioxidant enzyme activities were observed in transgenic tobacco plants compared to wild-type plants. In addition, Evans blue staining showed high cell viability of transgenic lines under drought stress. These results suggest that CcSDIR1 regulates various responses to drought stress by increasing antioxidant enzyme activities and reducing oxidative damage. From the study results, the CcSDIR1 gene will be very useful for drought stress research in plants.
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Affiliation(s)
- Hanting Chen
- College of Medical Technology, State Key Laboratory of Characteristic Chinese Medicine Resources in Southwest China, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Junjun Li
- College of Medical Technology, State Key Laboratory of Characteristic Chinese Medicine Resources in Southwest China, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Yang He
- College of Medical Technology, State Key Laboratory of Characteristic Chinese Medicine Resources in Southwest China, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
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Jia W, Liu Y, Shi L, Chu X. Investigation of Differentially Expressed Proteins Induced by Alteration of Natural Se Uptake with Ultrahigh-Performance Liquid Chromatography Quadrupole Orbitrap Uncovers the Potential Nutritional Value in Se-Enriched Green Tea. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:6316-6332. [PMID: 32407080 DOI: 10.1021/acs.jafc.0c02130] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Se-enriched green tea, with an increasing consumption, is the shoot of tea plants grown naturally in a seleniferous region. A label-free proteomic strategy based on ultrahigh-performance liquid chromatography quadrupole Orbitrap was applied to characterize and distinguish the difference between the Se-enriched and normal green tea with a total of 283 proteins identified and 264 proteins quantified, in which 96 proteins were observed different. The expressions of 10 proteins were upregulated and 40 proteins were downregulated (p < 0.05) in Se-enriched samples. Gene ontology, Kyoto Encyclopedia of Genes and Genomes pathway, and protein-protein interaction (PPI) network analysis results indicated that these differentially expressed proteins significantly interacted and were involved in secondary metabolites and inflammatory response biological processes. Furthermore, the expression of methyl-jasmonate- and ethylene-related genes changed significantly in Se-enriched green tea, and catalase proteins were employed as the center of the pathway that changed significantly in the PPI network. These results associating with the current knowledge of selenium in soil-plant cycling revealed that organic selenium was synthesized in green tea, which provided novel information on Se assimilation in Camellia sinensis and improved the understanding of Se-enriched green tea as a possible ideal selenium supplement in daily life.
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Affiliation(s)
- Wei Jia
- School of Food and Biological Engineering, Shaanxi University of Science & Technology, Xi'an, Shaanxi 710021, People's Republic of China
| | - Yuyang Liu
- School of Food and Biological Engineering, Shaanxi University of Science & Technology, Xi'an, Shaanxi 710021, People's Republic of China
| | - Lin Shi
- School of Food and Biological Engineering, Shaanxi University of Science & Technology, Xi'an, Shaanxi 710021, People's Republic of China
| | - Xiaogang Chu
- School of Food and Biological Engineering, Shaanxi University of Science & Technology, Xi'an, Shaanxi 710021, People's Republic of China
- Chinese Academy of Inspection and Quarantine, Beijing 100123, People's Republic of China
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Tiwari JK, Buckseth T, Zinta R, Saraswati A, Singh RK, Rawat S, Dua VK, Chakrabarti SK. Transcriptome analysis of potato shoots, roots and stolons under nitrogen stress. Sci Rep 2020; 10:1152. [PMID: 31980689 PMCID: PMC6981199 DOI: 10.1038/s41598-020-58167-4] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 01/13/2020] [Indexed: 12/19/2022] Open
Abstract
Potato crop requires high dose of nitrogen (N) to produce high tuber yield. Excessive application of N causes environmental pollution and increases cost of production. Hence, knowledge about genes and regulatory elements is essential to strengthen research on N metabolism in this crop. In this study, we analysed transcriptomes (RNA-seq) in potato tissues (shoot, root and stolon) collected from plants grown in aeroponic culture under controlled conditions with varied N supplies i.e. low N (0.2 milli molar N) and high N (4 milli molar N). High quality data ranging between 3.25 to 4.93 Gb per sample were generated using Illumina NextSeq500 that resulted in 83.60-86.50% mapping of the reads to the reference potato genome. Differentially expressed genes (DEGs) were observed in the tissues based on statistically significance (p ≤ 0.05) and up-regulation with ≥ 2 log2 fold change (FC) and down-regulation with ≤ -2 log2 FC values. In shoots, of total 19730 DEGs, 761 up-regulated and 280 down-regulated significant DEGs were identified. Of total 20736 DEGs in roots, 572 (up-regulated) and 292 (down-regulated) were significant DEGs. In stolons, of total 21494 DEG, 688 and 230 DEGs were significantly up-regulated and down-regulated, respectively. Venn diagram analysis showed tissue specific and common genes. The DEGs were functionally assigned with the GO terms, in which molecular function domain was predominant in all the tissues. Further, DEGs were classified into 24 KEGG pathways, in which 5385, 5572 and 5594 DEGs were annotated in shoots, roots and stolons, respectively. The RT-qPCR analysis validated gene expression of RNA-seq data for selected genes. We identified a few potential DEGs responsive to N deficiency in potato such as glutaredoxin, Myb-like DNA-binding protein, WRKY transcription factor 16 and FLOWERING LOCUS T in shoots; high-affinity nitrate transporter, protein phosphatase-2c, glutaredoxin family protein, malate synthase, CLE7, 2-oxoglutarate-dependent dioxygenase and transcription factor in roots; and glucose-6-phosphate/phosphate translocator 2, BTB/POZ domain-containing protein, F-box family protein and aquaporin TIP1;3 in stolons, and many genes of unknown function. Our study highlights that these potential genes play very crucial roles in N stress tolerance, which could be useful in augmenting research on N metabolism in potato.
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Affiliation(s)
- Jagesh Kumar Tiwari
- Indian Council of Agricultural Research-Central Potato Research Institute, Shimla, Himachal Pradesh, 171001, India.
| | - Tanuja Buckseth
- Indian Council of Agricultural Research-Central Potato Research Institute, Shimla, Himachal Pradesh, 171001, India
| | - Rasna Zinta
- Indian Council of Agricultural Research-Central Potato Research Institute, Shimla, Himachal Pradesh, 171001, India
| | - Aastha Saraswati
- Indian Council of Agricultural Research-Central Potato Research Institute, Shimla, Himachal Pradesh, 171001, India
| | - Rajesh Kumar Singh
- Indian Council of Agricultural Research-Central Potato Research Institute, Shimla, Himachal Pradesh, 171001, India
| | - Shashi Rawat
- Indian Council of Agricultural Research-Central Potato Research Institute, Shimla, Himachal Pradesh, 171001, India
| | - Vijay Kumar Dua
- Indian Council of Agricultural Research-Central Potato Research Institute, Shimla, Himachal Pradesh, 171001, India
| | - Swarup Kumar Chakrabarti
- Indian Council of Agricultural Research-Central Potato Research Institute, Shimla, Himachal Pradesh, 171001, India
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Mangena P. Phytocystatins and their Potential Application in the Development of Drought Tolerance Plants in Soybeans (Glycine max L.). Protein Pept Lett 2020; 27:135-144. [PMID: 31612812 DOI: 10.2174/0929866526666191014125453] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 02/06/2019] [Accepted: 08/07/2019] [Indexed: 11/22/2022]
Abstract
Plant cystatins, also called phytocystatins constitute a family of specific cysteine protease inhibitors found in several monocots and dicots. In soybean, phytocystatins regulate several endogenous processes contributing immensely to this crop's tolerance to abiotic stress factors. Soybeans offer numerous nutritional, pharmaceutical and industrial benefits; however, their growth and yields is hampered by drought, which causes more than 10% yield losses recorded every harvest period worldwide. This review analyses the role of papain-like cysteine proteases and their inhibitors in soybean plant growth and development under drought stress. It also describes their localisation, regulation, target organs and tissues, and the overall impact of cystatins on generating drought tolerance soybean plants. These proteins have many functions that remain poorly characterized, particularly under abiotic stress. Although much information is available on the utilisation of proteases for industrial applications, very few reports have focused on the impact of proteases on plant stress responses. The exploitation of cystatins in plant engineering, as competitive proteases inhibitors is one of the means that will guarantee the continued utilisation of soybeans as an important oilseed crop.
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Affiliation(s)
- Phetole Mangena
- Department of Biodiversity, School of Molecular and Life Sciences, Faculty of Science and Agriculture, University of Limpopo, Private Bag X1106, Sovenga, 0727,South Africa
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Jamil HMA, Ahmed A, Irshad U, Al-Ghamdi AA, Elshikh MS, Alaraidh IA, Al-Dosary MA, Abbasi AM, Ahmad R. Identification and inoculation of fungal strains from Cedrus deodara rhizosphere involve in growth and alleviation of high nitrogen stress. Saudi J Biol Sci 2020; 27:524-534. [PMID: 31889878 PMCID: PMC6933180 DOI: 10.1016/j.sjbs.2019.11.016] [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: 09/19/2019] [Revised: 11/13/2019] [Accepted: 11/17/2019] [Indexed: 11/29/2022] Open
Abstract
Cedrus deodara is economically and ethnobotanically an important forest tree and is shown to be at decline in Northern areas of Pakistan in recent years mainly due to high concentration of Nitrogen in forests. Ectomycorrhizal (ECM) association forming fungi enables the forest trees to develop optimally by absorbing water from the rhizosphere through their absorptive hyphae and by making available the nutrients by mobilization of N and P from the organic substrates. This study was conducted to identify the ECM strains from C. deodara rhizosphere and to analyse the impact of high N load on the C. deodara seedlings to establish N critical load value for coniferous forests of Pakistan. Six new fungal strains were identified from the rhizosphere of C. deodara and were registered at GenBank (NCBI) as Emmia latemarginata strain ACE1, Aspergillus terreus strain ACE2, Purpureocillium lilacinum strain ACE3, Talaromyces pinophilus strain ACE4, A. fumigatus strain ACE5 and T. pinophilus strain ACE6 with accession numbers MH145426, MH145427, MH145428, MH145429, MH145430 and MH547115. Four out of six isolated strains were inoculated with seedlings of C. deodara singly and in consortium (CN) in combination with nitrogen load of 0 (C), 25 (T1), 50 (T2), 100 kg N ha−1 yr−1 (T3). Agronomic, physiological and gene expression studies for ExpansinA4 (EXPA4) and Cystatins (Cys) were made to analyse the impact of fungal strains in relation to high N stress. This study suggests a positive impact of T1 (25 kg N ha−1 yr−1) Nitrogen load and a negative impact of T3 (100 kg N ha−1 yr−1) on growth parameters and expression patterns of EXPA4 and Cys genes. Peroxidase (POX) activity decreased in the order ACE5 > ACE2 > C > ACE3 > ACE1 > CN. However, the results of Superoxide dismutase (SOD) showed decreasing trend in the order ACE5 > C > CN > ACE1 > ACE2 > ACE3. Strain ACE3 was shown to have a positive impact on the seedlings in terms of growth, physiology and expression of genes. Present study suggests that newly identified fungal strains showing positive impact on the growth and physiology of C. deodara could be used for the propagation of this economically important plant in Pakistan after pathogenicity test.
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Affiliation(s)
- Hafiz Muhammad Ansab Jamil
- Department of Biotechnology, COMSATS University Islamabad, Abbottabad Campus, Abbottabad 22060, Pakistan
| | - Awais Ahmed
- Department of Biotechnology, COMSATS University Islamabad, Abbottabad Campus, Abbottabad 22060, Pakistan
| | - Usman Irshad
- Department of Environmental Sciences, COMSATS University Islamabad, Abbottabad Campus, Abbottabad 22060, Pakistan
| | - Abdullah Ahmed Al-Ghamdi
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Mohamed S Elshikh
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Ibrahim A Alaraidh
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Monerah A Al-Dosary
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Arshad Mehmood Abbasi
- Department of Environmental Sciences, COMSATS University Islamabad, Abbottabad Campus, Abbottabad 22060, Pakistan
| | - Rafiq Ahmad
- Department of Biotechnology, COMSATS University Islamabad, Abbottabad Campus, Abbottabad 22060, Pakistan
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Single-nucleotide polymorphism markers within MVA and MEP pathways among Hevea brasiliensis clones through transcriptomic analysis. 3 Biotech 2019; 9:388. [PMID: 31656726 DOI: 10.1007/s13205-019-1921-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 09/24/2019] [Indexed: 10/25/2022] Open
Abstract
In this study, RNA sequencing of several Hevea brasiliensis clones grown in Malaysia with different annual rubber production yields and disease resistance was performed on the Illumina platform. A total of 29,862,548 reads were generated, resulting in 101,269 assembled transcripts that were used as the reference transcripts. A similarity search against the non-redundant (nr) protein databases presented 83,771 (83%) positive BLASTx hits. The transcriptome was annotated using gene ontology (GO), the Kyoto Encyclopedia of Genes and Genomes (KEGG) and the Pfam database. A search for putative molecular markers was performed to identify single-nucleotide polymorphisms (SNPs). Overall, 3,210,629 SNPs were detected and a total of 1314 SNPs associated with the genes involved in MVA and MEP pathways were identified. A total of 176 SNP primer pairs were designed from sequences that were related to the MVA and MEP pathways. The transcriptome of RRIM 3001 and RRIM 712 were subjected to pairwise comparison and the results revealed that there were 1262 significantly differentially expressed genes unique to RRIM 3001, 1499 significantly differentially expressed genes unique to RRIM 712 and several genes related to the MVA and MEP pathways such as AACT, HMGS, PMK, MVD, DXS and HDS were included. The results will facilitate the characterization of H. brasiliensis transcriptomes and the development of a new set of molecular markers in the form of SNPs from transcriptome assembly for the genotype identification of various rubber varieties with superior traits in Malaysia.
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Ji S, Liu Z, Liu B, Wang Y. Comparative analysis of biocontrol agent Trichoderma asperellum ACCC30536 transcriptome during its interaction with Populus davidiana × P. alba var. pyramidalis. Microbiol Res 2019; 227:126294. [PMID: 31421718 DOI: 10.1016/j.micres.2019.126294] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 06/13/2019] [Accepted: 06/18/2019] [Indexed: 12/11/2022]
Abstract
After exposure to with Populus davidiana × P. alba var. pyramidalis, the expression of genes in Trichoderma asperellum were compared in four transcriptomes. The top 20 high expression genes included six heat shock proteins and three hydrophobins, indicating that Trichoderma can rapidly adapt to environment stresses and elicit a plant defense response. The genes, involved in the interaction between Trichoderma and plant, showed an increasing expression level, for example sugar transporters, EPL1s, endoxylanases, pectin lyases, and nitrilases. Interestingly, sugar transporters also showed high expression when T. asperellum was cultured on medium lacking a carbon substrate, which would contribute to T. asperellum's survival and domination in ecological niche competition. And the genes related to mycoparasitism were expressed abundantly following T. asperellum's interaction with PdPap, indicating the PdPap induction could enhance the mycoparasitic ability of T. asperellum. Twelve chitinases and five glucanases showed higher expression in transcriptome Cs, indicating that T. asperellum secretes both types of enzyme before interacting with pathogens, allowing T. asperellum to implement mycoparasitism and obtain more energy. Many novel transcripts were obtained in each transcriptome, which may play important roles in the biocontrol process of T. asperellum. Interestingly, T. asperellum undergo constitutive alternative splicing in the biocontrol process: Seven biocontrol genes were alternative spliced via intron retention. qRT-PCR analysis proved that intron retention is negatively associated with the expression of chitinase, oligopeptide transporters, and beta-lactamase. However, the percentage of MAPK intron retention was quite low, suggesting that intron retention has little effect on the function of MAPK.
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Affiliation(s)
- Shida Ji
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China
| | - Zhihua Liu
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), 26 Hexing Road, 150040, Harbin, China
| | - Bin Liu
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), 26 Hexing Road, 150040, Harbin, China
| | - Yucheng Wang
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China; State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), 26 Hexing Road, 150040, Harbin, China.
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11
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Prasad KVSK, Xing D, Reddy ASN. Vascular Plant One-Zinc-Finger (VOZ) Transcription Factors Are Positive Regulators of Salt Tolerance in Arabidopsis. Int J Mol Sci 2018; 19:ijms19123731. [PMID: 30477148 PMCID: PMC6321167 DOI: 10.3390/ijms19123731] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Revised: 11/19/2018] [Accepted: 11/20/2018] [Indexed: 11/16/2022] Open
Abstract
Soil salinity, a significant problem in agriculture, severely limits the productivity of crop plants. Plants respond to and cope with salt stress by reprogramming gene expression via multiple signaling pathways that converge on transcription factors. To develop strategies to generate salt-tolerant crops, it is necessary to identify transcription factors that modulate salt stress responses in plants. In this study, we investigated the role of VOZ (VASCULAR PLANT ONE-ZINC FINGER PROTEIN) transcription factors (VOZs) in salt stress response. Transcriptome analysis in WT (wild-type), voz1-1, voz2-1 double mutant and a VOZ2 complemented line revealed that many stress-responsive genes are regulated by VOZs. Enrichment analysis for gene ontology terms in misregulated genes in voz double mutant confirmed previously identified roles of VOZs and suggested a new role for them in salt stress. To confirm VOZs role in salt stress, we analyzed seed germination and seedling growth of WT, voz1, voz2-1, voz2-2 single mutants, voz1-1voz2-1 double mutant and a complemented line under different concentrations of NaCl. Only the double mutant exhibited hypersensitivity to salt stress as compared to WT, single mutants, and a complemented line. Expression analysis showed that hypersensitivity of the double mutant was accompanied by reduced expression of salt-inducible genes. These results suggest that VOZ transcription factors act as positive regulators of several salt-responsive genes and that the two VOZs are functionally redundant in salt stress.
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Affiliation(s)
- Kasavajhala V S K Prasad
- Department of Biology and Cell and Molecular Biology Program, Colorado State University, Fort Collins, CO 80523, USA.
| | - Denghui Xing
- Department of Biology and Cell and Molecular Biology Program, Colorado State University, Fort Collins, CO 80523, USA.
- Genomics Core Lab, Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA.
| | - Anireddy S N Reddy
- Department of Biology and Cell and Molecular Biology Program, Colorado State University, Fort Collins, CO 80523, USA.
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Albaladejo I, Egea I, Morales B, Flores FB, Capel C, Lozano R, Bolarin MC. Identification of key genes involved in the phenotypic alterations of res (restored cell structure by salinity) tomato mutant and its recovery induced by salt stress through transcriptomic analysis. BMC PLANT BIOLOGY 2018; 18:213. [PMID: 30285698 PMCID: PMC6167845 DOI: 10.1186/s12870-018-1436-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 09/23/2018] [Indexed: 05/05/2023]
Abstract
BACKGROUND The res (restored cell structure by salinity) mutant, recently identified as the first tomato mutant accumulating jasmonate in roots under non-stressful conditions, exhibits a remarkable growth inhibition and morphological alterations in roots and leaves, which are suppressed when the mutant plants are exposed to salinity. In order to understand the molecular basis of the phenotype recovery induced by salt stress in the res mutant, we carried out a comparative transcriptomic analysis in roots and leaves of wild-type and res plants in absence of stress (control) and when the phenotypic recovery of res mutant began to be observed upon salt stress (5 days of 200 mM NaCl). RESULTS The number of differentially expressed genes was three times greater in roots than in leaves of res vs WT plants grown in control, and included the down-regulation of growth-promoting genes and the up-regulation of genes involved in Ca2+ signalling, transcription factors and others related to stress responses. However, these expression differences were attenuated under salt stress, coinciding with the phenotypic normalisation of the mutant. Contrarily to the attenuated response observed in roots, an enhanced response was found in leaves under salt stress. This included drastic expression changes in several circadian clock genes, such as GIGANTEA1, which was down-regulated in res vs WT plants. Moreover, the higher photosynthetic efficiency of res leaves under salt stress was accompanied by specific salt-upregulation of the genes RUBISCO ACTIVASE1 and ALTERNATIVE OXIDASE1A. Very few genes were found to be differentially expressed in both tissues (root and leaf) and conditions (control and salt), but this group included SlWRKY39 and SlMYB14 transcription factors, as well as genes related to protein homeostasis, especially protease inhibitors such as METALLOCARBOXYPEPTIDASE INHIBITOR, which also seem to play a role in the phenotype recovery and salt tolerance of res mutant. CONCLUSIONS In summary, in this study we have identified genes which seem to have a prominent role in salt tolerance. Moreover, we think this work could contribute to future breeding of tomato crops with increased stress tolerance.
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Affiliation(s)
- Irene Albaladejo
- Departamento de Biología del Estrés y Patología Vegetal, Centro de Edafología y Biología Aplicada del Segura, CSIC, Campus Universitario Espinardo, 30100 Murcia, Spain
| | - Isabel Egea
- Departamento de Biología del Estrés y Patología Vegetal, Centro de Edafología y Biología Aplicada del Segura, CSIC, Campus Universitario Espinardo, 30100 Murcia, Spain
| | - Belen Morales
- Departamento de Biología del Estrés y Patología Vegetal, Centro de Edafología y Biología Aplicada del Segura, CSIC, Campus Universitario Espinardo, 30100 Murcia, Spain
| | - Francisco B. Flores
- Departamento de Biología del Estrés y Patología Vegetal, Centro de Edafología y Biología Aplicada del Segura, CSIC, Campus Universitario Espinardo, 30100 Murcia, Spain
| | - Carmen Capel
- Centro de Investigación en Biotecnología Agroalimentaria (BITAL), Universidad de Almería, 04120 Almería, Spain
| | - Rafael Lozano
- Centro de Investigación en Biotecnología Agroalimentaria (BITAL), Universidad de Almería, 04120 Almería, Spain
| | - Maria C. Bolarin
- Departamento de Biología del Estrés y Patología Vegetal, Centro de Edafología y Biología Aplicada del Segura, CSIC, Campus Universitario Espinardo, 30100 Murcia, Spain
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GA 3 application in grapes (Vitis vinifera L.) modulates different sets of genes at cluster emergence, full bloom, and berry stage as revealed by RNA sequence-based transcriptome analysis. Funct Integr Genomics 2018; 18:439-455. [PMID: 29626310 DOI: 10.1007/s10142-018-0605-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 12/06/2017] [Accepted: 03/20/2018] [Indexed: 01/10/2023]
Abstract
In grapes (Vitis vinifera L.), exogenous gibberellic acid (GA3) is applied at different stages of bunch development to achieve desirable bunch shape and berry size in seedless grapes used for table purpose. RNA sequence-based transcriptome analysis was used to understand the mechanism of GA3 action at cluster emergence, full bloom, and berry stage in table grape variety Thompson Seedless. At cluster emergence, rachis samples were collected at 6 and 24 h after application of GA3, whereas flower clusters and berry samples were collected at 6, 24, and 48 h after application at full bloom and 3-4 mm berry stages. Seven hundred thirty-three genes were differentially expressed in GA3-treated samples. At rachis and flower cluster stage respectively, 126 and 264 genes were found to be significantly differentially expressed within 6 h of GA3 application. The number of DEG reduced considerably at 24 h. However, at berry stage, major changes occurred even at 24 h and a number of DEGs at 6 and 24 h were 174 and 191, respectively. As compared to upregulated genes, larger numbers of genes were downregulated. Stage-specific response to the GA3 application was observed as evident from the unique set of DEGs at each stage and only a few common genes among three stages. Among the DEGs, 67 were transcription factors. Functional categorization and enrichment analysis revealed that several transcripts involved in sucrose and hexose metabolism, hormone and secondary metabolism, and abiotic and biotic stimuli were enriched in response to application of GA3. A high correlation was recorded for real-time PCR and transcriptome data for selected DEGs, thus indicating the robustness of transcriptome data obtained in this study for understanding the GA3 response at different stages of berry development in grape. Chromosomal localization of DEGs and identification of polymorphic microsatellite markers in selected genes have potential for their use in breeding for varieties with improved bunch architecture.
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Khan S, Khan NA, Bano B. In-sights into the effect of heavy metal stress on the endogenous mustard cystatin. Int J Biol Macromol 2017; 105:1138-1147. [PMID: 28754626 DOI: 10.1016/j.ijbiomac.2017.07.146] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2017] [Revised: 06/04/2017] [Accepted: 07/24/2017] [Indexed: 01/07/2023]
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Yang Q, Shohag MJI, Feng Y, He Z, Yang X. Transcriptome Comparison Reveals the Adaptive Evolution of Two Contrasting Ecotypes of Zn/Cd Hyperaccumulator Sedum alfredii Hance. FRONTIERS IN PLANT SCIENCE 2017; 8:425. [PMID: 28439276 PMCID: PMC5383727 DOI: 10.3389/fpls.2017.00425] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 03/13/2017] [Indexed: 05/29/2023]
Abstract
Hyperaccumulating ecotype (HE) and non-hyperaccumulating ecotype (NHE) of Sedum alfredii Hance belong to the same species but exhibit contrasting characteristics regarding hyperaccumulation and hypertolerance to cadmium and zinc. The Illumina Hiseq 2500 platform was employed to sequence HE and NHE to study the genetic evolution of this contrasting trait. Greater than 90 million clean reads were obtained and 118,479/228,051 unigenes of HE/NHE were annotated based on seven existing databases. We identified 149,668/319,830 single nucleotide polymorphisms (SNPs) and 12,691/14,428 simple sequence repeats (SSRs) of HE/NHE. We used a branch-site model to identify 18 divergent orthologous genes and 57 conserved orthologous genes of S. alfredii Hance. The divergent orthologous genes were mainly involved in the transcription and translation processes, protein metabolism process, calcium (Ca2+) pathway, stress response process and signal transduction process. To the best of our knowledge, this is the first study to use RNA-seq to compare the genetic evolution of hyperaccumulating and non-hyperaccumulating plants from the same species. In addition, this study made the sole concrete for further studies on molecular markers and divergent orthologous genes to depict the evolution process and formation of the hyperaccumulation and hypertolerance traits in S. alfredii Hance.
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Affiliation(s)
- Qianying Yang
- Ministry of Education Key Laboratory of Environmental Remediation and Ecosystem Health, College of Environmental and Resources Science, Zhejiang UniversityHangzhou, China
| | - M. J. I. Shohag
- Ministry of Education Key Laboratory of Environmental Remediation and Ecosystem Health, College of Environmental and Resources Science, Zhejiang UniversityHangzhou, China
- Department of Agriculture, Bangabandhu Sheikh Mujibur Rahman Science and Technology UniversityGopalganj, Bangladesh
| | - Ying Feng
- Ministry of Education Key Laboratory of Environmental Remediation and Ecosystem Health, College of Environmental and Resources Science, Zhejiang UniversityHangzhou, China
| | - Zhenli He
- Institute of Food and Agricultural Sciences, Indian River Research and Education Center, University of FloridaFort Pierce, FL, USA
| | - Xiaoe Yang
- Ministry of Education Key Laboratory of Environmental Remediation and Ecosystem Health, College of Environmental and Resources Science, Zhejiang UniversityHangzhou, China
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Protein Dynamics in the Plant Extracellular Space. Proteomes 2016; 4:proteomes4030022. [PMID: 28248232 PMCID: PMC5217353 DOI: 10.3390/proteomes4030022] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2016] [Revised: 07/07/2016] [Accepted: 07/07/2016] [Indexed: 12/15/2022] Open
Abstract
The extracellular space (ECS or apoplast) is the plant cell compartment external to the plasma membrane, which includes the cell walls, the intercellular space and the apoplastic fluid (APF). The present review is focused on APF proteomics papers and intends to draw information on the metabolic processes occurring in the ECS under abiotic and biotic stresses, as well as under non-challenged conditions. The large majority of the proteins detected are involved in "cell wall organization and biogenesis", "response to stimulus" and "protein metabolism". It becomes apparent that some proteins are always detected, irrespective of the experimental conditions, although with different relative contribution. This fact suggests that non-challenged plants have intrinsic constitutive metabolic processes of stress/defense in the ECS. In addition to the multiple functions ascribed to the ECS proteins, should be considered the interactions established between themselves and with the plasma membrane and its components. These interactions are crucial in connecting exterior and interior of the cell, and even simple protein actions in the ECS can have profound effects on plant performance. The proteins of the ECS are permanently contributing to the high dynamic nature of this plant compartment, which seems fundamental to plant development and adaptation to the environmental conditions.
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