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Tombuloglu G, Tombuloglu H, Slimani Y, Almessiere MA, Baykal A, Bostancioglu SM, Kirat G, Ercan I. Effects of foliar iron oxide nanoparticles (Fe 3O 4) application on photosynthetic parameters, distribution of mineral elements, magnetic behaviour, and photosynthetic genes in tomato (Solanum lycopersicum var. cerasiforme) plants. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 210:108616. [PMID: 38615444 DOI: 10.1016/j.plaphy.2024.108616] [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: 02/11/2024] [Revised: 04/04/2024] [Accepted: 04/06/2024] [Indexed: 04/16/2024]
Abstract
This study aims to examine the effect of foliar magnetic iron oxide (Fe3O4) nanoparticles (IONP) application on the physiology, photosynthetic parameters, magnetic character, and mineral element distribution of cherry tomatoes (Solanum lycopersicum var. cerasiforme). The IONP suspension (500 mg L-1) was sprayed once (S1), twice (S2), thrice (S3), and four times (S4) a week on seedlings. Upon 21 days of the treatments, photosynthetic parameters (chlorophyll, carotenoids, photosynthetic yield, electron transport rate) were elucidated. Inductively-coupled plasma-optical emission spectrometer (ICP-OES) and vibrating sample magnetometer (VSM) were used to determine the mineral elements and abundance of magnetic power in the seedlings. In addition, the RT-qPCR method was performed to quantify the expressions of photosystem-related (PsaC, PsbP6, and PsbQ) and ferritin-coding (Fer-1 and Fer-2) genes. Results revealed that the physiological and photosynthetic indices were improved upon S1 treatment. The optimal dosage of IONP spraying enhances chlorophyll, carotenoid, electron transport rate (ETR), and effective photochemical quantum yield of photosystem II (Y(II)) but substantially diminishes non-photochemical quenching (NPQ). However, frequent IONP applications (S2, S3, and S4) caused growth retardation and suppressed the photosynthetic parameters, suggesting a toxic effect of IONP in recurrent treatments. Fer-1 and Fer-2 expressions were strikingly increased by IONP applications, suggesting an attempt to neutralize the excess amount of Fe ions by ferritin. Nevertheless, frequent IONP treatment fluctuated the mineral distribution and caused growth inhibition. Although low-repeat foliar applications of IONP (S1 in this study) may help improve plant growth, consecutive applications (S2, S3, and S4) should be avoided.
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Affiliation(s)
- Guzin Tombuloglu
- Department of Biophysics, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, P.O. Box 1982, 34221, Dammam, Saudi Arabia
| | - Huseyin Tombuloglu
- Department of Genetics Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, P.O. Box 1982, 34221, Dammam, Saudi Arabia.
| | - Yassine Slimani
- Department of Biophysics, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, P.O. Box 1982, 34221, Dammam, Saudi Arabia
| | - Munirah A Almessiere
- Department of Biophysics, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, P.O. Box 1982, 34221, Dammam, Saudi Arabia
| | - Abdulhadi Baykal
- Food Engineering Department, Faculty of Engineering, Istanbul Aydin University, Istanbul, 34295, Turkey
| | - Safiye Merve Bostancioglu
- Department of Biology, Faculty of Arts and Sciences, Marmara University, Goztepe Campus, Goztepe, 34722, Istanbul, Turkey
| | - Gokhan Kirat
- Scientific and Technological Research Center, Inonu University, Malatya, 44280, Turkey
| | - Ismail Ercan
- Department of Electrical and Electronics Engineering, Faculty of Engineering, Duzce University, 81010, Duzce, Turkey
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Tombuloglu G, Aldahnem A, Tombuloglu H, Slimani Y, Akhtar S, Hakeem KR, Almessiere MA, Baykal A, Ercan I, Manikandan A. Uptake and bioaccumulation of iron oxide nanoparticles (Fe 3O 4) in barley (Hordeum vulgare L.): effect of particle-size. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:22171-22186. [PMID: 38403831 DOI: 10.1007/s11356-024-32378-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 02/04/2024] [Indexed: 02/27/2024]
Abstract
Root-to-shoot translocation of nanoparticles (NPs) is a matter of interest due to their possible unprecedented effects on biota. Properties of NPs, such as structure, surface charge or coating, and size, determine their uptake by cells. This study investigates the size effect of iron oxide (Fe3O4) NPs on plant uptake, translocation, and physiology. For this purpose, Fe3O4 NPs having about 10 and 100 nm in average sizes (namely NP10 and NP100) were hydroponically subjected to barley (Hordeum vulgare L.) in different doses (50, 100, and 200 mg/L) at germination (5 days) and seedling (3 weeks) stages. Results revealed that particle size does not significantly influence the seedlings' growth but improves germination. The iron content in root and leaf tissues gradually increased with increasing NP10 and NP100 concentrations, revealing their root-to-shoot translocation. This result was confirmed by vibrating sample magnetometry analysis, where the magnetic signals increased with increasing NP doses. The translocation of NPs enhanced chlorophyll and carotenoid contents, suggesting their contribution to plant pigmentation. On the other hand, catalase activity and H2O2 production were higher in NP10-treated roots compared to NP100-treated ones. Besides, confocal microscopy revealed that NP10 leads to cell membrane damages. These findings showed that Fe3O4 NPs were efficiently taken up by the roots and transported to the leaves regardless of the size factor. However, small-sized Fe3O4 NPs may be more reactive due to their size properties and may cause cell stress and membrane damage. This study may help us better understand the size effect of NPs in nanoparticle-plant interaction.
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Affiliation(s)
- Guzin Tombuloglu
- Department of Biophysics, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam, 31441, Saudi Arabia
| | - Anwar Aldahnem
- Department of Genetics Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam, 31441, Saudi Arabia
| | - Huseyin Tombuloglu
- Department of Genetics Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam, 31441, Saudi Arabia.
| | - Yassine Slimani
- Department of Biophysics, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam, 31441, Saudi Arabia
| | - Sultan Akhtar
- Department of Biophysics, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam, 31441, Saudi Arabia
| | - Khalid Rehman Hakeem
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
- Princess Dr. Najla Bint Saud Al-Saud Center for Excellence Research in Biotechnology, King Abdulaziz University, P.O. Box 80200, Jeddah, 21589, Saudi Arabia
| | - Munirah A Almessiere
- Department of Biophysics, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam, 31441, Saudi Arabia
- Department of Physics, College of Science, Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam, 31441, Saudi Arabia
| | - Abdulhadi Baykal
- Food Engineering Department, Faculty of Engineering, Istanbul Aydin University, Istanbul, 34295, Türkiye
| | - Ismail Ercan
- Department of Electrical and Electronics Engineering, Faculty of Engineering, Duzce University, 81010, Duzce, Türkiye
| | - Ayyar Manikandan
- Department of Chemistry, Bharath Institute of Higher Education and Research (BIHER), Bharath University, Chennai, Tamil Nadu, 600073, India
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Tombuloglu H, Ercan I, Alqahtani N, Alotaibi B, Bamhrez M, Alshumrani R, Turumtay H, Ergin I, Demirci T, Ozcelik S, Kayed TS, Ercan F. Impact of magnetic field on the translocation of iron oxide nanoparticles (Fe 3O 4) in barley seedlings ( Hordeum vulgare L.). 3 Biotech 2023; 13:296. [PMID: 37564274 PMCID: PMC10409972 DOI: 10.1007/s13205-023-03727-4] [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: 09/29/2022] [Accepted: 08/01/2023] [Indexed: 08/12/2023] Open
Abstract
The effect and contribution of an external magnetic field (MF) on the uptake and translocation of nanoparticles (NPs) in plants have been investigated in this study. Barley was treated with iron oxide NPs (Fe3O4, 500 mg/L, 50-100 nm) and grown under various MF strengths (20, 42, 125, and 250 mT). The root-to-shoot translocation of NPs was assessed using a vibrating sample magnetometer (VSM) and inductively coupled plasma optical emission spectrometry (ICP-OES). Additionally, plant phenological parameters, such as germination, protein and chlorophyll content, and photosynthetic and nutritional status, were examined. The results demonstrated that the external MF significantly enhances the uptake of NPs through the roots. The uptake was higher at lower MF strengths (20 and 42 mT) than at higher MF strengths (125 and 250 mT). The root and shoot iron (Fe) contents were approximately 2.5-3-fold higher in the 250 mT application compared to the control. Furthermore, the MF treatments significantly increased micro-elements such as Mn, Zn, Cu, Mo, and B (P < 0.005). This effect could be attributed to the disruption of cell membranes at the root tip cells caused by both the MF and NPs. Moreover, the MF treatments improved germination rates by 28%, total protein content, and photosynthetic parameters. These findings show that magnetic field application helps the effective transport of magnetic NPs, which could be essential for NPs-mediated drug delivery, plant nutrition, and genetic transformation applications. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03727-4.
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Affiliation(s)
- Huseyin Tombuloglu
- Department of Genetics Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, P.O. Box 1982, 34221 Dammam, Saudi Arabia
| | - Ismail Ercan
- Department of Electrical and Electronics Engineering, Faculty of Engineering, Duzce University, 81010 Düzce, Turkey
| | - Noha Alqahtani
- Department of Genetics Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, P.O. Box 1982, 34221 Dammam, Saudi Arabia
| | - Bayan Alotaibi
- Department of Genetics Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, P.O. Box 1982, 34221 Dammam, Saudi Arabia
| | - Muruj Bamhrez
- Department of Genetics Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, P.O. Box 1982, 34221 Dammam, Saudi Arabia
| | - Raghdah Alshumrani
- Department of Genetics Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, P.O. Box 1982, 34221 Dammam, Saudi Arabia
| | - Halbay Turumtay
- Joint BioEnergy Institute, Emeryville, CA 94608 USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
- Department of Energy System Engineering, Karadeniz Technical University, 61830 Trabzon, Turkey
| | - Ibrahim Ergin
- Department of Physics, Faculty of Art and Sciences, Cukurova University, 01330 Balcali-Adana, Turkey
| | - Tuna Demirci
- Scientific and Technological Research Laboratory, Düzce University, 81560 Düzce, Turkey
| | - Sezen Ozcelik
- Department of Food Engineering, Faculty of Engineering, Hakkari University, 30000 Hakkari, Turkey
| | - Tarek Said Kayed
- Department of Basic Engineering Sciences, College of Engineering, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Filiz Ercan
- Basic and Applied Scientific Research Center, Imam Abdulrahman Bin Faisal University, PO Box 1982, 31441 Dammam, Saudi Arabia
- Department of Physics, College of Science, Imam Abdulrahman Bin Faisal University, PO Box 1982, 31441 Dammam, Saudi Arabia
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Pech R, Volná A, Hunt L, Bartas M, Červeň J, Pečinka P, Špunda V, Nezval J. Regulation of Phenolic Compound Production by Light Varying in Spectral Quality and Total Irradiance. Int J Mol Sci 2022; 23:ijms23126533. [PMID: 35742975 PMCID: PMC9223736 DOI: 10.3390/ijms23126533] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 06/01/2022] [Accepted: 06/02/2022] [Indexed: 11/16/2022] Open
Abstract
Photosynthetically active radiation (PAR) is an important environmental cue inducing the production of many secondary metabolites involved in plant oxidative stress avoidance and tolerance. To examine the complex role of PAR irradiance and specific spectral components on the accumulation of phenolic compounds (PheCs), we acclimated spring barley (Hordeum vulgare) to different spectral qualities (white, blue, green, red) at three irradiances (100, 200, 400 µmol m−2 s−1). We confirmed that blue light irradiance is essential for the accumulation of PheCs in secondary barley leaves (in UV-lacking conditions), which underpins the importance of photoreceptor signals (especially cryptochrome). Increasing blue light irradiance most effectively induced the accumulation of B-dihydroxylated flavonoids, probably due to the significantly enhanced expression of the F3′H gene. These changes in PheC metabolism led to a steeper increase in antioxidant activity than epidermal UV-A shielding in leaf extracts containing PheCs. In addition, we examined the possible role of miRNAs in the complex regulation of gene expression related to PheC biosynthesis.
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Affiliation(s)
- Radomír Pech
- Department of Physics, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic; (R.P.); (A.V.)
| | - Adriana Volná
- Department of Physics, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic; (R.P.); (A.V.)
| | - Lena Hunt
- Department of Experimental Plant Biology, Faculty of Science, Charles University, 128 00 Praha, Czech Republic;
| | - Martin Bartas
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic; (M.B.); (J.Č.); (P.P.)
| | - Jiří Červeň
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic; (M.B.); (J.Č.); (P.P.)
| | - Petr Pečinka
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic; (M.B.); (J.Č.); (P.P.)
| | - Vladimír Špunda
- Department of Physics, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic; (R.P.); (A.V.)
- Global Change Research Institute, Czech Academy of Sciences, 603 00 Brno, Czech Republic
- Correspondence: (V.Š.); (J.N.)
| | - Jakub Nezval
- Department of Physics, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic; (R.P.); (A.V.)
- Correspondence: (V.Š.); (J.N.)
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Kolozsváriné Nagy J, Schwarczinger I, Király L, Bacsó R, Ádám AL, Künstler A. Near-Isogenic Barley Lines Show Enhanced Susceptibility to Powdery Mildew Infection Following High-Temperature Stress. PLANTS 2022; 11:plants11070903. [PMID: 35406883 PMCID: PMC9003484 DOI: 10.3390/plants11070903] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 03/23/2022] [Accepted: 03/25/2022] [Indexed: 11/16/2022]
Abstract
Barley cultivation is adversely affected by high-temperature stress, which may modulate plant defense responses to pathogens such as barley powdery mildew (Blumeria graminis f. sp. hordei, Bgh). Earlier research focused mainly on the influence of short-term heat stress (heat shock) of barley on Bgh infection. In this study, our aim was to investigate the effects of both short- and long-term heat stress (35 °C from 30 s to 5 days) on Bgh infection in the barley cultivar Ingrid and its near-isogenic lines containing different powdery mildew resistance genes (Mla12, Mlg, and mlo5) by analyzing symptom severity and Bgh biomass with RT-qPCR. The expression of selected barley defense genes (BAX inhibitor-1, Pathogenesis- related protein-1b, Respiratory burst oxidase homologue F2, and Heat shock protein 90-1) was also monitored in plants previously exposed to heat stress followed by inoculation with Bgh. We demonstrated that pre-exposure to short- and long-term heat stress negatively affects the resistance of all resistant lines manifested by the appearance of powdery mildew symptoms and increased Bgh biomass. Furthermore, prolonged heat stress (48 and 120 h) enhanced both Bgh symptoms and biomass in susceptible wild-type Ingrid. Heat stress suppressed and delayed early defense gene activation in resistant lines, which is a possible reason why resistant barley became partially susceptible to Bgh.
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Ercan I, Tombuloglu H, Alqahtani N, Alotaibi B, Bamhrez M, Alshumrani R, Ozcelik S, Kayed TS. Magnetic field effects on the magnetic properties, germination, chlorophyll fluorescence, and nutrient content of barley (Hordeum vulgare L.). PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 170:36-48. [PMID: 34844116 DOI: 10.1016/j.plaphy.2021.11.033] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 11/01/2021] [Accepted: 11/17/2021] [Indexed: 06/13/2023]
Abstract
The magnetic field (MF) interacts with biological systems and has the potential to increase germination, plant growth and productivity. Although it is known as a low cost and promising approach, the mechanism that increases growth is not fully understood yet. In this study, the effect of different MF strengths (20, 42, 125, and 250 mT) was investigated on barley (Hordeum vulgare L.). In addition to phenological parameters, possible cell damage, electron transport rate, chlorophyll fluorescence, magnetic character and elemental status of tissues were determined. Results showed that lower strengths (≤125 mT) of MF treatment improve germination. Confocal microscopy analyzes revealed MF-induced cell membrane damage in roots that could alter the elemental content of tissues. Elemental analyzes found that the content of macroelements (Ca, Mg, P, and K) are gradually reduced with increasing MF forces; in opposite the microelement contents (Fe, B, Cu, Mn, Zn, and Mo) are increased in roots. Diamagnetism is the dominant magnetic character in all root and leaf samples. However, the roots became surprisingly superparamagnetic in 250 mT application. It seems that MF treatment at higher strength (250 mT in this study) could influence the orientation of magnetic moments. These findings suggest that MF application: i) can alter the magnetic character of plants, ii) enhances the germination, photosynthetic machinery, and growth, and iii) affects the nutrient uptake and abundance in tissues, depending on the MF strength. This comprehensive study can help in understanding the interaction of magnetic field with plants.
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Affiliation(s)
- Ismail Ercan
- Department of Biophysics, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam, 34221, Saudi Arabia.
| | - Huseyin Tombuloglu
- Department of Genetics Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam, 34221, Saudi Arabia
| | - Noha Alqahtani
- Department of Genetics Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam, 34221, Saudi Arabia
| | - Bayan Alotaibi
- Department of Genetics Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam, 34221, Saudi Arabia
| | - Muruj Bamhrez
- Department of Genetics Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam, 34221, Saudi Arabia
| | - Raghdah Alshumrani
- Department of Genetics Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam, 34221, Saudi Arabia
| | - Sezen Ozcelik
- Department of Food Engineering, Faculty of Engineering, Hakkari University, 30000, Hakkari, Turkey
| | - Tarek Said Kayed
- Department of Basic Engineering Sciences, College of Engineering, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
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Saada S, Solomon CU, Drea S. Programmed Cell Death in Developing Brachypodium distachyon Grain. Int J Mol Sci 2021; 22:ijms22169086. [PMID: 34445790 PMCID: PMC8396479 DOI: 10.3390/ijms22169086] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 08/14/2021] [Accepted: 08/19/2021] [Indexed: 01/01/2023] Open
Abstract
The normal developmental sequence in a grass grain entails the death of several maternal and filial tissues in a genetically regulated process termed programmed cell death (PCD). The progression and molecular aspects of PCD in developing grains have been reported for domesticated species such as barley, rice, maize and wheat. Here, we report a detailed investigation of PCD in the developing grain of the wild model species Brachypodium distachyon. We detected PCD in developing Brachypodium grains using molecular and histological approaches. We also identified in Brachypodium the orthologs of protease genes known to contribute to grain PCD and surveyed their expression. We found that, similar to cereals, PCD in the Brachypodium nucellus occurs in a centrifugal pattern following anthesis. However, compared to cereals, the rate of post-mortem clearance in the Brachypodium nucellus is slower. However, compared to wheat and barley, mesocarp PCD in Brachypodium proceeds more rapidly in lateral cells. Remarkably, Brachypodium mesocarp PCD is not coordinated with endosperm development. Phylogenetic analysis suggests that barley and wheat possess more vacuolar processing enzymes that drive nucellar PCD compared to Brachypodium and rice. Our expression analysis highlighted putative grain-specific PCD proteases in Brachypodium. Combined with existing knowledge on grain PCD, our study suggests that the rate of nucellar PCD moderates grain size and that the pattern of mesocarp PCD influences grain shape.
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Affiliation(s)
- Safia Saada
- Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester LE1 7RH, UK; (S.S.); (S.D.)
| | - Charles Ugochukwu Solomon
- Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester LE1 7RH, UK; (S.S.); (S.D.)
- Department of Plant Science and Biotechnology, Abia State University, Uturu PMB 2000, Nigeria
- Correspondence:
| | - Sinéad Drea
- Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester LE1 7RH, UK; (S.S.); (S.D.)
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Evolutionary Understanding of Metacaspase Genes in Cultivated and Wild Oryza Species and Its Role in Disease Resistance Mechanism in Rice. Genes (Basel) 2020; 11:genes11121412. [PMID: 33256228 PMCID: PMC7760854 DOI: 10.3390/genes11121412] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 11/18/2020] [Accepted: 11/24/2020] [Indexed: 12/16/2022] Open
Abstract
Metacaspases (MCs), a class of cysteine-dependent proteases found in plants, fungi, and protozoa, are predominately involved in programmed cell death processes. In this study, we identified metacaspase genes in cultivated and wild rice species. Characterization of metacaspase genes identified both in cultivated subspecies of Oryza sativa, japonica, and indica and in nine wild rice species was performed. Extensive computational analysis was conducted to understand gene structures, phylogenetic relationships, cis-regulatory elements, expression patterns, and haplotypic variations. Further, the haplotyping study of metacaspase genes was conducted using the whole-genome resequencing data publicly available for 4726 diverse genotype and in-house resequencing data generated for north-east Indian rice lines. Sequence variations observed among wild and cultivated rice species for metacaspase genes were used to understand the duplication and neofunctionalization events. The expression profiles of metacaspase genes were analyzed using RNA-seq transcriptome profiling in rice during different developmental stages and stress conditions. Real-time quantitative PCR analysis of candidate metacaspase genes in rice cultivars Pusa Basmati-1 in response to Magnaporthe oryzae infection indicated a significant role in the disease resistance mechanism. The information provided here will help to understand the evolution of metacaspases and their role under stress conditions in rice.
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Shireen F, Nawaz MA, Xiong M, Ahmad A, Sohail H, Chen Z, Abouseif Y, Huang Y, Bie Z. Pumpkin rootstock improves the growth and development of watermelon by enhancing uptake and transport of boron and regulating the gene expression. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 154:204-218. [PMID: 32563044 DOI: 10.1016/j.plaphy.2020.06.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 05/31/2020] [Accepted: 06/01/2020] [Indexed: 06/11/2023]
Abstract
Boron (B) is an essential trace element that plays a vital role in metabolic and physiological functions of higher plants. The adequate supply of B is important for plant growth and development. Grafting is a technique used to improve the ion uptake and plant growth. In this study, a commercial watermelon cultivar "Zaojia 8424" [Citrullus lanatus (Thunb.) Matsum. and Nakai.] was grafted onto pumpkin (Cucurbita maxima × Cucurbita moschata) rootstock cv. "Qingyan Zhenmu No.1" with an aim to investigate the response of grafted plants to different levels of B supply (0.25 μM, 25 μM and 75 μM B) in the nutrient solution. Self-grafted watermelon plants were used as control. Pumpkin rootstock improved the plant growth, chlorophyll and carotenoid contents, photosynthetic assimilation, stomatal conductance, transpiration rate, B accumulation and up-regulated the expression of NIP5;1, NIP6;1 and B transporter (BOR2, BOR4) genes in the roots and leaves at 25 μM B compared with self-grafted watermelon plants. Moreover, pumpkin rootstock reduced the oxidative stress and cell damage by reducing H2O2 and MDA contents, and down-regulating the expression of PDCD2-1, PDCD2-2 genes. Moreover, it enhanced the antioxidant activity of watermelon by up-regulating the expression of SOD1, SOD2, CAT2-1, and CAT2-2 genes. Based on these observations, we concluded that pumpkin rootstock has ability to improve the plant growth of watermelon by enhancing the B uptake. This study may help adjust the B concentration in the nutrient medium for watermelon production where pumpkin grafted plants are utilized.
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Affiliation(s)
- Fareeha Shireen
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University/Key Laboratory of Horticultural Plant Biology, Ministry of Education, Wuhan, 430070, PR China
| | - Muhammad Azher Nawaz
- Department of Horticulture, College of Agriculture, University of Sargodha, Sargodha, 40100, Pakistan
| | - Mu Xiong
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University/Key Laboratory of Horticultural Plant Biology, Ministry of Education, Wuhan, 430070, PR China
| | - Adeel Ahmad
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University/Key Laboratory of Horticultural Plant Biology, Ministry of Education, Wuhan, 430070, PR China
| | - Hamza Sohail
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University/Key Laboratory of Horticultural Plant Biology, Ministry of Education, Wuhan, 430070, PR China
| | - Zhi Chen
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University/Key Laboratory of Horticultural Plant Biology, Ministry of Education, Wuhan, 430070, PR China
| | - Yehia Abouseif
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University/Key Laboratory of Horticultural Plant Biology, Ministry of Education, Wuhan, 430070, PR China
| | - Yuan Huang
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University/Key Laboratory of Horticultural Plant Biology, Ministry of Education, Wuhan, 430070, PR China
| | - Zhilong Bie
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University/Key Laboratory of Horticultural Plant Biology, Ministry of Education, Wuhan, 430070, PR China.
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10
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Tombuloglu H, Slimani Y, Tombuloglu G, Alshammari T, Almessiere M, Korkmaz AD, Baykal A, Samia ACS. Engineered magnetic nanoparticles enhance chlorophyll content and growth of barley through the induction of photosystem genes. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:34311-34321. [PMID: 32542569 DOI: 10.1007/s11356-020-09693-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 06/10/2020] [Indexed: 06/11/2023]
Abstract
This study investigates the impact of an engineered magnetic nanoparticle (MNP) on a crop plant. For this purpose, a sonochemical synthetic approach was utilized in order to dope magnetic elements (Co and Nd) into technologically important iron oxide NPs. After being characterized by using TEM, SEM, and XRD instruments, the MNPs were hydroponically applied to barley plants with varying doses (from 125 to 1000 mg/L) both in germination (4 days) and early growing stages (3 weeks). Physiological responses, as well as expression of photosystem marker genes, were assessed. Compared to the untreated control, MNP treatment enhanced germination rate (~ 31%), tissue growth (8% in roots, 16% in shoots), biomass (~ 21%), and chlorophyll (a, b) (~ 20%), and carotenoids (~ 22%) pigments. In general, plants showed the highest growth enhancement at 125 or 250 mg/L treatment. However, higher doses diminished the growth indices. Compared to the control, the catalase activity was significantly reduced in the leaves (~ 33%, p < 0.005) but stimulated in the roots (~ 46%, p < 0.005). All tested photosystem marker genes (BCA, psbA, and psaA) were overexpressed in MNP-treated leaves than non-treated control. Moreover, the gene expressions were found to be proportionally increased with increasing MNP doses, indicating a positive correlation between MNPs and the photosynthetic machinery, which could contribute to the enhancement of plant growth.
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Affiliation(s)
- Huseyin Tombuloglu
- Department of Genetics Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, P.O. Box 34221, Dammam, Saudi Arabia.
| | - Yassine Slimani
- Department of Biophysics, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, P.O. Box 34221, Dammam, Saudi Arabia
| | - Guzin Tombuloglu
- Adnan Kahveci Mah., Mimar Sinan Cad., Mavisu evl, 7/28 Beylikduzu-, Istanbul, Turkey
| | - Thamer Alshammari
- Department of Genetics Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, P.O. Box 34221, Dammam, Saudi Arabia
| | - Munirah Almessiere
- Department of Biophysics, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, P.O. Box 34221, Dammam, Saudi Arabia
- Department of Physics, College of Science, Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam, 31441, Saudi Arabia
| | - Ayşe Demir Korkmaz
- Department of Chemistry, Istanbul Medeniyet University, 34700 Uskudar, Istanbul, Turkey
| | - Abdulhadi Baykal
- Department of Nanomedicine, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, P.O. Box 34221, Dammam, Saudi Arabia
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11
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Shamloo-Dashtpagerdi R, Lindlöf A, Aliakbari M, Pirasteh-Anosheh H. Plausible association between drought stress tolerance of barley (Hordeum vulgare L.) and programmed cell death via MC1 and TSN1 genes. PHYSIOLOGIA PLANTARUM 2020; 170:46-59. [PMID: 32246464 DOI: 10.1111/ppl.13102] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 03/17/2020] [Accepted: 03/27/2020] [Indexed: 06/11/2023]
Abstract
Studying the drought-responsive transcriptome is of high interest as it can serve as a blueprint for stress adaptation strategies. Despite extensive studies in this area, there are still many details to be uncovered, such as the importance of each gene involved in the stress response as well as the relationship between these genes and the physiochemical processes governing stress tolerance. This study was designed to address such important details and to gain insights into molecular responses of barley (Hordeum vulgare L.) to drought stress. To that, we combined RNA-seq data analysis with field and greenhouse drought experiments in a systems biology approach. RNA-sequence analysis identified a total of 665 differentially expressed genes (DEGs) belonging to diverse functional categories. A gene network was derived from the DEGs, which comprised of a total of 131 nodes and 257 edges. Gene network topology analysis highlighted two programmed cell death (PCD) modulating genes, MC1 (metacaspase 1) and TSN1 (Tudor-SN 1), as important (hub) genes in the predicted network. Based on the field trial, a drought-tolerant and a drought-susceptible barley genotype was identified from eight tested cultivars. Identified genotypes exhibited different physiochemical characteristics, including proline content, chlorophyll concentration, percentage of electrolyte leakage and malondialdehyde content as well as expression profiles of MC1 and TSN1 genes. Machine learning and correspondence analysis revealed a significant relationship between drought tolerance and measured characteristics in the context of PCD. Our study provides new insights which bridge barley drought tolerance to PCD through MC1 and TSN1 pathway.
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Affiliation(s)
| | | | - Massume Aliakbari
- Department of Crop Production and Plant Breeding, Shiraz University, Shiraz, Iran
| | - Hadi Pirasteh-Anosheh
- National Salinity Research Center, Agricultural Research, Education and Extension Organization, Yazd, Iran
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12
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Ye H, Ren F, Guo H, Guo L, Bai J, Wang Y. Identification of key genes and transcription factors in ageing Arabidopsis papilla cells by transcriptome analysis. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 147:1-9. [PMID: 31837555 DOI: 10.1016/j.plaphy.2019.12.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 12/04/2019] [Accepted: 12/06/2019] [Indexed: 06/10/2023]
Abstract
Programmed cell death (PCD) play essential roles in plant growth and development. Stigmatic papilla cells form an indispensable organ for plant reproduction. The lifetime of papilla cells is tightly controlled, and the developmental PCD (dPCD) process is involved in papilla cell death. Hence, papilla cell death is a good model for studying on PCD process. In this study, the dPCD signal was visualized in dying papilla cells by detecting the GUS signal of the PCD-related reporter gene BIFUNCTIONAL NUCLEASE 1 (BFN1). We found that the GUS was not expressed at young stage, but strongly expressed in papilla cells at the ageing stage, indicating the PCD process was triggered to terminate the papilla cell fate. Given this, the RNA-Seq data set, which covered the information of the whole lifespan of papilla cells, was analyzed aiming to understand which genes and pathways were involved in papilla cell death. 37 differential expressed genes (DEGs) were isolated. Moreover, the pathways related to energy production and transportation, autophagy, and plant hormone signal transduction were considered as the key pathways involved in the papilla cell death. 9 types, total of 104 transcriptional factors (TFs) were identified as well. Finally, a putative working model of papilla cell death was integrated. The findings herein will enrich the knowledge of the dPCD-mediated pathway in regulating plant organ/tissue growth, development, senescence, and death. Our study will provide some referential gene resources for studying on the dPCD in other plant organs or tissues.
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Affiliation(s)
- Hong Ye
- Division of Biological Science, Nara Institute of Science and Technology, Ikoma, 6300192, Japan
| | - Fei Ren
- School of Agricultural Science and Engineering, Shaoguan University, 288 Daxue Road, Zhenjiang District, Shaoguan, 512000, PR China
| | - Haoyu Guo
- College of Life Science, Capital Normal University, Beijing, 100048, PR China
| | - Liping Guo
- School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, PR China
| | - Jianfang Bai
- Beijing Engineering Research Center for Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, PR China.
| | - Yukun Wang
- Division of Biological Science, Nara Institute of Science and Technology, Ikoma, 6300192, Japan.
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13
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Unver T, Tombuloglu H. Barley long non-coding RNAs (lncRNA) responsive to excess boron. Genomics 2019; 112:1947-1955. [PMID: 31730798 DOI: 10.1016/j.ygeno.2019.11.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Revised: 11/06/2019] [Accepted: 11/11/2019] [Indexed: 02/01/2023]
Abstract
Long non-coding RNA (lncRNA) has a misleading name, since although they do not encode proteins, they may encode small peptides. Such transcripts are emerging as regulatory molecules. With the advent of next-generation sequencing technologies and novel bioinformatics tools, a tremendous amount of lncRNAs have been identified in several plant species. Recent reports demonstrated roles of plant lncRNAs such as development and environmental response. Here, we reported a genome-wide discovery of ~8000 barley lncRNAs and measured their expression pattern upon excessive boron (B) treatment. According to the tissue-based comparison, leaves have a greater number of B-responsive differentially expressed lncRNAs than the root. Functional annotation of the coding transcripts, which were co-expressed with lncRNAs, revealed that molecular function of the ion transport, establishment of localization, and response to stimulus significantly enriched only in the leaf. On the other hand, 32 barley endogenous target mimics (eTM) as lncRNAs, which potentially decoy the transcriptional suppression activity of 18 miRNAs, were obtained. Also, six lncRNAs, differentially expressed upon B-treatment, were selected and quantitatively analyzed in both B-sensitive and B-tolerant cultivars treated by excess B-level. Quantitative real-time polymerase chain reaction (qRT-PCR) analysis confirmed the B-responsive expressional changes obtained by RNA sequencing. Notably, some lncRNAs (i.e., TCONS_00045190 and TCONS_00056415) over-expressed only in B-tolerant cultivar upon excess B treatment. Presented data including identification, expression measurement, and functional characterization of barley lncRNAs suggest that B-stress response might also be regulated by lncRNA expression, via cooperative interaction of miRNA-eTM-coding target transcript modules.
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Affiliation(s)
- Turgay Unver
- Ficus Biotechnology, Ostim Teknopark, No: 1/1/76, 06378, Yenimahalle, Ankara, Turkey.
| | - Huseyin Tombuloglu
- Department of Genetics Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam 31441, Saudi Arabia
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14
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Tombuloglu H, Slimani Y, Tombuloglu G, Almessiere M, Baykal A. Uptake and translocation of magnetite (Fe 3O 4) nanoparticles and its impact on photosynthetic genes in barley (Hordeum vulgare L.). CHEMOSPHERE 2019; 226:110-122. [PMID: 30925403 DOI: 10.1016/j.chemosphere.2019.03.075] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2018] [Revised: 03/03/2019] [Accepted: 03/12/2019] [Indexed: 05/23/2023]
Abstract
This study investigates the fate and impact of iron oxide or magnetite (Fe3O4, ∼13 nm in size) nanoparticles (NPs) in barley (Hordeum vulgare L.), a common crop cultivated around the world. Barley seedlings were grown in hydroponic culture for three weeks to include NPs (125, 250, 500, and 1000 mg/L). Transmission electron microscopy (TEM) and vibrating sample magnetometer (VSM) techniques were used to assess their uptake and translocation. Photosynthesis marker genes were quantified by RT-qPCR. Results revealed that increasing doses of Fe3O4 NPs were gradually enhanced the plant growth up to 500 mg/L, which promoted the fresh weight (FW) respectively ∼19% and ∼88% for leaf and root tissues than the ones for control. No phytotoxic effect was recorded even at high NPs doses. NPs inclusion increased some phenological parameters such as chlorophyll, total soluble protein, number of chloroplasts, and dry weight. High NPs doses dramatically reduced the catalase activity and hydrogen peroxide content, suggesting a possible function of NPs as nanozyme in vivo. TEM observations showed that Fe3O4 NPs penetrated and internalized in the root cells. In leaves, they were mostly existed at the surrounding cell wall, suggesting their translocation from root to shoot without cellular penetration. Further analysis by using VSM confirmed the existence of Fe3O4 NPs in leaves which result in dramatic alterations of the photosystem genes (PetA, psaA, BCA and psbA). In conclusion, barley plants uptake and translocate Fe3O4 NPs, which promoted the plant growth probably due to the promoted gene expression and efficient photosynthetic activity.
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Affiliation(s)
- Huseyin Tombuloglu
- Department of Genetics Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, P.O. Box 34221, Dammam, Saudi Arabia.
| | - Yassine Slimani
- Department of Biophysics, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, P.O. Box 34221, Dammam, Saudi Arabia
| | - Guzin Tombuloglu
- Adnan Kahveci Mah., Mimar Sinan Cad., Mavisu evl., 7/28 Beylikduzu, Istanbul, Turkey
| | - Munirah Almessiere
- Department of Nanomedicine, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, P.O. Box 34221, Dammam, Saudi Arabia; Department of Physics, College of Science, Imam Abdulrahman Bin Faisal University, P.O. Box 1982, 31441, Dammam, Saudi Arabia
| | - Abdulhadi Baykal
- Department of Nanomedicine, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, P.O. Box 34221, Dammam, Saudi Arabia
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15
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Tombuloglu H. Genome-wide identification and expression analysis of R2R3, 3R- and 4R-MYB transcription factors during lignin biosynthesis in flax (Linum usitatissimum). Genomics 2019; 112:782-795. [PMID: 31128265 DOI: 10.1016/j.ygeno.2019.05.017] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 05/06/2019] [Accepted: 05/20/2019] [Indexed: 11/19/2022]
Abstract
MYB transcription factors (TFs) have vital roles in regulating lignin or fiber development. Flax (Linum usitatissimum) is known as one of the plants with high fiber production capacity. However, no studies have been conducted to identify and characterize MYB TFs in the flax genome. Results showed that flax genome harbours 167 R2R3, seven 3R, and one 4R-type MYB TFs. 22 MYB genes (%13) were estimated to be tandem duplicated dated around 13.3-86.98 Mya. 130 flax MYB members have apparent orthologous with Arabidopsis, in which 17 R2R3 MYBs are associated with lignin biosynthesis. MYB062, MYB072, MYB096, MYB141, and MYB146 genes were up-regulated in tissues having higher lignin production capacity. In opposite, MYB012 and MYB113 genes were down-regulated which points out the involvement of those genes in the lignin biosynthesis mechanism. This comprehensive study can provide a basis for understanding the role of MYBs in fiber or lignin production in flax.
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Affiliation(s)
- Huseyin Tombuloglu
- Department of Genetics Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, P.O. Box 1982, 31441 Dammam, Saudi Arabia.
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16
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Cao Y, Meng D, Chen T, Chen Y, Zeng W, Zhang L, Wang Q, Hen W, Abdullah M, Jin Q, Lin Y, Cai Y. Metacaspase gene family in Rosaceae genomes: Comparative genomic analysis and their expression during pear pollen tube and fruit development. PLoS One 2019; 14:e0211635. [PMID: 30794567 PMCID: PMC6386261 DOI: 10.1371/journal.pone.0211635] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 01/17/2019] [Indexed: 12/11/2022] Open
Abstract
Metacaspase (MC), which is discovered gene family with distant caspase homologs in plants, fungi, and protozoa, may be involved in programmed cell death (PCD) processes during plant development and respond abiotic and biotic stresses. To reveal the evolutionary relationship of MC gene family in Rosaceae genomes, we identified 8, 7, 8, 12, 12, and 23 MC genes in the genomes of Fragaria vesca, Prunus mume, Prunus persica, Pyrus communis, Pyrus bretschneideri and Malus domestica, respectively. Phylogenetic analysis suggested that the MC genes could be grouped into three clades: Type I*, Type I and Type II, which was supported by gene structure and conserved motif analysis. Microsynteny analysis revealed that MC genes present in the corresponding syntenic blocks of P. communis, P. bretschneideri and M. domestica, and further suggested that large-scale duplication events play an important role in the expansion of MC gene family members in these three genomes than other Rosaceae plants (F. vesca, P. mume and P. persica). RNA-seq data showed the specific expression patterns of PbMC genes in response to drought stress. The expression analysis of MC genes demonstrated that PbMC01 and PbMC03 were able to be detected in all four pear pollen tubes and seven fruit development stages. The current study highlighted the evolutionary relationship and duplication of the MC gene family in these six Rosaceae genomes and provided appropriate candidate genes for further studies in P. bretschneideri.
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Affiliation(s)
- Yunpeng Cao
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Dandan Meng
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Tianzhe Chen
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Yu Chen
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Wei Zeng
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Lei Zhang
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Qi Wang
- College of Horticulture, Anhui Agricultural University, Hefei, China
| | - Wei Hen
- College of Horticulture, Anhui Agricultural University, Hefei, China
| | - Muhammad Abdullah
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Qing Jin
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Yi Lin
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Yongping Cai
- School of Life Sciences, Anhui Agricultural University, Hefei, China
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17
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Kong W, Zhang Y, Deng X, Li S, Zhang C, Li Y. Comparative Genomic and Transcriptomic Analysis Suggests the Evolutionary Dynamic of GH3 Genes in Gramineae Crops. FRONTIERS IN PLANT SCIENCE 2019; 10:1297. [PMID: 31681387 PMCID: PMC6803601 DOI: 10.3389/fpls.2019.01297] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 09/18/2019] [Indexed: 05/18/2023]
Abstract
Glycoside hydrolase 3 (GH3) gene family belongs to auxin-responsive gene families and is tightly linked with hormone homeostasis and signaling pathways. However, our knowledge about the evolutionary dynamic of GH3 genes in Gramineae crops is limited. In this study, a comparative genomic and transcriptomic analysis was conducted to study evolutionary patterns and the driving selective forces of GH3 gene family in six representative Gramineae crops, namely, Setaria italica (Si), Zea mays (Zm), Sorghum bicolor (Sb), Hordeum vulgare (Hv), Brachypodium distachyon (Bd), and Oryza sativa ssp. japonica (Os). A total of 17, 13, 11, 9, 8, and 11 GH3 proteins (GH3s) were identified in Si, Zm, Sb, Hv, Bd, and Os, respectively. Phylogenetic, conserved motif, and gene structural analyses could divide all GH3s into two groups (I and II), and all GH3s consisted of seven orthogroups (Ors) on the basis of Or identification result. We further found that genes in the same Or showed similar sequence and structural features, whereas genes in the same groups exhibited intrinsic differences in exon numbers and intron lengths. These results revealed GH3 genes in the same groups have been differentiated. Obvious differences in total numbers of GH3 genes, Ors, and duplication events among these six tested Gramineae crops reflected lineage-specific expansions and homologous gene loss/gain of GH3 gene family during the evolutionary process. In addition, selective force and expression analyses indicated that all GH3 genes were constrained by strong purifying selection, and GH3 genes in conserved Ors showed higher expression levels than that in unconserved Ors. The current study highlighted different evolutionary patterns of GH3 genes in Gramineae crops resulted from different evolutionary rates and duplication events and provided a vital insight into the functional divergence of GH3 genes.
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