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Nawaz MA, Khalil HK, Azeem F, Ali MA, Pamirsky IE, Golokhvast KS, Yang SH, Atif RM, Chung G. In Silico Comparison of WRKY Transcription Factors in Wild and Cultivated Soybean and Their Co-expression Network Arbitrating Disease Resistance. Biochem Genet 2024:10.1007/s10528-024-10701-z. [PMID: 38411942 DOI: 10.1007/s10528-024-10701-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 01/15/2024] [Indexed: 02/28/2024]
Abstract
WRKY Transcription factors (TFs) play critical roles in plant defence mechanisms that are activated in response to biotic and abiotic stresses. However, information on the Glycine soja WRKYs (GsoWRKYs) is scarce. Owing to its importance in soybean breeding, here we identified putative WRKY TFs in wild soybean, and compared the results with Glycine max WRKYs (GmaWRKYs) by phylogenetic, conserved motif, and duplication analyses. Moreover, we explored the expression trends of WRKYs in G. max (oomycete, fungi, virus, bacteria, and soybean cyst nematode) and G. soja (soybean cyst nematode), and identified commonly expressed WRKYs and their co-expressed genes. We identified, 181 and 180 putative WRKYs in G. max and G. soja, respectively. Though the number of WRKYs in both studied species is almost the same, they differ in many ways, i.e., the number of WRKYs on corresponding chromosomes, conserved domain structures, WRKYGQK motif variants, and zinc-finger motifs. WRKYs in both species grouped in three major clads, i.e., I-III, where group-II had sub-clads IIa-IIe. We found that GsoWRKYs expanded mostly through segmental duplication. A large number of WRKYs were expressed in response to biotic stresses, i.e., Phakospora pachyrhizi, Phytoplasma, Heterodera glycines, Macrophomina phaseolina, and Soybean mosaic virus; 56 GmaWRKYs were commonly expressed in soybean plants infected with these diseases. Finally, 30 and 63 GmaWRKYs and GsoWRKYs co-expressed with 205 and 123 non-WRKY genes, respectively, indicating that WRKYs play essential roles in biotic stress tolerance in Glycine species.
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Affiliation(s)
- Muhammad Amjad Nawaz
- Advanced Engineering School (Agrobiotek), Tomsk State University, Lenin Ave, 36, Tomsk Oblast, Russia, 634050.
- Center for Research in the Field of Materials and Technologies, Tomsk State University, Tomsk, Russia.
| | - Hafiz Kashif Khalil
- Department of Plant Breeding and Genetics / CAS-AFS, University of Agriculture, Faisalabad, Pakistan
| | - Farrukh Azeem
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Faisalabad, Pakistan
| | - Muhammad Amjad Ali
- Department of Plant Pathology, University of Agriculture, Faisalabad, Pakistan
| | - Igor Eduardovich Pamirsky
- Siberian Federal Scientific Centre of AgrobiotechnologyCentralnaya, Presidium, Krasnoobsk, Russia, 633501
| | - Kirill S Golokhvast
- Advanced Engineering School (Agrobiotek), Tomsk State University, Lenin Ave, 36, Tomsk Oblast, Russia, 634050
- Siberian Federal Scientific Centre of AgrobiotechnologyCentralnaya, Presidium, Krasnoobsk, Russia, 633501
- Laboratory of Supercritical Fluid Research and Application in Agrobiotechnology, Tomsk State University, Lenin Str. 36, Tomsk, Russia, 634050
| | - Seung Hwan Yang
- Department of Biotechnology, Chonnam National University, Yeosu Campus, Yeosu-si, 59626, South Korea
| | - Rana Muhammad Atif
- Department of Plant Breeding and Genetics / CAS-AFS, University of Agriculture, Faisalabad, Pakistan.
- Precision Agriculture and Analytics Lab, National Centre in Big Data and Cloud Computing, Centre for Advanced Studies in Agriculture and Food Security, University of Agriculture Faisalabad, Faisalabad, Pakistan.
- Department of Plant Pathology, University of California, Davis, CA, USA.
| | - Gyuhwa Chung
- Department of Biotechnology, Chonnam National University, Yeosu Campus, Yeosu-si, 59626, South Korea.
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Sadaqat M, Umer B, Attia KA, Abdelkhalik AF, Azeem F, Javed MR, Fatima K, Zameer R, Nadeem M, Tanveer MH, Sun S, Ercisli S, Nawaz MA. Genome-wide identification and expression profiling of two-component system (TCS) genes in Brassica oleracea in response to shade stress. Front Genet 2023; 14:1142544. [PMID: 37323660 PMCID: PMC10267837 DOI: 10.3389/fgene.2023.1142544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 04/26/2023] [Indexed: 06/17/2023] Open
Abstract
The Two-component system (TCS) consists of Histidine kinases (HKs), Phosphotransfers (HPs), and response regulator (RR) proteins. It has an important role in signal transduction to respond to a wide variety of abiotic stresses and hence in plant development. Brassica oleracea (cabbage) is a leafy vegetable, which is used for food and medicinal purposes. Although this system was identified in several plants, it had not been identified in Brassica oleracea yet. This genome-wide study identified 80 BoTCS genes consisting of 21 HKs, 8 HPs, 39 RRs, and 12 PRRs. This classification was done based on conserved domains and motif structure. Phylogenetic relationships of BoTCS genes with Arabidopsis thaliana, Oryza sativa, Glycine max, and Cicer arietinum showed conservation in TCS genes. Gene structure analysis revealed that each subfamily had conserved introns and exons. Both tandem and segmental duplication led to the expansion of this gene family. Almost all of the HPs and RRs were expanded through segmental duplication. Chromosomal analysis showed that BoTCS genes were dispersed across all nine chromosomes. The promoter regions of these genes were found to contain a variety of cis-regulatory elements. The 3D structure prediction of proteins also confirmed the conservation of structure within subfamilies. MicroRNAs (miRNAs) involved in the regulation of BoTCSs were also predicted and their regulatory roles were also evaluated. Moreover, BoTCSs were docked with abscisic acid to evaluate their binding. RNA-seq-based expression analysis and validation by qRT-PCR showed significant variation of expression for BoPHYs, BoERS1.1, BoERS2.1, BoERS2.2, BoRR10.2, and BoRR7.1 suggesting their importance in stress response. These genes showing unique expression can be further used in manipulating the plant's genome to make the plant more resistant the environmental stresses which will ultimately help in the increase of plant's yield. More specifically, these genes have altered expression in shade stress which clearly indicates their importance in biological functions. These findings are important for future functional characterization of TCS genes in generating stress-responsive cultivars.
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Affiliation(s)
- Muhammad Sadaqat
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Faisalabad, Pakistan
| | - Basit Umer
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Faisalabad, Pakistan
| | - Kotb A. Attia
- Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Amr F. Abdelkhalik
- Biotechnology School, Nile University, Giza, Egypt
- Rice Biotechnology Lab, Rice Research and Training Center, Field Crops Research Institute, ARC, Kafrelshikh, Egypt
| | - Farrukh Azeem
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Faisalabad, Pakistan
| | - Muhammad Rizwan Javed
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Faisalabad, Pakistan
| | - Kinza Fatima
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Faisalabad, Pakistan
| | - Roshan Zameer
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Faisalabad, Pakistan
| | - Majid Nadeem
- Wheat Research Institute, Ayub Agriculture Research Institute, Faisalabad, Pakistan
| | | | - Sangmi Sun
- Department of Biotechnology, Chonnam National University, Yesosu Campus, Yesosu Si, Republic of Korea
| | - Sezai Ercisli
- Department of Horticulture, Faculty of Agriculture, Ataturk University, Erzurum, Türkiye
- HGF Agro, Ata Teknokent, Erzurum, Türkiye
| | - Muhammad Amjad Nawaz
- Advanced Engineering School (Agrobiotek), Tomsk State University, Tomsk, Russia
- Center for Research in the Field of Materials and Technologies, Tomsk State University, Tomsk, Russia
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Baloch FS, Altaf MT, Liaqat W, Bedir M, Nadeem MA, Cömertpay G, Çoban N, Habyarimana E, Barutçular C, Cerit I, Ludidi N, Karaköy T, Aasim M, Chung YS, Nawaz MA, Hatipoğlu R, Kökten K, Sun HJ. Recent advancements in the breeding of sorghum crop: current status and future strategies for marker-assisted breeding. Front Genet 2023; 14:1150616. [PMID: 37252661 PMCID: PMC10213934 DOI: 10.3389/fgene.2023.1150616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 04/17/2023] [Indexed: 05/31/2023] Open
Abstract
Sorghum is emerging as a model crop for functional genetics and genomics of tropical grasses with abundant uses, including food, feed, and fuel, among others. It is currently the fifth most significant primary cereal crop. Crops are subjected to various biotic and abiotic stresses, which negatively impact on agricultural production. Developing high-yielding, disease-resistant, and climate-resilient cultivars can be achieved through marker-assisted breeding. Such selection has considerably reduced the time to market new crop varieties adapted to challenging conditions. In the recent years, extensive knowledge was gained about genetic markers. We are providing an overview of current advances in sorghum breeding initiatives, with a special focus on early breeders who may not be familiar with DNA markers. Advancements in molecular plant breeding, genetics, genomics selection, and genome editing have contributed to a thorough understanding of DNA markers, provided various proofs of the genetic variety accessible in crop plants, and have substantially enhanced plant breeding technologies. Marker-assisted selection has accelerated and precised the plant breeding process, empowering plant breeders all around the world.
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Affiliation(s)
- Faheem Shehzad Baloch
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Türkiye
| | - Muhammad Tanveer Altaf
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Türkiye
| | - Waqas Liaqat
- Department of Field Crops, Faculty of Agriculture, Çukurova University, Adana, Türkiye
| | - Mehmet Bedir
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Türkiye
| | - Muhammad Azhar Nadeem
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Türkiye
| | - Gönül Cömertpay
- Eastern Mediterranean Agricultural Research Institute, Adana, Türkiye
| | - Nergiz Çoban
- Eastern Mediterranean Agricultural Research Institute, Adana, Türkiye
| | - Ephrem Habyarimana
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, Telangana, India
| | - Celaleddin Barutçular
- Department of Field Crops, Faculty of Agriculture, Çukurova University, Adana, Türkiye
| | - Ibrahim Cerit
- Eastern Mediterranean Agricultural Research Institute, Adana, Türkiye
| | - Ndomelele Ludidi
- Plant Stress Tolerance Laboratory, Department of Biotechnology, University of the Western Cape, Bellville, South Africa
- DSI-NRF Centre of Excellence in Food Security, University of the Western Cape, Bellville, South Africa
| | - Tolga Karaköy
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Türkiye
| | - Muhammad Aasim
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Türkiye
| | - Yong Suk Chung
- Department of Plant Resources and Environment, Jeju National University, Jeju, Republic of Korea
| | | | - Rüştü Hatipoğlu
- Kırşehir Ahi Evran Universitesi Ziraat Fakultesi Tarla Bitkileri Bolumu, Kırşehir, Türkiye
| | - Kağan Kökten
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Türkiye
| | - Hyeon-Jin Sun
- Subtropical Horticulture Research Institute, Jeju National University, Jeju, Republic of Korea
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Hawamda AIM, Reichert S, Ali MA, Nawaz MA, Austerlitz T, Schekahn P, Abbas A, Tenhaken R, Bohlmann H. Characterization of an Arabidopsis Defensin-like Gene Conferring Resistance against Nematodes. Plants 2022; 11:plants11030280. [PMID: 35161268 PMCID: PMC8838067 DOI: 10.3390/plants11030280] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 01/15/2022] [Accepted: 01/18/2022] [Indexed: 12/15/2022]
Abstract
Arabidopsis contains 317 genes for defensin-like (DEFL) peptides. DEFLs have been grouped into different families based mainly on cysteine motifs. The DEFL0770 group contains seven genes, of which four are strongly expressed in roots. We found that the expression of these genes is downregulated in syncytia induced by the beet cyst nematode Heterodera schachtii as revealed by RNAseq analysis. We have studied one gene of this group, At3g59930, in detail. A promoter::GUS line revealed that the gene is only expressed in roots but not in other plant organs. Infection of the GUS line with larvae of H. schachtii showed a strong downregulation of GUS expression in infection sites as early as 1 dpi, confirming the RNAseq data. The At3g59930 peptide had only weak antimicrobial activity against Botrytis cinerea. Overexpression lines had no enhanced resistance against this fungus but were more resistant to H. schachtii infection. Our data indicate that At3g59930 is involved in resistance to nematodes which is probably not due to direct nematicidal activity.
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Affiliation(s)
- Abdalmenem I. M. Hawamda
- Institute of Plant Protection, Department of Crop Sciences, University of Natural Resources and Life Sciences, 1180 Vienna, Austria; (A.I.M.H.); (S.R.); (M.A.A.); (T.A.); (P.S.); (A.A.)
- Department of Agricultural Biotechnology, Faculty of Agricultural Science and Technology, Palestine Technical University-Kadoorie (PTUK), Tulkarm P.O. Box 7, Palestine
| | - Susanne Reichert
- Institute of Plant Protection, Department of Crop Sciences, University of Natural Resources and Life Sciences, 1180 Vienna, Austria; (A.I.M.H.); (S.R.); (M.A.A.); (T.A.); (P.S.); (A.A.)
| | - Muhammad Amjad Ali
- Institute of Plant Protection, Department of Crop Sciences, University of Natural Resources and Life Sciences, 1180 Vienna, Austria; (A.I.M.H.); (S.R.); (M.A.A.); (T.A.); (P.S.); (A.A.)
- Department of Plant Pathology, University of Agriculture, Faisalabad 38040, Pakistan
- Centre of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad 38040, Pakistan
| | - Muhammad Amjad Nawaz
- Siberian Federal Scientific Centre of Agrobiotechnology, Russian Academy of Sciences, 630501 Krasnoobsk, Russia;
- Laboratory of Supercritical Fluid Research and Application in Agrobiotechnology, The National Research Tomsk State University, 36, Lenin Avenue, 634050 Tomsk, Russia
| | - Tina Austerlitz
- Institute of Plant Protection, Department of Crop Sciences, University of Natural Resources and Life Sciences, 1180 Vienna, Austria; (A.I.M.H.); (S.R.); (M.A.A.); (T.A.); (P.S.); (A.A.)
| | - Patricia Schekahn
- Institute of Plant Protection, Department of Crop Sciences, University of Natural Resources and Life Sciences, 1180 Vienna, Austria; (A.I.M.H.); (S.R.); (M.A.A.); (T.A.); (P.S.); (A.A.)
| | - Amjad Abbas
- Institute of Plant Protection, Department of Crop Sciences, University of Natural Resources and Life Sciences, 1180 Vienna, Austria; (A.I.M.H.); (S.R.); (M.A.A.); (T.A.); (P.S.); (A.A.)
- Department of Plant Pathology, University of Agriculture, Faisalabad 38040, Pakistan
| | - Raimund Tenhaken
- Plant Physiology, University of Salzburg, 5020 Salzburg, Austria;
| | - Holger Bohlmann
- Institute of Plant Protection, Department of Crop Sciences, University of Natural Resources and Life Sciences, 1180 Vienna, Austria; (A.I.M.H.); (S.R.); (M.A.A.); (T.A.); (P.S.); (A.A.)
- Correspondence:
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Azeem F, Ijaz U, Ali MA, Hussain S, Zubair M, Manzoor H, Abid M, Zameer R, Kim DS, Golokhvast KS, Chung G, Sun S, Nawaz MA. Genome-Wide Identification and Expression Profiling of Potassium Transport-Related Genes in Vigna radiata under Abiotic Stresses. Plants (Basel) 2021; 11:2. [PMID: 35009006 PMCID: PMC8747342 DOI: 10.3390/plants11010002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 11/25/2021] [Accepted: 12/10/2021] [Indexed: 06/14/2023]
Abstract
Potassium (K+) is one of the most important cations that plays a significant role in plants and constitutes up to 10% of plants' dry weight. Plants exhibit complex systems of transporters and channels for the distribution of K+ from soil to numerous parts of plants. In this study, we have identified 39 genes encoding putative K+ transport-related genes in Vigna radiata. Chromosomal mapping of these genes indicated an uneven distribution across eight out of 11 chromosomes. Comparative phylogenetic analysis of different plant species, i.e., V. radiata, Glycine max, Cicer arietinum, Oryza sativa, and Arabidopsis thaliana, showed their strong conservation in different plant species. Evolutionary analysis of these genes suggests that gene duplication is a major route of expansion for this family in V. radiata. Comprehensive promoter analysis identified several abiotic stresses related to cis-elements in the promoter regions of these genes, suggesting their role in abiotic stress tolerance. Our additional analyses indicated that abiotic stresses adversely affected the chlorophyll concentration, carotenoids, catalase, total soluble protein concentration, and the activities of superoxide and peroxidase in V. radiata. It also disturbs the ionic balance by decreasing the uptake of K+ content and increasing the uptake of Na+. Expression analysis from high-throughput sequencing data and quantitative real-time PCR experiments revealed that several K+ transport genes were expressed in different tissues (seed, flower, and pod) and in abiotic stress-responsive manners. A highly significant variation of expression was observed for VrHKT (1.1 and 1.2), VrKAT (1 and 2) VrAKT1.1, VrAKT2, VrSKOR, VrKEA5, VrTPK3, and VrKUP/HAK/KT (4, 5, and 8.1) in response to drought, heat or salinity stress. It reflected their potential roles in plant growth, development, or stress adaptations. The present study gives an in-depth understanding of K+ transport system genes in V. radiata and will serve as a basis for a functional analysis of these genes.
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Affiliation(s)
- Farrukh Azeem
- Department of Bioinformatics and Biotechnology, GC University, Faisalabad 38000, Pakistan; (F.A.); (U.I.); (M.Z.); (R.Z.)
| | - Usman Ijaz
- Department of Bioinformatics and Biotechnology, GC University, Faisalabad 38000, Pakistan; (F.A.); (U.I.); (M.Z.); (R.Z.)
| | - Muhammad Amjad Ali
- Department of Plant Pathology, University of Agriculture, Faisalabad 38000, Pakistan;
| | - Sabir Hussain
- Department of Environmental Science and Engineering, GC University, Faisalabad 38000, Pakistan;
| | - Muhammad Zubair
- Department of Bioinformatics and Biotechnology, GC University, Faisalabad 38000, Pakistan; (F.A.); (U.I.); (M.Z.); (R.Z.)
| | - Hamid Manzoor
- Institute of Molecular Biology & Biotechnology, Bahauddin Zakariya University, Multan 60800, Pakistan;
| | - Muhammad Abid
- Department of Plant Pathology, Bahauddin Zakariya University, Multan 60800, Pakistan;
| | - Roshan Zameer
- Department of Bioinformatics and Biotechnology, GC University, Faisalabad 38000, Pakistan; (F.A.); (U.I.); (M.Z.); (R.Z.)
| | - Dong-Seon Kim
- KM Research Science Division, Korea Institute of Oriental Medicine (KIOM), Daejeon 34054, Korea;
| | - Kirill S. Golokhvast
- N.I. Vavilov All-Russian Research Institute of Plant Genetic Resources, 190000 Saint Petersburg, Russia;
- SEC in Nanotechnology, Engineering School, Far Eastern Federal University, 690922 Vladivostok, Russia
- Siberian Federal Scientific Center of Agrobiotechnology, Russian Academy of Sciences, Krasnoobsk, 630501 Novosibirsk, Russia
| | - Gyuhwa Chung
- Department of Biotechnology, Chonnam National University, Yeosu Campus, Gwangju 52626, Korea;
| | - Sangmi Sun
- Department of Biotechnology, Chonnam National University, Yeosu Campus, Gwangju 52626, Korea;
| | - Muhammad Amjad Nawaz
- Siberian Federal Scientific Center of Agrobiotechnology, Russian Academy of Sciences, Krasnoobsk, 630501 Novosibirsk, Russia
- Laboratory of Supercritical Fluid Research and Application in Agrobiotechnology, The National Research Tomsk State University, 36, Lenin Avenue, 634050 Tomsk, Russia
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Khan W, Rafiq N, Nawaz MA, Kabir M, Farooqi ZUR, Romman M, Parvez R, Alfarraj S, Noor A, Ujjan AA. Parasitic contamination of fresh vegetables sold in open markets: a public health threat. BRAZ J BIOL 2021; 82:e242614. [PMID: 34816974 DOI: 10.1590/1519-6984.242614] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Accepted: 10/16/2020] [Indexed: 11/21/2022] Open
Abstract
Vegetables eating raw are a leading source of transmission of infective forms of pathogenic internal parasites among human beings. This research was conducted from April to October, 2017 to assess the parasitic contamination of vegetables sold at main vegetable markets in districts Lower Dir and Peshawar, Pakistan. Eight hundred specimens of different vegetables were purchased and soaked in physiological saline solution, shaken with a mechanical shaker for 20 minutes and processed by sedimentation concentration method. Results revealed that only 19.7% (n=158/800) of the vegetables were found to be contaminated with single or multiple parasite species. Ascaris lumbricoides (the large round worm) 12.3% (n=99/800) was the most commonly detected pathogen and Taenia saginata (the beef tapeworm) 1.62% (n=13/800) was the least frequently detected one. Interestingly, significant p value (p>0.05 at 95%CI) between the number of examined and contaminated for all the variables studied including education status of the vendors, markets location, type of vegetables, means of display, washed before display, washing source of water and market type. The findings of this study evidenced that consumption of raw vegetables possesses great risk of getting parasitic infections in Lower Dir and Peshawar districts, Pakistan. Instructing the sellers and the public about parasitic disease transfer and their hygiene can reduce the infection rate of parasites of human origin.
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Affiliation(s)
- W Khan
- University of Malakand, Department of Zoology, Lower Dir, KP, Pakistan
| | - N Rafiq
- Abdul Wali Khan University, Department of Zoology, Mardan, KP, Pakistan
| | - M A Nawaz
- Shaheed Benazir Bhutto University, Department of Biotechnology, Sheringal, Dir (Upper), KPK, Pakistan
| | - M Kabir
- University of Sargodha, Department of Biological Sciences, Punjab, Pakistan
| | - Z Ur R Farooqi
- University of Karachi, Department of Botany, Karachi, Pakistan
| | - M Romman
- University of Chitral, Department of Botany, KP, Pakistan
| | - R Parvez
- Government Girls Degree College Dargai, Department of Botany, Malakand, KP, Pakistan
| | - S Alfarraj
- King Saud University, College of Science, Zoology Department, Riyadh, Saudi Arabia
| | - A Noor
- Karakoram International University Gilgit, Biological Sciences Department, Baltistan, Pakistan
| | - A A Ujjan
- University of Sindh, Institute of Plant Sciences, Jamshoro, Pakistan
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Jan T, Gul S, Khan A, Pervez S, Noor A, Amin H, Bibi S, Nawaz MA, Rahim A, Ahmad MS, Azam R, Ullah H. Range of factors in the reduction of hyperhydricity associated with in vitro shoots of Salvia santolinifolia Bioss. BRAZ J BIOL 2021; 83:e246904. [PMID: 34706025 DOI: 10.1590/1519-6984.246904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 07/05/2021] [Indexed: 11/22/2022] Open
Abstract
Hyperhydricity is a serious physiological disorder and affects In vitro propagation of many plants and as well of Salvia santolinifolia. The donor material to initiate the in vitro culture was the callus taken from the in vitro shoots produced on Murashig and Skoogs (MS) medium at 4.0 mg/l BA. This callus formed numerous hyperhydric shoots on culturing upon the medium of the same composition. The aim was to systematically evaluate the effect of cytokinins (Benzyladnine (BA) and N6-(-2-isopentenyl) adenine (2iP), culture vessels magnitude, medium solidification, source of nitrogen and calcium chloride for the alleviation of hyperhydricity. In the tissue cultures of S. santolinifolia BA and 2iP induced severe hyperhydricity, when other factors i.e. culture vessels magnitude and a suitable concentration of agar, ammonium nitrate (NH4NO3), potassium nitrate (KNO3) & calcium chloride (CaCl2.2H2O) were not optimized. After 30 days' culture, we observed 83.82% hyperhydric shoots at increased level (1.5 mg/l 2iP) and 81.59% at decreased levels (1.0 mg/l 2iP). On the other hand, hyperhydricity percentage at decreased (0.4%) and at increased (0.8%) levels of agar were 72.37% and 39.08%, respectively. MS medium modification with NH4NO3 (412 mg/l), KNO3 (475 mg/l) and CaCl2.2H2O (880 mg/l) was found the best medium to reduced hyperhydricity (23.6%).
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Affiliation(s)
- T Jan
- University of Malakand, Department of Botany, Plant Tissue Culture Laboratory, Dir lower, Khyber Pakhtunkhwa, Pakistan
| | - S Gul
- University of Malakand, Department of Botany, Plant Tissue Culture Laboratory, Dir lower, Khyber Pakhtunkhwa, Pakistan
| | - A Khan
- University of Lakki Marwat, Department of Biological Sciences, Khyber Pakhtunkhwa, Pakistan
| | - S Pervez
- Shaheed Benazir Bhutto Women University, Department of Biochemistry, Peshawar, Khyber Pakhtunkhwa, Pakistan
| | - A Noor
- Karakoram International University, Department of Biological Sciences, Gilgit-Baltistan, Pakistan
| | - H Amin
- University of Malakand, Department of Botany, Plant Tissue Culture Laboratory, Dir lower, Khyber Pakhtunkhwa, Pakistan
| | - S Bibi
- University of Malakand, Department of Botany, Plant Tissue Culture Laboratory, Dir lower, Khyber Pakhtunkhwa, Pakistan
| | - M A Nawaz
- Shaheed Benazir Bhutto University, Department of Biotechnology, Sheringal, Dir Upper, Pakistan
| | - A Rahim
- University of Malakand, Department of Zoology, Dir lower, Khyber Pakhtunkhwa, Pakistan
| | - M S Ahmad
- University of Malakand, Department of Botany, Plant Tissue Culture Laboratory, Dir lower, Khyber Pakhtunkhwa, Pakistan
| | - R Azam
- University of Malakand, Department of Botany, Plant Tissue Culture Laboratory, Dir lower, Khyber Pakhtunkhwa, Pakistan
| | - H Ullah
- University of Malakand, Department of Botany, Plant Tissue Culture Laboratory, Dir lower, Khyber Pakhtunkhwa, Pakistan
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Attaullah M, Nawaz MA, Ilahi I, Ali H, Jan T, Khwaja S, Hazrat A, Ullah I, Ullah Z, Ullah S, Ahmad B, Ullah R. Honey as a bioindicator of environmental organochlorine insecticides contamination. BRAZ J BIOL 2021; 83:e250373. [PMID: 34550295 DOI: 10.1590/1519-6984.250373] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Accepted: 05/25/2021] [Indexed: 11/22/2022] Open
Abstract
Honey is a suitable matrix for the evaluation of environmental contaminants including organochlorine insecticides. The present study was conducted to evaluate residues of fifteen organochlorine insecticides in honey samples of unifloral and multifloral origins from Dir, Pakistan. Honey samples (5 g each) were extracted with GC grade organic solvents and then subjected to Rotary Evaporator till dryness. The extracts were then mixed with n-Hexane (5 ml) and purified through Column Chromatography. Purified extracts (1μl each) were processed through Gas Chromatograph coupled with Electron Capture Detector (GC-ECD) for identification and quantification of the insecticides. Of the 15 insecticides tested, 46.7% were detected while 53.3% were not detected in the honey samples. Heptachlor was the most prevalent insecticide with a mean level of 0.0018 mg/kg detected in 80% of the samples followed by β-HCH with a mean level of 0.0016 mg/kg detected in 71.4% of the honey samples. Honey samples from Acacia modesta Wall. were 100% positive for Heptachlor with a mean level of 0.0048 mg/kg followed by β-HCH with a mean level of 0.003 mg/kg and frequency of 83.3%. Minimum levels of the tested insecticides were detected in the unifloral honey from Ziziphus jujuba Mill. Methoxychlor, Endosulfan, Endrin and metabolites of DDT were not detected in the studied honey samples. Some of the tested insecticides are banned in Pakistan but are still detected in honey samples indicating their use in the study area. The detected levels of all insecticides were below the Maximum Residue Levels (MRLs) and safe for consumers. However, the levels detected can cause mortality in insect fauna. The use of banned insecticides is one of the main factors responsible for the declining populations of important insect pollinators including honeybees.
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Affiliation(s)
- M Attaullah
- University of Malakand, Department of Zoology, Chakdara, Dir Lower, Pakistan
| | - M A Nawaz
- Shaheed Benazir Bhutto University, Department of Biotechnology, Dir Upper, Pakistan
| | - I Ilahi
- University of Malakand, Department of Zoology, Chakdara, Dir Lower, Pakistan
| | - H Ali
- University of Malakand, Department of Chemistry, Chakdara, Dir Lower, Pakistan
| | - T Jan
- University of Malakand, Department of Botany, Chakdara, Dir Lower, Pakistan
| | - S Khwaja
- Federal Urdu University of Arts, Science and Technology, Department of Zoology, Karachi, Pakistan
| | - A Hazrat
- University of Malakand, Department of Botany, Chakdara, Dir Lower, Pakistan
| | - I Ullah
- University of Malakand, Department of Zoology, Chakdara, Dir Lower, Pakistan
| | - Z Ullah
- University of Malakand, Department of Zoology, Chakdara, Dir Lower, Pakistan
| | - S Ullah
- University of Malakand, Department of Botany, Chakdara, Dir Lower, Pakistan
| | - B Ahmad
- University of Malakand, Department of Zoology, Chakdara, Dir Lower, Pakistan
| | - R Ullah
- Shaheed Benazir Bhutto University, Department of Zoology, Dir Upper, Pakistan
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Kurt C, Demirbas A, Nawaz MA, Chung G, Baloch FS, Altunay N. Determination of Se content of 78 sesame accessions with different geographical origin. J Food Compost Anal 2020. [DOI: 10.1016/j.jfca.2020.103621] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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10
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Nawaz MA, Azeem F, Zakharenko AM, Lin X, Atif RM, Baloch FS, Chan TF, Chung G, Ham J, Sun S, Golokhvast KS. In-silico Exploration of Channel Type and Efflux Silicon Transporters and Silicification Proteins in 80 Sequenced Viridiplantae Genomes. Plants (Basel) 2020; 9:plants9111612. [PMID: 33233677 PMCID: PMC7709012 DOI: 10.3390/plants9111612] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Revised: 11/17/2020] [Accepted: 11/18/2020] [Indexed: 12/29/2022]
Abstract
Silicon (Si) accumulation protects plants from biotic and abiotic stresses. It is transported and distributed within the plant body through a cooperative system of channel type (e.g., OsLsi1) and efflux (Lsi2s e.g., OsLsi2) Si transporters (SITs) that belong to Noduline-26 like intrinsic protein family of aquaporins and an uncharacterized anion transporter family, respectively. Si is deposited in plant tissues as phytoliths and the process is known as biosilicification but the knowledge about the proteins involved in this process is limited. In the present study, we explored channel type SITs and Lsi2s, and siliplant1 protein (Slp1) in 80 green plant species. We found 80 channel type SITs and 133 Lsi2s. The channel type SITs characterized by the presence of two NPA motifs, GSGR or STAR selectivity filter, and 108 amino acids between two NPA motifs were absent from Chlorophytes, while Streptophytes evolved two different types of channel type SITs with different selectivity filters. Both channel type SITs and Lsi2s evolved two types of gene structures each, however, Lsi2s are ancient and were also found in Chlorophyta. Homologs of Slp1 (225) were present in almost all Streptophytes regardless of their Si accumulation capacity. In Si accumulator plant species, the Slp1s were characterized by the presence of H, D-rich domain, P, K, E-rich domain, and P, T, Y-rich domain, while moderate Si accumulators lacked H, D-rich domain and P, T, Y-rich domains. The digital expression analysis and coexpression networks highlighted the role of channel type and Lsi2s, and how Slp1 homologs were ameliorating plants’ ability to withstand different stresses by co-expressing with genes related to structural integrity and signaling. Together, the in-silico exploration made in this study increases our knowledge of the process of biosilicification in plants.
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Affiliation(s)
- Muhammad Amjad Nawaz
- Laboratory of Bio-Economics and Biotechnology, Department of Bio-Economics and Food Safety, School of Economics and Management, Far Eastern Federal University, 690950 Vladivostok, Russia;
| | - Farrukh Azeem
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad 38000, Pakistan;
| | | | - Xiao Lin
- Center for Soybean Research, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong SAR, Hong Kong 999077, China; (X.L.); (T.-F.C.)
| | - Rana Muhammad Atif
- US-Pakistan Centre for Advanced Studies in Agriculture and Food Security, University of Agriculture, Faisalabad 38040, Pakistan;
| | - Faheem Shehzad Baloch
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas 58140, Turkey;
| | - Ting-Fung Chan
- Center for Soybean Research, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong SAR, Hong Kong 999077, China; (X.L.); (T.-F.C.)
| | - Gyuhwa Chung
- Department of Biotechnology, Chonnam National University, Chonnam 59626, Korea;
| | - Junghee Ham
- Department of Health Policy and Management, Wonkwang University, Iksan, Jeonbuk 54538, Korea;
| | - Sangmi Sun
- Department of Biotechnology, Chonnam National University, Chonnam 59626, Korea;
- Correspondence: (S.S.); (K.S.G.)
| | - Kirill S. Golokhvast
- N.I. Vavilov All-Russian Institute of Plant Genetic Resources, 42, 44 Bolshaya Morskaya Street, 190000 St. Petersburg, Russia;
- Education and Scientific Center of Nanotechnology, Far Eastern Federal University, 690950 Vladivostok, Russia
- Pacific Geographical Institute, FEB RAS, 7 Radio street, 690014 Vladivostok, Russia
- Correspondence: (S.S.); (K.S.G.)
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11
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Lavrent'yeva SI, Chernyshuk DK, Martinenko NV, Ivachenko LE, Arsene AL, Ercisli S, Tsatsakis AM, Golokhvast KS, Nawaz MA. Biochemical adaptation of wild and cultivated soybean against toxicity of lead salts. Environ Toxicol Pharmacol 2020; 79:103429. [PMID: 32473423 DOI: 10.1016/j.etap.2020.103429] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 05/22/2020] [Accepted: 05/25/2020] [Indexed: 06/11/2023]
Abstract
Agricultural production is becoming increasingly dependent on the environmental factors that alter soil properties, plant productivity, and product quality. Environment pollution caused by heavy metals because of human activities are among the most dangerous pollutants on the biosphere. Here, we have studied the biochemical adaptation of wild and cultivated soybeans to the simulated effects of lead nitrate and lead acetate. Lead in the form of acetate had a relevant toxic effect, as evidenced by a significant increase in the concentration of malonic dialdehyde in the treated samples relative to control samples. Catalase and peroxidase, possibly performing a signaling function, are involved in the adaptation to the toxicity of Pb salts. The studied Pb salts showed a predominant stimulating effect on the specific activity of acid phosphatases in cultivated soybean, while the ribonuclease activity changed in both Glycine species. Moreover, in wild soybean, it was mostly suppressive, except for the first day. We found that the electrophoretic spectra of acid phosphatases of soybean seedlings was highly stabile, while that of ribonucleases varied depending on the salt. On the seventh day of exposure, lead nitrate caused a decrease in the specific activity of the studied hydrolases of seedlings of cultivated and wild soybeans. A change in the number or electrophoretic mobility of multiple forms of enzymes during treatment with Pb salts was revealed, which indicates the adaptation of the plants at the molecular genetic level. These results imply that the observed enzymes can be used as sensitive indicators for predicting the effects of heavy metals on soybean.
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Affiliation(s)
- Svetlana Igorevna Lavrent'yeva
- Blagoveshchensk State Pedagogical University, Blagoveshchensk, Russia; All-Russian Scientific Research Institute of Soybean, Blagoveshchensk, Russia; Education and Scientific Center of Nanotechnology, Far Eastern Federal University, Vladivostok, 690950, Russia
| | - Darya Konstantinovna Chernyshuk
- Blagoveshchensk State Pedagogical University, Blagoveshchensk, Russia; All-Russian Scientific Research Institute of Soybean, Blagoveshchensk, Russia
| | | | - Lubov Egorovna Ivachenko
- Blagoveshchensk State Pedagogical University, Blagoveshchensk, Russia; All-Russian Scientific Research Institute of Soybean, Blagoveshchensk, Russia
| | - Andreea L Arsene
- Department of General and Pharmaceutical Microbiology, Faculty of Pharmacy, University of Medicine and Pharmacy, Romania
| | - Sezai Ercisli
- Department of Horticulture, Faculty of Agriculture, Ataturk University, 25240, Erzurum, Turkey
| | | | - Kirill Sergeyvich Golokhvast
- Education and Scientific Center of Nanotechnology, Far Eastern Federal University, Vladivostok, 690950, Russia; Pacific Institute of Geography, Far Eastern Branch of the Russian Academy of Sciences, 690041, Vladivostok, Russia; N.I. Vavilov All-Russian Institute of Plant Genetic Resources, 42 Bolshaya Morskaya St., 44, St. Petersburg, Russia
| | - Muhammad Amjad Nawaz
- Education and Scientific Center of Nanotechnology, Far Eastern Federal University, Vladivostok, 690950, Russia.
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Ahmad B, Azeem F, Ali MA, Nawaz MA, Nadeem H, Abbas A, Batool R, Atif RM, Ijaz U, Nieves-Cordones M, Chung G. Genome-wide identification and expression analysis of two component system genes in Cicer arietinum. Genomics 2020; 112:1371-1383. [DOI: 10.1016/j.ygeno.2019.08.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 07/19/2019] [Accepted: 08/11/2019] [Indexed: 10/26/2022]
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13
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Babar U, Nawaz MA, Arshad U, Azhar MT, Atif RM, Golokhvast KS, Tsatsakis AM, Shcerbakova K, Chung G, Rana IA. Transgenic crops for the agricultural improvement in Pakistan: a perspective of environmental stresses and the current status of genetically modified crops. GM Crops Food 2019; 11:1-29. [PMID: 31679447 DOI: 10.1080/21645698.2019.1680078] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Transgenic technologies have emerged as a powerful tool for crop improvement in terms of yield, quality, and quantity in many countries of the world. However, concerns also exist about the possible risks involved in transgenic crop cultivation. In this review, literature is analyzed to gauge the real intensity of the issues caused by environmental stresses in Pakistan. In addition, the research work on genetically modified organisms (GMOs) development and their performance is analyzed to serve as a guide for the scientists to help them select useful genes for crop transformation in Pakistan. The funding of GMOs research in Pakistan shows that it does not follow the global trend. We also present socio-economic impact of GM crops and political dimensions in the seed sector and the policies of the government. We envisage that this review provides guidelines for public and private sectors as well as the policy makers in Pakistan and in other countries that face similar environmental threats posed by the changing climate.
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Affiliation(s)
- Usman Babar
- Center of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Pakistan
| | - Muhammad Amjad Nawaz
- Education and Scientific Center of Nanotechnology, Far Eastern Federal University, Vladivostok, Russian Federation
| | - Usama Arshad
- Center of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Pakistan
| | - Muhammad Tehseen Azhar
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, Pakistan
| | - Rana Muhammad Atif
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, Pakistan.,Centre for Advanced Studies in Agriculture and Food Security, University of Agriculture, Faisalabad, Pakistan
| | - Kirill S Golokhvast
- Education and Scientific Center of Nanotechnology, Far Eastern Federal University, Vladivostok, Russian Federation
| | - Aristides M Tsatsakis
- Department of Toxicology and Forensics, School of Medicine, University of Crete, Heraklion, Greece
| | - Kseniia Shcerbakova
- Education and Scientific Center of Nanotechnology, Far Eastern Federal University, Vladivostok, Russian Federation
| | - Gyuhwa Chung
- Department of Biotechnology, Chonnam National University, Yeosu, Republic of Korea
| | - Iqrar Ahmad Rana
- Center of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Pakistan.,Centre for Advanced Studies in Agriculture and Food Security, University of Agriculture, Faisalabad, Pakistan
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14
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Atif RM, Shahid L, Waqas M, Ali B, Rashid MAR, Azeem F, Nawaz MA, Wani SH, Chung G. Insights on Calcium-Dependent Protein Kinases (CPKs) Signaling for Abiotic Stress Tolerance in Plants. Int J Mol Sci 2019; 20:E5298. [PMID: 31653073 PMCID: PMC6862689 DOI: 10.3390/ijms20215298] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 10/16/2019] [Accepted: 10/17/2019] [Indexed: 12/18/2022] Open
Abstract
Abiotic stresses are the major limiting factors influencing the growth and productivity of plants species. To combat these stresses, plants can modify numerous physiological, biochemical, and molecular processes through cellular and subcellular signaling pathways. Calcium-dependent protein kinases (CDPKs or CPKs) are the unique and key calcium-binding proteins, which act as a sensor for the increase and decrease in the calcium (Ca) concentrations. These Ca flux signals are decrypted and interpreted into the phosphorylation events, which are crucial for signal transduction processes. Several functional and expression studies of different CPKs and their encoding genes validated their versatile role for abiotic stress tolerance in plants. CPKs are indispensable for modulating abiotic stress tolerance through activation and regulation of several genes, transcription factors, enzymes, and ion channels. CPKs have been involved in supporting plant adaptation under drought, salinity, and heat and cold stress environments. Diverse functions of plant CPKs have been reported against various abiotic stresses in numerous research studies. In this review, we have described the evaluated functions of plant CPKs against various abiotic stresses and their role in stress response signaling pathways.
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Affiliation(s)
- Rana Muhammad Atif
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad 38000, Pakistan.
- Center for Advanced Studies in Agriculture and Food Security, University of Agriculture, Faisalabad 38040, Pakistan.
| | - Luqman Shahid
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad 38000, Pakistan.
| | - Muhammad Waqas
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad 38000, Pakistan.
| | - Babar Ali
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad 38000, Pakistan.
| | - Muhammad Abdul Rehman Rashid
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad 38000, Pakistan.
- Industrial Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming 650200, China.
| | - Farrukh Azeem
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad 38040, Pakistan.
| | - Muhammad Amjad Nawaz
- Education Scientific Center of Nanotechnology, Far Eastern Federal University, 690950 Vladivostok, Russia.
| | - Shabir Hussain Wani
- Mountain Research Centre for Field Crops, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar 190001, India.
| | - Gyuhwa Chung
- Department of Biotechnology, Chonnam National University, Chonnam 59626, Korea.
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15
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Nawaz MA, Zakharenko AM, Zemchenko IV, Haider MS, Ali MA, Imtiaz M, Chung G, Tsatsakis A, Sun S, Golokhvast KS. Phytolith Formation in Plants: From Soil to Cell. Plants (Basel) 2019; 8:E249. [PMID: 31357485 PMCID: PMC6724085 DOI: 10.3390/plants8080249] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Revised: 07/22/2019] [Accepted: 07/23/2019] [Indexed: 01/19/2023]
Abstract
Silica is deposited extra- and intracellularly in plants in solid form, as phytoliths. Phytoliths have emerged as accepted taxonomic tools and proxies for reconstructing ancient flora, agricultural economies, environment, and climate. The discovery of silicon transporter genes has aided in the understanding of the mechanism of silicon transport and deposition within the plant body and reconstructing plant phylogeny that is based on the ability of plants to accumulate silica. However, a precise understanding of the process of silica deposition and the formation of phytoliths is still an enigma and the information regarding the proteins that are involved in plant biosilicification is still scarce. With the observation of various shapes and morphologies of phytoliths, it is essential to understand which factors control this mechanism. During the last two decades, significant research has been done in this regard and silicon research has expanded as an Earth-life science superdiscipline. We review and integrate the recent knowledge and concepts on the uptake and transport of silica and its deposition as phytoliths in plants. We also discuss how different factors define the shape, size, and chemistry of the phytoliths and how biosilicification evolved in plants. The role of channel-type and efflux silicon transporters, proline-rich proteins, and siliplant1 protein in transport and deposition of silica is presented. The role of phytoliths against biotic and abiotic stress, as mechanical barriers, and their use as taxonomic tools and proxies, is highlighted.
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Affiliation(s)
- Muhammad Amjad Nawaz
- Education and Scientific Center of Nanotechnology, Far Eastern Federal University, 690950 Vladivostok, Russia
| | | | | | - Muhammad Sajjad Haider
- Department of Forestry, College of Agriculture, University of Sargodha, 40100 Sargodha, Pakistan
| | - Muhammad Amjad Ali
- Department of Plant Pathology, University of Agriculture, 38040 Faisalabad, Pakistan
- Center of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, 38040 Faisalabad, Pakistan
| | - Muhammad Imtiaz
- Soil and Environmental Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, 38040 Faisalabad, Pakistan
| | - Gyuhwa Chung
- Department of Biotechnology, Chonnam National University, 59626 Yeosu-Si, Korea
| | - Aristides Tsatsakis
- Department of Toxicology and Forensics, School of Medicine, University of Crete, Heraklion GR-71003, Crete, Greece
| | - Sangmi Sun
- Department of Biotechnology, Chonnam National University, 59626 Yeosu-Si, Korea.
| | - Kirill Sergeyevich Golokhvast
- Education and Scientific Center of Nanotechnology, Far Eastern Federal University, 690950 Vladivostok, Russia.
- Pacific Geographical Institute, FEB RAS, 7 Radio street, Vladivostok 690014, Russia.
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16
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Lavrent`yeva SI, Ivachenko LY, Golokhvast KS, Nawaz MA. Ribonuclease activity of Glycine max and Glycine soja sprouts as a marker adaptation to copper sulphate and zinc sulphate toxicity. BIOCHEM SYST ECOL 2019. [DOI: 10.1016/j.bse.2019.01.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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17
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Nadeem MA, Habyarimana E, Çiftçi V, Nawaz MA, Karaköy T, Comertpay G, Shahid MQ, Hatipoğlu R, Yeken MZ, Ali F, Ercişli S, Chung G, Baloch FS. Characterization of genetic diversity in Turkish common bean gene pool using phenotypic and whole-genome DArTseq-generated silicoDArT marker information. PLoS One 2018; 13:e0205363. [PMID: 30308006 PMCID: PMC6181364 DOI: 10.1371/journal.pone.0205363] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2018] [Accepted: 09/20/2018] [Indexed: 12/31/2022] Open
Abstract
Turkey presents a great diversity of common bean landraces in farmers' fields. We collected 183 common bean accessions from 19 different Turkish geographic regions and 5 scarlet runner bean accessions to investigate their genetic diversity and population structure using phenotypic information (growth habit, and seed weight, flower color, bracteole shape and size, pod shape and leaf shape and color), geographic provenance and 12,557 silicoDArT markers. A total of 24.14% markers were found novel. For the entire population (188 accessions), the expected heterozygosity was 0.078 and overall gene diversity, Fst and Fis were 0.14, 0.55 and 1, respectively. Using marker information, model-based structure, principal coordinate analysis (PCoA) and unweighted pair-group method with arithmetic means (UPGMA) algorithms clustered the 188 accessions into two main populations A (predominant) and B, and 5 unclassified genotypes, representing 3 meaningful heterotic groups for breeding purposes. Phenotypic information clearly distinguished these populations; population A and B, respectively, were bigger (>40g/100 seeds) and smaller (<40g/100 seeds) seed-sized. The unclassified population was pure and only contained climbing genotypes with 100 seed weight 2-3 times greater than populations A and B. Clustering was mainly based on A: seed weight, B: growth habit, C: geographical provinces and D: flower color. Mean kinship was generally low, but population B was more diverse than population A. Overall, a useful level of gene and genotypic diversity was observed in this work and can be used by the scientific community in breeding efforts to develop superior common bean strains.
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Affiliation(s)
- Muhammad Azhar Nadeem
- Department of field crops, Faculty of Agricultural and Natural Science, Abant Izzet Baysal University, Bolu, Turkey
| | - Ephrem Habyarimana
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria–Centro di ricerca cerealicoltura e colture industriali, Bologna, Italy
| | - Vahdettin Çiftçi
- Department of field crops, Faculty of Agricultural and Natural Science, Abant Izzet Baysal University, Bolu, Turkey
| | - Muhammad Amjad Nawaz
- Department of Biotechnology, Chonnam National University, Chonnam, Republic of Korea
| | - Tolga Karaköy
- Organic Agriculture Program, Vocational School of Sivas, University of Cumhuriyet, Sivas, Turkey
| | - Gonul Comertpay
- Eastern Mediterranean Agricultural Research Institute, Turkey
| | - Muhammad Qasim Shahid
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bio resources, South China Agricultural University, Guangzhou, China
| | - Rüştü Hatipoğlu
- Department of Field Crops, Faculty of Agricultural, University of Cukurova, Adana, Turkey
| | - Mehmet Zahit Yeken
- Department of field crops, Faculty of Agricultural and Natural Science, Abant Izzet Baysal University, Bolu, Turkey
| | - Fawad Ali
- Department of field crops, Faculty of Agricultural and Natural Science, Abant Izzet Baysal University, Bolu, Turkey
| | - Sezai Ercişli
- Department of Horticulture, Faculty of Agriculture, Ataturk University, Erzurum, Turkey
| | - Gyuhwa Chung
- Department of Biotechnology, Chonnam National University, Chonnam, Republic of Korea
| | - Faheem Shehzad Baloch
- Department of field crops, Faculty of Agricultural and Natural Science, Abant Izzet Baysal University, Bolu, Turkey
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18
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Nawaz MA, Lin X, Chan TF, Imtiaz M, Rehman HM, Ali MA, Baloch FS, Atif RM, Yang SH, Chung G. Characterization of Cellulose Synthase A (CESA) Gene Family in Eudicots. Biochem Genet 2018; 57:248-272. [PMID: 30267258 DOI: 10.1007/s10528-018-9888-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 09/20/2018] [Indexed: 12/30/2022]
Abstract
Cellulose synthase A (CESA) is a key enzyme involved in the complex process of plant cell wall biosynthesis, and it remains a productive subject for research. We employed systems biology approaches to explore structural diversity of eudicot CESAs by exon-intron organization, mode of duplication, synteny, and splice site analyses. Using a combined phylogenetics and comparative genomics approach coupled with co-expression networks we reconciled the evolution of cellulose synthase gene family in eudicots and found that the basic forms of CESA proteins are retained in angiosperms. Duplications have played an important role in expansion of CESA gene family members in eudicots. Co-expression networks showed that primary and secondary cell wall modules are duplicated in eudicots. We also identified 230 simple sequence repeat markers in 103 eudicot CESAs. The 13 identified conserved motifs in eudicots will provide a basis for gene identification and functional characterization in other plants. Furthermore, we characterized (in silico) eudicot CESAs against senescence and found that expression levels of CESAs decreased during leaf senescence.
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Affiliation(s)
- Muhammad Amjad Nawaz
- Department of Biotechnology, Chonnam National University, Chonnam, 59626, Republic of Korea
| | - Xiao Lin
- Center for Soybean Research, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, SAR, China
| | - Ting-Fung Chan
- Center for Soybean Research, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, SAR, China
| | - Muhammad Imtiaz
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510275, China
| | - Hafiz Mamoon Rehman
- Department of Biotechnology, Chonnam National University, Chonnam, 59626, Republic of Korea
| | - Muhammad Amjad Ali
- Department of Plant Pathology, University of Agriculture, Faisalabad, 38040, Pakistan
| | - Faheem Shehzad Baloch
- Department of Field Crops, Faculty of Agricultural and Natural Science, Abant Izzet Baysal University, 14280, Bolu, Turkey
| | - Rana Muhammad Atif
- US-Pakistan Centre for Advanced Studies in Agriculture and Food Security, University of Agriculture, Faisalabad, 38040, Pakistan
| | - Seung Hwan Yang
- Department of Biotechnology, Chonnam National University, Chonnam, 59626, Republic of Korea.
| | - Gyuhwa Chung
- Department of Biotechnology, Chonnam National University, Chonnam, 59626, Republic of Korea.
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Imtiaz M, Mushtaq MA, Nawaz MA, Ashraf M, Rizwan MS, Mehmood S, Aziz O, Rizwan M, Virk MS, Shakeel Q, Ijaz R, Androutsopoulos VP, Tsatsakis AM, Coleman MD. Physiological and anthocyanin biosynthesis genes response induced by vanadium stress in mustard genotypes with distinct photosynthetic activity. Environ Toxicol Pharmacol 2018; 62:20-29. [PMID: 29935434 DOI: 10.1016/j.etap.2018.06.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 06/06/2018] [Accepted: 06/12/2018] [Indexed: 06/08/2023]
Abstract
The present study aimed to elucidate the photosynthetic performance, antioxidant enzyme activities, anthocyanin contents, anthocyanin biosynthetic gene expression, and vanadium uptake in mustard genotypes (purple and green) that differ in photosynthetic capacity under vanadium stress. The results indicated that vanadium significantly reduced photosynthetic activity in both genotypes. The activities of the antioxidant enzymes were increased significantly in response to vanadium in both genotypes, although the purple exhibited higher. The anthocyanin contents were also reduced under vanadium stress. The anthocyanin biosynthetic genes were highly expressed in the purple genotype, notably the genes TT8, F3H, and MYBL2 under vanadium stress. The results indicate that induction of TT8, F3H, and MYBL2 genes was associated with upregulation of the biosynthetic genes required for higher anthocyanin biosynthesis in purple compared with the green mustard. The roots accumulated higher vanadium than shoots in both mustard genotypes. The results indicate that the purple mustard had higher vanadium tolerance.
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Affiliation(s)
- Muhammad Imtiaz
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China; Soil and Environmental Sciences Division, Nuclear Institute for Food and Agriculture, Peshawar, Pakistan.
| | - Muhammad Adnan Mushtaq
- College of Plant Sciences and Technology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Muhammad Amjad Nawaz
- Department of Biotechnology, Chonnam National University, Chonnam, 59626, Republic of Korea.
| | - Muhammad Ashraf
- Department of Soil and Environmental Sciences, University College of Agriculture, University of Sargodha, Sargodha, 40100, Pakistan.
| | - Muhammad Shahid Rizwan
- Cholistan Institute of Desert Studies, The Islamia University of Bahawalpur, 63100, Pakistan.
| | - Sajid Mehmood
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Omar Aziz
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Muhammad Rizwan
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Muhammad Safiullah Virk
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Qaiser Shakeel
- Discipline of Plant Pathology, University College of Agriculture and Environmental Sciences, The Islamia University of Bahawalpur, 63100, Pakistan.
| | - Raina Ijaz
- Department of Horticulture, The University of Poonch Rawalakot, Azad Kashmir, Pakistan.
| | - Vasilis P Androutsopoulos
- Department of Toxicology and Foresnsics, School of Medicine, University of Crete, Herakion, 71003, Greece.
| | - Aristides M Tsatsakis
- Department of Toxicology and Foresnsics, School of Medicine, University of Crete, Herakion, 71003, Greece.
| | - Michael D Coleman
- School of Life and Health Sciences, Aston University, Birmingham, United Kingdom.
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20
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Imtiaz M, Ashraf M, Rizwan MS, Nawaz MA, Rizwan M, Mehmood S, Yousaf B, Yuan Y, Ditta A, Mumtaz MA, Ali M, Mahmood S, Tu S. Vanadium toxicity in chickpea (Cicer arietinum L.) grown in red soil: Effects on cell death, ROS and antioxidative systems. Ecotoxicol Environ Saf 2018; 158:139-144. [PMID: 29677596 DOI: 10.1016/j.ecoenv.2018.04.022] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 04/06/2018] [Accepted: 04/09/2018] [Indexed: 06/08/2023]
Abstract
The agricultural soil contaminated with heavy metals induces toxic effects on plant growth. The present study was conducted to evaluate the effects of vanadium (V) on growth, H2O2 and enzyme activities, cell death, ion leakage, and at which concentration; V induces the toxic effects in chickpea plants grown in red soil. The obtained results indicated that the biomass (fresh and dry) and lengths of roots and shoots were significantly decreased by V application, and roots accumulated more V than shoots. The enzyme activities (SOD, CAT, and POD) and ion leakage were increased linearly with increasing V concentrations. However, the protein contents, and tolerance indices were significantly declined with the increasing levels of V. The results about the cell death indicated that the cell viability was badly damaged when plants were exposed to higher V, and induction of H2O2 might be involved in this cell death. In conclusion, all the applied V levels affected the enzymatic activities, and induced the cell death of chickpea plants. Furthermore, our results also confirmed that vanadium ≥ 130 mg kg-1 induced detrimental effects on chickpea plants. Additional investigation is needed to clarify the mechanistic explanations of V toxicity at the molecular level and gene expression involved in plant cell death.
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Affiliation(s)
- Muhammad Imtiaz
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou 510006, China; Soil and Environmental Sciences Division, Nuclear Institute for Food and Agriculture, Peshawar, Pakistan.
| | - Muhammad Ashraf
- Department of Soil and Environmental Sciences, University College of Agriculture, University of Sargodha, Sargodha 40100, Pakistan.
| | - Muhammad Shahid Rizwan
- Cholistan Institute of Desert Studies, The Islamia University of Bahawalpur, 63100, Pakistan.
| | - Muhammad Amjad Nawaz
- Department of Biotechnology, Chonnam National University, Chonnam 59626, Republic of Korea.
| | - Muhammad Rizwan
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China.
| | - Sajid Mehmood
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China.
| | - Balal Yousaf
- CAS-Key Laboratory of Crust-Mantle Materials and the Environments, School of Earth and Space Sciences, University of Science and Technology of China, Hefei 230026, China.
| | - Yuan Yuan
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China.
| | - Allah Ditta
- Department of Environmental Sciences, Shaheed Benazir Bhutto University, Sheringal, Dir (U) 18000, Pakistan.
| | - Muhammad Ali Mumtaz
- Key Laboratory of Horticultural Plant Biology, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China.
| | - Muhammad Ali
- Biotechnology Program, Department of Environmental Sciences, COMSATS Institute of Information Technology, Abbottabad 22010, Pakistan.
| | - Sammina Mahmood
- Department of Botany, Government College Women University, Faisalabad 38000, Pakistan.
| | - Shuxin Tu
- Department of Biotechnology, Chonnam National University, Chonnam 59626, Republic of Korea.
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Ali MA, Azeem F, Nawaz MA, Acet T, Abbas A, Imran QM, Shah KH, Rehman HM, Chung G, Yang SH, Bohlmann H. Transcription factors WRKY11 and WRKY17 are involved in abiotic stress responses in Arabidopsis. J Plant Physiol 2018; 226:12-21. [PMID: 29689430 DOI: 10.1016/j.jplph.2018.04.007] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 03/14/2018] [Accepted: 04/14/2018] [Indexed: 05/28/2023]
Abstract
Plant WRKY transcription factors play a vital role in abiotic stress tolerance and regulation of plant defense responses. This study examined AtWRKY11 and AtWRKY17 expression under ABA, salt, and osmotic stress at different developmental stages in Arabidopsis. We used reverse transcriptase PCR, quantitative real-time PCR, and promoter:GUS lines to analyze expression. Both genes were upregulated in response to abiotic stress. Next, we applied the same stressors to seedlings of T-DNA insertion wrky11 and 17 knock-out mutants (single and double). Under stress, the mutants exhibited slower germination and compromised root growth compared with the wild type. In most cases, double-mutant seedlings were more affected than single mutants. These results suggest that wrky11 and wrky17 are not strictly limited to plant defense responses but are also involved in conferring stress tolerance.
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Affiliation(s)
- Muhammad Amjad Ali
- Department of Plant Pathology, University of Agriculture, 38040 Faisalabad, Pakistan; Centre of Agricultural Biochemistry and Biotechnology, University of Agriculture, 38040 Faisalabad, Pakistan.
| | - Farrukh Azeem
- Department of Bioinformatics and Biotechnology, Govt. College University, Faisalabad, Pakistan
| | - Muhammad Amjad Nawaz
- Department of Biotechnology, Chonnam National University, Yeosu, Chonnam, 59626, South Korea
| | - Tuba Acet
- Department of Genetic and Bioengineering, Faculty of Engineering and Natural Sciences, Gumusahne University, 29100, Gumushane, Turkey
| | - Amjad Abbas
- Department of Plant Pathology, University of Agriculture, 38040 Faisalabad, Pakistan
| | - Qari Muhammad Imran
- Laboratory of Plant Functional Genomics, College of Agriculture & Life Sciences, Kyngpook National University, Buk-gu Daegu, 702-701, South Korea
| | - Kausar Hussain Shah
- Institute of Pure and Applied Biology, Bahauddin Zakariya University, Multan, Pakistan
| | - Hafiz Mamoon Rehman
- Department of Biotechnology, Chonnam National University, Yeosu, Chonnam, 59626, South Korea
| | - Gyuhwa Chung
- Department of Biotechnology, Chonnam National University, Yeosu, Chonnam, 59626, South Korea
| | - Seung Hwan Yang
- Department of Biotechnology, Chonnam National University, Yeosu, Chonnam, 59626, South Korea.
| | - Holger Bohlmann
- Division of Plant Protection, Department of Crop Sciences, University of Natural Resources and Life Sciences, Vienna, Austria
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Ali MA, Anjam MS, Nawaz MA, Lam HM, Chung G. Signal Transduction in Plant⁻Nematode Interactions. Int J Mol Sci 2018; 19:ijms19061648. [PMID: 29865232 PMCID: PMC6032140 DOI: 10.3390/ijms19061648] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 05/26/2018] [Accepted: 05/29/2018] [Indexed: 12/26/2022] Open
Abstract
To successfully invade and infect their host plants, plant parasitic nematodes (PPNs) need to evolve molecular mechanisms to overcome the defense responses from the plants. Nematode-associated molecular patterns (NAMPs), including ascarosides and certain proteins, while instrumental in enabling the infection, can be perceived by the host plants, which then initiate a signaling cascade leading to the induction of basal defense responses. To combat host resistance, some nematodes can inject effectors into the cells of susceptible hosts to reprogram the basal resistance signaling and also modulate the hosts’ gene expression patterns to facilitate the establishment of nematode feeding sites (NFSs). In this review, we summarized all the known signaling pathways involved in plant–nematode interactions. Specifically, we placed particular focus on the effector proteins from PPNs that mimic the signaling of the defense responses in host plants. Furthermore, we gave an updated overview of the regulation by PPNs of different host defense pathways such as salicylic acid (SA)/jasmonic acid (JA), auxin, and cytokinin and reactive oxygen species (ROS) signaling to facilitate their parasitic successes in plants. This review will enhance the understanding of the molecular signaling pathways involved in both compatible and incompatible plant–nematode interactions.
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Affiliation(s)
- Muhammad Amjad Ali
- Department of Plant Pathology, University of Agriculture, Faisalabad 38040, Pakistan.
- Centre of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad 38040, Pakistan.
| | - Muhammad Shahzad Anjam
- Institute of Molecular Biology & Biotechnology, Bahauddin Zakariya University, Multan 66000, Pakistan.
| | | | - Hon-Ming Lam
- School of Life Sciences and Centre for Soybean Research of the Partner State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China.
| | - Gyuhwa Chung
- Department of Biotechnology, Chonnam National University, Yeosu 59626, Korea.
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Rehman HM, Nawaz MA, Shah ZH, Ludwig-Müller J, Chung G, Ahmad MQ, Yang SH, Lee SI. Author Correction: Comparative genomic and transcriptomic analyses of Family-1 UDP glycosyltransferase in three Brassica species and Arabidopsis indicates stress-responsive regulation. Sci Rep 2018; 8:6237. [PMID: 29651019 PMCID: PMC5897407 DOI: 10.1038/s41598-018-24107-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Hafiz Mamoon Rehman
- Department of Biotechnology, Chonnam National University, Yeosu, Chonnam, 59626, Korea
| | - Muhammad Amjad Nawaz
- Department of Biotechnology, Chonnam National University, Yeosu, Chonnam, 59626, Korea
| | - Zahid Hussain Shah
- Department of Arid Land Agriculture, King Abdul-Aziz University, Jeddah, Saudi Arabia
| | - Jutta Ludwig-Müller
- Institut für Botanik, Technische Universität Dresden, 01062, Dresden, Germany
| | - Gyuhwa Chung
- Department of Biotechnology, Chonnam National University, Yeosu, Chonnam, 59626, Korea
| | - Muhammad Qadir Ahmad
- Department of Plant Breeding and Genetics, Bahauddin Zakariya University, Multan, 6000, Pakistan
| | - Seung Hwan Yang
- Department of Biotechnology, Chonnam National University, Yeosu, Chonnam, 59626, Korea.
| | - Soo In Lee
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Jeonju, 54874, Republic of Korea.
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Nawaz MA, Golokhvast KS, Rehman HM, Tsukamoto C, Kim HS, Yang SH, Chung G. Soyisoflavone diversity in wild soybeans ( Glycine soja Sieb. & Zucc.) from the main centres of diversity. BIOCHEM SYST ECOL 2018. [DOI: 10.1016/j.bse.2018.01.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Rehman HM, Nawaz MA, Shah ZH, Yang SH, Chung G. Functional characterization of naturally occurring wild soybean mutant (sg-5) lacking astringent saponins using whole genome sequencing approach. Plant Sci 2018; 267:148-156. [PMID: 29362093 DOI: 10.1016/j.plantsci.2017.11.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 11/24/2017] [Accepted: 11/27/2017] [Indexed: 06/07/2023]
Abstract
Triterpenoid saponins are one of the most highly accumulated groups of functional components in soybean (Glycine max) and the oxidative reactions during their biosynthesis are required for their aglycone diversity. Natural mutants of soyasaponins in wild soybean (Glycine soja) are valuable resources for establishing the soyasaponin biosynthesis pathway and breeding new soybean varieties. In this study, we investigated the genetic mechanism behind the absence of group A saponins in a Korean wild soybean mutant, CWS5095. Whole genome sequencing (WGS) of CWS5095 identified four point mutations [Val6 → Asp, Ile231 → Thr, His294 → Gln, and Arg376 → Lys] in CYP72A69 (Glyma15g39090), which oxygenate the C-21 position of soyasapogenol B or other intermediates to produce soyasapogenol A, leading to group A saponin production. An in vitro enzyme activity assay of single-sited mutated clones indicated that the Arg376 > Lys mutation (a highly conserved mutation based on a nucleotide change from G → A at the 1,127th position) may lead to loss of gene function in the sg-5 mutant. A very high normalized expression value of 377 reads per kilo base per million (RPKM) of Glyma15g39090 in the hypocotyl axis at the early maturation seed-development stage confirmed their abundant presence in seed hypocotyls. A molecular dynamics analysis of the Arg376 > Lys mutation based on the CYP3A4 (a human CYP450) protein structure found that it was responsible for the increase in axis length toward the heme (active site), which is critically important for biological activity and ligand binding. Our results provide important information on how to eradicate bitter and astringent saponins in soybean by utilizing the reported mutation in Glyma15g39090, and its importance for seed hypocotyl development based on transcript abundance.
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Affiliation(s)
- Hafiz Mamoon Rehman
- Department of Biotechnology, Chonnam National University, Yeosu, Chonnam, 550-749, South Korea
| | - Muhammad Amjad Nawaz
- Department of Biotechnology, Chonnam National University, Yeosu, Chonnam, 550-749, South Korea
| | - Zahid Hussain Shah
- Department of Arid Land Agriculture, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Seung Hwan Yang
- Department of Biotechnology, Chonnam National University, Yeosu, Chonnam, 550-749, South Korea
| | - Gyuhwa Chung
- Department of Biotechnology, Chonnam National University, Yeosu, Chonnam, 550-749, South Korea.
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26
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Rehman HM, Nawaz MA, Shah ZH, Ludwig-Müller J, Chung G, Ahmad MQ, Yang SH, Lee SI. Comparative genomic and transcriptomic analyses of Family-1 UDP glycosyltransferase in three Brassica species and Arabidopsis indicates stress-responsive regulation. Sci Rep 2018; 8:1875. [PMID: 29382843 PMCID: PMC5789830 DOI: 10.1038/s41598-018-19535-3] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 01/03/2018] [Indexed: 12/25/2022] Open
Abstract
In plants, UGTs (UDP-glycosyltransferases) glycosylate various phytohormones and metabolites in response to biotic and abiotic stresses. Little is known about stress-responsive glycosyltransferases in plants. Therefore, it is important to understand the genomic and transcriptomic portfolio of plants with regard to biotic and abiotic stresses. Here, we identified 140, 154, and 251 putative UGTs in Brassica rapa, Brassica oleracea, and Brassica napus, respectively, and clustered them into 14 major phylogenetic groups (A–N). Fourteen major KEGG pathways and 24 biological processes were associated with the UGTs, highlighting them as unique modulators against environmental stimuli. Putative UGTs from B. rapa and B. oleracea showed a negative selection pressure and biased gene fractionation pattern during their evolution. Polyploidization increased the intron proportion and number of UGT-containing introns among Brassica. The putative UGTs were preferentially expressed in developing tissues and at the senescence stage. Differential expression of up- and down-regulated UGTs in response to phytohormone treatments, pathogen responsiveness and abiotic stresses, inferred from microarray and RNA-Seq data in Arabidopsis and Brassica broaden the glycosylation impact at the molecular level. This study identifies unique candidate UGTs for the manipulation of biotic and abiotic stress pathways in Brassica and Arabidopsis.
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Affiliation(s)
- Hafiz Mamoon Rehman
- Department of Biotechnology, Chonnam National University, Yeosu, Chonnam, 59626, Korea
| | - Muhammad Amjad Nawaz
- Department of Biotechnology, Chonnam National University, Yeosu, Chonnam, 59626, Korea
| | - Zahid Hussain Shah
- Department of Arid Land Agriculture, King Abdul-Aziz University, Jeddah, Saudi Arabia
| | - Jutta Ludwig-Müller
- Institut für Botanik, Technische Universität Dresden, 01062, Dresden, Germany
| | - Gyuhwa Chung
- Department of Biotechnology, Chonnam National University, Yeosu, Chonnam, 59626, Korea
| | - Muhammad Qadir Ahmad
- Department of Plant Breeding and Genetics, Bahauddin Zakariya University, Multan, 6000, Pakistan
| | - Seung Hwan Yang
- Department of Biotechnology, Chonnam National University, Yeosu, Chonnam, 59626, Korea.
| | - Soo In Lee
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Jeonju, 54874, Republic of Korea.
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Nadeem MA, Nawaz MA, Shahid MQ, Doğan Y, Comertpay G, Yıldız M, Hatipoğlu R, Ahmad F, Alsaleh A, Labhane N, Özkan H, Chung G, Baloch FS. DNA molecular markers in plant breeding: current status and recent advancements in genomic selection and genome editing. BIOTECHNOL BIOTEC EQ 2017. [DOI: 10.1080/13102818.2017.1400401] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Affiliation(s)
- Muhammad Azhar Nadeem
- Department of Field Crops, Faculty of Agricultural and Natural Sciences, Abant İzzet Baysal University, Bolu, Turkey
| | - Muhammad Amjad Nawaz
- Department of Biotechnology, School of Engineering, Chonnam National University, Yeosu, Korea
| | - Muhammad Qasim Shahid
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, South China Agricultural University, Guangzhou, P. R. China
| | - Yıldız Doğan
- Department of Field Crops, Eastern Mediterranean Agricultural Research Institute, Agricultural Ministry, Adana, Turkey
| | - Gonul Comertpay
- Department of Field Crops, Eastern Mediterranean Agricultural Research Institute, Agricultural Ministry, Adana, Turkey
| | - Mehtap Yıldız
- Department of Agricultural Biotechnology, Faculty of Agriculture, Yuzuncu Yıl University, Van, Turkey
| | - Rüştü Hatipoğlu
- Department of Field Crops, Faculty of Agriculture, University of Çukurova, Adana, Turkey
| | - Fiaz Ahmad
- Botany Division, Institute of Pure and Applied Biology, Bahauddin Zakariya University, Punjab, Pakistan
| | - Ahmad Alsaleh
- Molecular Genetics Laboratory, Science and Technology Application and Research Center, Bozok University, Yozgat, Turkey
| | - Nitin Labhane
- Department of Botany, Bhavan's College, University of Mumbai, Mumbai, India
| | - Hakan Özkan
- Department of Field Crops, Faculty of Agriculture, University of Çukurova, Adana, Turkey
| | - Gyuhwa Chung
- Department of Biotechnology, School of Engineering, Chonnam National University, Yeosu, Korea
| | - Faheem Shehzad Baloch
- Department of Field Crops, Faculty of Agricultural and Natural Sciences, Abant İzzet Baysal University, Bolu, Turkey
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28
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Nawaz MA, Rehman HM, Imtiaz M, Baloch FS, Lee JD, Yang SH, Lee SI, Chung G. Systems Identification and Characterization of Cell Wall Reassembly and Degradation Related Genes in Glycine max (L.) Merill, a Bioenergy Legume. Sci Rep 2017; 7:10862. [PMID: 28883533 PMCID: PMC5589831 DOI: 10.1038/s41598-017-11495-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 08/24/2017] [Indexed: 12/22/2022] Open
Abstract
Soybean is a promising biomass resource for generation of second-generation biofuels. Despite the utility of soybean cellulosic biomass and post-processing residues in biofuel generation, there is no comprehensive information available on cell wall loosening and degradation related gene families. In order to achieve enhanced lignocellulosic biomass with softened cell walls and reduced recalcitrance, it is important to identify genes involved in cell wall polymer loosening and degrading. Comprehensive genome-wide analysis of gene families involved in cell wall modifications is an efficient stratagem to find new candidate genes for soybean breeding for expanding biofuel industry. We report the identification of 505 genes distributed among 12 gene families related to cell wall loosening and degradation. 1262 tandem duplication events contributed towards expansion and diversification of studied gene families. We identified 687 Simple Sequence Repeat markers and 5 miRNA families distributed on 316 and 10 genes, respectively. Publically available microarray datasets were used to explore expression potential of identified genes in soybean plant developmental stages, 68 anatomical parts, abiotic and biotic stresses. Co-expression networks revealed transcriptional coordination of different gene families involved in cell wall loosening and degradation process.
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Affiliation(s)
- Muhammad Amjad Nawaz
- Department of Biotechnology, Chonnam National University, Chonnam, 59626, Republic of Korea
| | - Hafiz Mamoon Rehman
- Department of Biotechnology, Chonnam National University, Chonnam, 59626, Republic of Korea
| | - Muhammad Imtiaz
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510275, China
| | - Faheem Shehzad Baloch
- Department of Field Crops, Faculty of Agricultural and Natural Science, Abant Izzet Baysal University, 14280, Bolu, Turkey
| | - Jeong Dong Lee
- Division of Plant Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Seung Hwan Yang
- Department of Biotechnology, Chonnam National University, Chonnam, 59626, Republic of Korea
| | - Soo In Lee
- Metabolic Engineering Division, Department of Agricultural Biotechnology, National Institute of Agricultural Sciences (NAS), Jeonju, 54874, Republic of Korea.
| | - Gyuhwa Chung
- Department of Biotechnology, Chonnam National University, Chonnam, 59626, Republic of Korea.
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29
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Nawaz MA, Rehman HM, Baloch FS, Ijaz B, Ali MA, Khan IA, Lee JD, Chung G, Yang SH. Genome and transcriptome-wide analyses of cellulose synthase gene superfamily in soybean. J Plant Physiol 2017; 215:163-175. [PMID: 28704793 DOI: 10.1016/j.jplph.2017.04.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 04/12/2017] [Accepted: 04/14/2017] [Indexed: 05/28/2023]
Abstract
The plant cellulose synthase gene superfamily belongs to the category of type-2 glycosyltransferases, and is involved in cellulose and hemicellulose biosynthesis. These enzymes are vital for maintaining cell-wall structural integrity throughout plant life. Here, we identified 78 putative cellulose synthases (CS) in the soybean genome. Phylogenetic analysis against 40 reference Arabidopsis CS genes clustered soybean CSs into seven major groups (CESA, CSL A, B, C, D, E and G), located on 19 chromosomes (except chromosome 18). Soybean CS expansion occurred in 66 duplication events. Additionally, we identified 95 simple sequence repeat makers related to 44 CSs. We next performed digital expression analysis using publically available datasets to understand potential CS functions in soybean. We found that CSs were highly expressed during soybean seed development, a pattern confirmed with an Affymatrix soybean IVT array and validated with RNA-seq profiles. Within CS groups, CESAs had higher relative expression than CSLs. Soybean CS models were designed based on maximum average RPKM values. Gene co-expression networks were developed to explore which CSs could work together in soybean. Finally, RT-PCR analysis confirmed the expression of 15 selected CSs during all four seed developmental stages.
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Affiliation(s)
- Muhammad Amjad Nawaz
- Department of Biotechnology, Chonnam National University, Yeosu, Chonnam, 59626, Republic of Korea
| | - Hafiz Mamoon Rehman
- Department of Biotechnology, Chonnam National University, Yeosu, Chonnam, 59626, Republic of Korea
| | | | - Babar Ijaz
- Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
| | - Muhammad Amjad Ali
- Department of Plant Pathology, University of Agriculture, Faisalabad 38040, Pakistan
| | - Iqrar Ahmad Khan
- Institute of Horticultural Sciences, University of Agriculture, Faisalabad 38040, Pakistan
| | - Jeong Dong Lee
- Division of Plant Biosciences, Kyungpook National University, Daegu 702-701, Republic of Korea
| | - Gyuhwa Chung
- Department of Biotechnology, Chonnam National University, Yeosu, Chonnam, 59626, Republic of Korea.
| | - Seung Hwan Yang
- Department of Biotechnology, Chonnam National University, Yeosu, Chonnam, 59626, Republic of Korea.
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Tsatsakis AM, Nawaz MA, Kouretas D, Balias G, Savolainen K, Tutelyan VA, Golokhvast KS, Lee JD, Yang SH, Chung G. Environmental impacts of genetically modified plants: A review. Environ Res 2017; 156:818-833. [PMID: 28347490 DOI: 10.1016/j.envres.2017.03.011] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Revised: 03/07/2017] [Accepted: 03/08/2017] [Indexed: 06/06/2023]
Abstract
Powerful scientific techniques have caused dramatic expansion of genetically modified crops leading to altered agricultural practices posing direct and indirect environmental implications. Despite the enhanced yield potential, risks and biosafety concerns associated with such GM crops are the fundamental issues to be addressed. An increasing interest can be noted among the researchers and policy makers in exploring unintended effects of transgenes associated with gene flow, flow of naked DNA, weediness and chemical toxicity. The current state of knowledge reveals that GM crops impart damaging impacts on the environment such as modification in crop pervasiveness or invasiveness, the emergence of herbicide and insecticide tolerance, transgene stacking and disturbed biodiversity, but these impacts require a more in-depth view and critical research so as to unveil further facts. Most of the reviewed scientific resources provide similar conclusions and currently there is an insufficient amount of data available and up until today, the consumption of GM plant products are safe for consumption to a greater extent with few exceptions. This paper updates the undesirable impacts of GM crops and their products on target and non-target species and attempts to shed light on the emerging challenges and threats associated with it. Underpinning research also realizes the influence of GM crops on a disturbance in biodiversity, development of resistance and evolution slightly resembles with the effects of non-GM cultivation. Future prospects are also discussed.
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Affiliation(s)
- Aristidis M Tsatsakis
- Department of Toxicology and Forensics, School of Medicine, University of Crete, Heraklion, Crete, Greece; Educational Scientific Center of Nanotechnology, Far Eastern Federal University, Vladivostok 690950, Russian Federation
| | - Muhammad Amjad Nawaz
- Department of Biotechnology, Chonnam National University, Yeosu, Chonnam 59626, Republic of Korea
| | - Demetrios Kouretas
- Department of Biochemistry-Biotechnology, University of Thessaly, Larisa, Greece
| | | | - Kai Savolainen
- Finnish Institute of Occupational Health, POB 40 Helsinki, Finland
| | - Victor A Tutelyan
- Federal Research Centre of Nutrition, Biotechnology and Food Safety, Moscow, Russian Federation
| | - Kirill S Golokhvast
- Educational Scientific Center of Nanotechnology, Far Eastern Federal University, Vladivostok 690950, Russian Federation; Pacific Institute of Geography, FEB RAS, Vladivostok 690041, Russian Federation
| | - Jeong Dong Lee
- School of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Seung Hwan Yang
- Department of Biotechnology, Chonnam National University, Yeosu, Chonnam 59626, Republic of Korea
| | - Gyuhwa Chung
- Department of Biotechnology, Chonnam National University, Yeosu, Chonnam 59626, Republic of Korea.
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31
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Tsatsakis AM, Nawaz MA, Tutelyan VA, Golokhvast KS, Kalantzi OI, Chung DH, Kang SJ, Coleman MD, Tyshko N, Yang SH, Chung G. Impact on environment, ecosystem, diversity and health from culturing and using GMOs as feed and food. Food Chem Toxicol 2017. [PMID: 28645870 DOI: 10.1016/j.fct.2017.06.033] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Modern agriculture provides the potential for sustainable feeding of the world's increasing population. Up to the present moment, genetically modified (GM) products have enabled increased yields and reduced pesticide usage. Nevertheless, GM products are controversial amongst policy makers, scientists and the consumers, regarding their possible environmental, ecological, and health risks. Scientific-and-political debates can even influence legislation and prospective risk assessment procedure. Currently, the scientifically-assessed direct hazardous impacts of GM food and feed on fauna and flora are conflicting; indeed, a review of literature available data provides some evidence of GM environmental and health risks. Although the consequences of gene flow and risks to biodiversity are debatable. Risks to the environment and ecosystems can exist, such as the evolution of weed herbicide resistance during GM cultivation. A matter of high importance is to provide precise knowledge and adequate current information to regulatory agencies, governments, policy makers, researchers, and commercial GMO-releasing companies to enable them to thoroughly investigate the possible risks.
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Affiliation(s)
- Aristidis M Tsatsakis
- Laboratory of Toxicology, School of Medicine, University of Crete, Heraklion, Crete, Greece
| | - Muhammad Amjad Nawaz
- Department of Biotechnology, Chonnam National University, Yeosu, Chonnam, 59626, Republic of Korea
| | - Victor A Tutelyan
- Federal Research Centre of Nutrition, Biotechnology and Food Safety, Moscow, Russian Federation
| | - Kirill S Golokhvast
- Educational Scientific Center of Nanotechnology, Engineering School, Far Eastern Federal Univeristy, 37 Pushkinskaya Street, 690950, Vladivostok, Russian Federation
| | | | - Duck Hwa Chung
- Department of Agricultural Chemistry and Food Science and Technology, Gyeongsang National University, Jinju, Gyeongnam 52828, Republic of Korea
| | - Sung Jo Kang
- Institute of Agriculture and Life Science, Gyeongsang National University, Jinju, Geyongnam 52828, Republic of Korea
| | - Michael D Coleman
- School of Life and Health Sciences, Aston University, Birmingham, United Kingdom
| | - Nadia Tyshko
- Federal Research Centre of Nutrition, Biotechnology and Food Safety, Moscow, Russian Federation
| | - Seung Hwan Yang
- Department of Biotechnology, Chonnam National University, Yeosu, Chonnam, 59626, Republic of Korea
| | - Gyuhwa Chung
- Department of Biotechnology, Chonnam National University, Yeosu, Chonnam, 59626, Republic of Korea.
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Rehman HM, Shah ZH, Nawaz MA, Ahmad MQ, Yang SH, Kho KH, Chung G. RETRACTED ARTICLE: Beta-cyanoalanine synthase pathway as a homeostatic mechanism for cyanide detoxification as well as growth and development in higher plants. Planta 2017; 245:235. [PMID: 27744484 DOI: 10.1007/s00425-016-2606-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 10/09/2016] [Indexed: 06/06/2023]
Affiliation(s)
- Hafiz Mamoon Rehman
- Department of Biotechnology, Chonnam National University, Yeosu, Chonnam, 59626, South Korea
| | - Zahid Hussain Shah
- Department of Arid Land Agriculture, King Abdul-Aziz University, Jeddah, 21577, Saudi Arabia
| | - Muhammad Amjad Nawaz
- Department of Biotechnology, Chonnam National University, Yeosu, Chonnam, 59626, South Korea
| | - Muhammad Qadir Ahmad
- Department of Plant Breeding and Genetics, Bahauddin Zakariya University, Multan, 6000, Pakistan
| | - Seung Hwan Yang
- Department of Biotechnology, Chonnam National University, Yeosu, Chonnam, 59626, South Korea
| | - Kang Hee Kho
- Department of Aquatic Biology, Chonnam National University, Yeosu, Chonnam, 59626, South Korea
| | - Gyuhwa Chung
- Department of Biotechnology, Chonnam National University, Yeosu, Chonnam, 59626, South Korea.
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Mamoon Rehman H, Amjad Nawaz M, Bao L, Hussain Shah Z, Lee JM, Ahmad MQ, Chung G, Yang SH. Genome-wide analysis of Family-1 UDP-glycosyltransferases in soybean confirms their abundance and varied expression during seed development. J Plant Physiol 2016; 206:87-97. [PMID: 27721120 DOI: 10.1016/j.jplph.2016.08.017] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2016] [Revised: 08/23/2016] [Accepted: 08/28/2016] [Indexed: 05/13/2023]
Abstract
Family-1 UDP-glycosyltransferases (EC 2.4.1.x; UGTs) are enzymes that glycosylate aglycones into glycoside-associated compounds with improved transport and water solubility. This glycosylation mechanism is vital to plant functions, such as regulation of hormonal homeostasis, growth and development, xenobiotic detoxification, stress response, and biosynthesis of secondary metabolites. Here, we report a genome-wide analysis of soybean that identified 149 putative UGTs based on 44 conserved plant secondary product glycosyl-transferase (PSPG) motif amino acid sequences. Phylogenetic analysis against 22 referenced UGTs from Arabidopsis and maize clustered the putative UGTs into 15 major groups (A-O); J, K, and N were not represented, but the UGTs were distributed across all chromosomes except chromosome 04. Leucine was the most abundant amino acid across all 149 UGT peptide sequences. Two conserved introns (C1 and C2) were detected in the most intron-containing UGTs. Publicly available microarray data on their maximum expression in the seed developmental stage were further confirmed using Affymetrix soybean IVT array and RNA sequencing data. The UGT expression models were designed, based on reads per kilobase of gene model per million mapped read (RPKM) values confirmed their maximally varied expression at globular and early maturation stages of seed development.
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Affiliation(s)
- Hafiz Mamoon Rehman
- Department of Biotechnology, Chonnam National University, Yeosu, Chonnam 550-749, Republic of Korea
| | - Muhammad Amjad Nawaz
- Department of Biotechnology, Chonnam National University, Yeosu, Chonnam 550-749, Republic of Korea
| | - Le Bao
- Department of Biotechnology, Chonnam National University, Yeosu, Chonnam 550-749, Republic of Korea
| | - Zahid Hussain Shah
- Department of Arid Land Agriculture, King Abdul-Aziz University Jeddah, Saudi Arabia
| | - Jae-Min Lee
- Department of Biotechnology, Chonnam National University, Yeosu, Chonnam 550-749, Republic of Korea
| | - Muhammad Qadir Ahmad
- Department of Plant Breeding and Genetics, Bahauddin Zakariya University, Multan 6000, Pakistan
| | - Gyuhwa Chung
- Department of Biotechnology, Chonnam National University, Yeosu, Chonnam 550-749, Republic of Korea.
| | - Seung Hwan Yang
- Department of Biotechnology, Chonnam National University, Yeosu, Chonnam 550-749, Republic of Korea
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Le B, Nawaz MA, Rehman HM, Le T, Yang SH, Golokhvast KS, Son E, Chung G. Genome-wide characterization and expression pattern of auxin response factor (ARF) gene family in soybean and common bean. Genes Genomics 2016. [DOI: 10.1007/s13258-016-0462-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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