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Sharma AR, Vohra M, Vinay CM, Paul B, Chakrabarty S, Rai PS. Development of DNA markers using next-generation sequencing approach for molecular authentication of Boerhavia diffusa L. and Tinospora cordifolia (Willd.) Miers. 3 Biotech 2023; 13:304. [PMID: 37593204 PMCID: PMC10427588 DOI: 10.1007/s13205-023-03732-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 06/11/2023] [Indexed: 08/19/2023] Open
Abstract
The adulteration of plants and their materials used in herbal formulations poses a severe health concern. Hence, there is a need to establish a reliable, cost-effective, and robust molecular biomarker to distinguish among species and identify herbal plants and raw drugs from adulterants. The present study used suppressive subtractive hybridization and next-generation sequencing technology to identify novel DNA markers for Boerhavia diffusa L. and Tinospora cordifolia (Willd.) Miers. We identified two primer sets for B. diffusa and one for T. cordifolia. The DNA markers were validated in different accessions of B. diffusa and T. cordifolia and their common adulterants to determine the sensitivity and specificity of developed DNA markers. The designed DNA markers showed 100% sensitivity and specificity in detecting B. diffusa and T. cordifolia from their adulterants. The strategy described here can be extrapolated for developing DNA markers to authenticate other plant species. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03732-7.
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Affiliation(s)
- Anu Radha Sharma
- Department of Biotechnology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, 576104 India
| | - Manik Vohra
- Department of Biotechnology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, 576104 India
| | - Chigateri M. Vinay
- Department of Biotechnology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, 576104 India
| | - Bobby Paul
- Department of Bioinformatics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, India
| | - Sanjiban Chakrabarty
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, India
| | - Padmalatha S. Rai
- Department of Biotechnology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, 576104 India
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Balkanska R, Shumkova R, Atsenova N, Salkova D, Dundarova H, Radoslavov G, Hristov P. Molecular Detection and Phylogenetic Analysis of Deformed Wing Virus and Sacbrood Virus Isolated from Pollen. Vet Sci 2023; 10:vetsci10020140. [PMID: 36851444 PMCID: PMC9965827 DOI: 10.3390/vetsci10020140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 02/03/2023] [Accepted: 02/08/2023] [Indexed: 02/12/2023] Open
Abstract
Among many pathogens and pests, honey bee viruses are known as one of the most common cause of diseases in honey bee colonies. In this study, we demonstrate that pollen grains and bee bread are potential sources of viral DNA. We extracted DNA from 3 types of pollen samples: directly provided by beekeepers (n = 12), purchased from trade markets (n = 5), and obtained from honeycombs (bee bread, n = 10). The extracted DNA was used for molecular detection (RT-PCR analysis) of six of the most widely distributed honey bee viruses: deformed wing virus, sacbrood virus, acute bee paralysis virus, black queen cell virus, Kashmir bee virus, Israeli acute paralysis virus, and chronic bee paralysis virus. We successfully managed to establish only the deformed wing virus (DWV) and the sacbrood virus (SBV), with different distribution frequencies depending on the territory of the country. The phylogenetic analyses of Bulgarian isolates were performed with the most similar sequences available in molecular databases from other countries. Phylogenies of Bulgarian viral strains demonstrated genetically heterogeneous populations of DWV and relatively homogenous populations of SBV. In conclusion, the results obtained from the current study have shown that pollen is a valuable source for molecular detection of honey bee pathogens. This allows epidemiological monitoring of honey bee diseases at a regional and a national level.
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Affiliation(s)
- Ralitsa Balkanska
- Department “Special Branches”, Institute of Animal Science, Agricultural Academy, 2230 Kostinbrod, Bulgaria
| | - Rositsa Shumkova
- Research Centre of Stockbreeding and Agriculture, Agricultural Academy, 4700 Smolyan, Bulgaria
| | - Nedyalka Atsenova
- Department of Animal Diversity and Resources, Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Delka Salkova
- Department of Experimental Parasitology, Institute of Experimental Morphology, Pathology and Anthropology with Museum, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Heliana Dundarova
- Department of Animal Diversity and Resources, Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
- Department of Ecosystem Research, Environmental Risk Assessment and Conservation Biology, Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Georgi Radoslavov
- Department of Animal Diversity and Resources, Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Peter Hristov
- Department of Animal Diversity and Resources, Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
- Correspondence:
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Liu Y, Cao G, Xie Y, Chu M. Identification of differentially expressed genes associated with precocious puberty by suppression subtractive hybridization in goat pituitary tissues. Anim Biotechnol 2021:1-14. [PMID: 34747679 DOI: 10.1080/10495398.2021.1990940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The aim of this study was to identify genes related to precocious puberty expressed in the pituitary of goats at different growth stages by suppression subtractive hybridization (SSH). The pituitary glands from Jining Gray (JG) goats (early puberty) and Liaoning Cashmere (LC) goats (late puberty) at 30, 90, and 180 days were used in this study. To identify differentially expressed genes (DEGs) in the pituitary glands, mRNA was extracted from these tissues, and SSH libraries were constructed and divided into the following groups: juvenile group (30-JG vs. 30-LC, API), puberty group (90-JG vs. 180-LC, BPI), and control group (90-JG vs. 90-LC, EPI). A total of 60, 49, and 58 DEGs were annotated by 222 Gene Ontology (GO) terms and 75 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Most of the DEGs were significantly enriched in GO terms related to 'structural constituent of ribosome', 'translation' and 'GTP binding', and numerous DEGs were also significantly enriched in KEGG terms related to the Jak-STAT signaling and oocyte meiosis pathways. Candidate genes associated with precocious puberty and sexual development were screened from the SSH libraries. These genes were analyzed to determine if they were expressed in the pituitary tissues of the goats at different growth stages and to identify genes that may influence the hypothalamic-pituitary-gonadal (HPG) axis. In this study, we found precocious puberty-related genes (such as PRLP0, EIF5A, and YWHAH) that may be interesting from an evolutionary perspective and that could be investigated for use in future goat breeding programs. Our results provide a valuable dataset that will facilitate further research into the reproductive biology of goats.
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Affiliation(s)
- Yufang Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.,College of Life Sciences and Food Engineering, Hebei University of Engineering, Handan, China
| | - Guiling Cao
- College of Agriculture, Liaocheng University, Liaocheng, China
| | - Yujing Xie
- College of Agriculture, Liaocheng University, Liaocheng, China
| | - Mingxing Chu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
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Iqbal Z, Iqbal MS, Khan MIR, Ansari MI. Toward Integrated Multi-Omics Intervention: Rice Trait Improvement and Stress Management. FRONTIERS IN PLANT SCIENCE 2021; 12:741419. [PMID: 34721467 PMCID: PMC8554098 DOI: 10.3389/fpls.2021.741419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 09/20/2021] [Indexed: 05/04/2023]
Abstract
Rice (Oryza sativa) is an imperative staple crop for nearly half of the world's population. Challenging environmental conditions encompassing abiotic and biotic stresses negatively impact the quality and yield of rice. To assure food supply for the unprecedented ever-growing world population, the improvement of rice as a crop is of utmost importance. In this era, "omics" techniques have been comprehensively utilized to decipher the regulatory mechanisms and cellular intricacies in rice. Advancements in omics technologies have provided a strong platform for the reliable exploration of genetic resources involved in rice trait development. Omics disciplines like genomics, transcriptomics, proteomics, and metabolomics have significantly contributed toward the achievement of desired improvements in rice under optimal and stressful environments. The present review recapitulates the basic and applied multi-omics technologies in providing new orchestration toward the improvement of rice desirable traits. The article also provides a catalog of current scenario of omics applications in comprehending this imperative crop in relation to yield enhancement and various environmental stresses. Further, the appropriate databases in the field of data science to analyze big data, and retrieve relevant information vis-à-vis rice trait improvement and stress management are described.
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Affiliation(s)
- Zahra Iqbal
- Molecular Crop Research Unit, Department of Biochemistry, Chulalongkorn University, Bangkok, Thailand
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Fu J, Gong Z, Bae S. Ecotoxicogenomic analysis of zebrafish embryos exposed to triclosan and mixture triclosan and methyl triclosan using suppression subtractive hybridization and next-generation sequencing. JOURNAL OF HAZARDOUS MATERIALS 2021; 414:125450. [PMID: 33676256 DOI: 10.1016/j.jhazmat.2021.125450] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 02/11/2021] [Accepted: 02/12/2021] [Indexed: 06/12/2023]
Abstract
Triclosan (TCS) and methyl-triclosan (MTCS), an environmental transformation product of biocide of TCS, have been detected in water, sediment, fish, and invertebrates. In this study, the key pathway perturbation in zebrafish (Danio rerio) embryos exposed to TCS (300 μg/L) and TCS/MTCS mixture (300 μg/L TCS + 30 μg/L MTCS) was assessed by integrating the metabolomic and transcriptomic dysregulation. The differential expressed genes (DEGs) were obtained from the subtracted cDNA libraries by using the suppression subtractive hybridization and next-generation sequencing approach. The dysregulation of twenty-eight GO terms and four KEGG pathways, including oxidative phosphorylation and cardiac muscle contraction, were shown in the TCS treatment group, indicating that TCS could disrupt the mitochondrial inner membrane function by downshifting the electrochemical gradient. Meanwhile, the addition of MTCS in the exposure would cause fourteen additional significant KEGG pathway changes, demonstrating the different effects between two exposure. A pathway-based analysis using the identified DEGs and the altered metabolites in zebrafish embryos treated with TCS and TCS/MTCS mixture, collectively, has been applied. This study demonstrated that the integration of SSH-NGS and metabolomics could reveal toxic effects and potential diseases associated with the exposures of TCS and MTCS in aquatic environments.
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Affiliation(s)
- Jing Fu
- Department of Civil and Environmental Engineering, National University of Singapore, Singapore
| | - Zhiyuan Gong
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Sungwoo Bae
- Department of Civil and Environmental Engineering, National University of Singapore, Singapore.
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Duan L, Zhang S, Yang Y, Wang Q, Lan Q, Wang Y, Xu W, Jin W, Li L, Chen R. A feasible method for detecting unknown GMOs via a combined strategy of PCR-based suppression subtractive hybridization and next-generation sequencing. Food Control 2021. [DOI: 10.1016/j.foodcont.2020.107448] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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Xie ZY, Gong XX, Xu XD, Mei B, Xuan XZ, Long H, Zhang X, Cai XN. Identification of Vibrio alginolyticus virulent strain-specific DNA regions by suppression subtractive hybridization and PCR. J Appl Microbiol 2020; 129:1472-1485. [PMID: 32510751 DOI: 10.1111/jam.14739] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 05/23/2020] [Accepted: 06/02/2020] [Indexed: 12/25/2022]
Abstract
AIMS Vibrio alginolyticus was frequently isolated from diseased farmed fish in the coaster waters of Hainan Island over the past two decades. In this study, we attempted to identify candidates of virulent strain-specific DNA regions for this pathogen. METHODS AND RESULTS Suppression subtractive hybridization (SSH) and PCR were successively performed between the typical virulent strain and avirulent strain of V. alginolyticus, in which they shared 99·54% homology of 16S rDNAs. Out of 2873 subtracted clones, nine clones were finally indicated to harbour virulent strain-specific DNA fragments. The receivable functions of the major fragments in the nine clones were believed to encode methyl-accepting chemotaxis protein (n = 1), type VI secretion system-associated FHA domain protein TagH (n = 1), diguanylate cyclase (n = 1), AraC family transcriptional regulator (n = 1), ABC-type uncharacterized transport system permease component (n = 1) and hypothetical proteins (n = 4). Two hypothetical proteins contain several disordered regions. CONCLUSIONS Some specific DNA regions existed in the virulent strain of V. alginolyticus, and the SSH assay could be a highly sensitive method for identifying virulent regions in pathogens. SIGNIFICANCE AND IMPACT OF THE STUDY This report is the first to describe the identification of virulent strain-specific DNA regions in the V. alginolyticus genome, which is helpful in developing virulent strain-specific rapid detection methods and is a pivotal precondition for clarifying the molecular virulence mechanism of V. alginolyticus.
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Affiliation(s)
- Z-Y Xie
- State Key Laboratory of Marine Resource Utilization in the South China Sea, Hainan University, Haikou, Hainan Province, China.,Hainan Provincial Key Laboratory for Tropical Hydrobiology and Biotechnology, Hainan University, Haikou, Hainan Province, China.,College of Marine Sciences, Hainan University, Haikou, Hainan Province, China
| | - X-X Gong
- State Key Laboratory of Marine Resource Utilization in the South China Sea, Hainan University, Haikou, Hainan Province, China.,Hainan Provincial Key Laboratory for Tropical Hydrobiology and Biotechnology, Hainan University, Haikou, Hainan Province, China.,College of Marine Sciences, Hainan University, Haikou, Hainan Province, China
| | - X-D Xu
- College of Marine Sciences, Hainan University, Haikou, Hainan Province, China
| | - B Mei
- College of Marine Sciences, Hainan University, Haikou, Hainan Province, China
| | - X-Z Xuan
- College of Marine Sciences, Hainan University, Haikou, Hainan Province, China
| | - H Long
- State Key Laboratory of Marine Resource Utilization in the South China Sea, Hainan University, Haikou, Hainan Province, China
| | - X Zhang
- State Key Laboratory of Marine Resource Utilization in the South China Sea, Hainan University, Haikou, Hainan Province, China.,Hainan Provincial Key Laboratory for Tropical Hydrobiology and Biotechnology, Hainan University, Haikou, Hainan Province, China.,College of Marine Sciences, Hainan University, Haikou, Hainan Province, China
| | - X-N Cai
- State Key Laboratory of Marine Resource Utilization in the South China Sea, Hainan University, Haikou, Hainan Province, China.,Hainan Provincial Key Laboratory for Tropical Hydrobiology and Biotechnology, Hainan University, Haikou, Hainan Province, China.,College of Marine Sciences, Hainan University, Haikou, Hainan Province, China
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8
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Mechanisms of Sugar Beet Response to Biotic and Abiotic Stresses. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1241:167-194. [PMID: 32383121 DOI: 10.1007/978-3-030-41283-8_10] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Sugar beet is used not only in the sugar production, but also in a wide range of industries including the production of bioethanol as a source of renewable energy, extraction of pectin and production of molasses. The red beetroot has attracted much attention as health-promoting and disease-preventing functional food. The negative effects of environmental stresses, including abiotic and biotic ones, significantly decrease the cash crop sugar beet productivity. In this paper, we outline the mechanisms of sugar beet response to biotic and abiotic stresses at the levels of physiological change, the genes' functions, transcription and translation. Regarding the physiological changes, most research has been carried out on salt and drought stress. The functions of genes from sugar beet in response to salt, cold and heavy metal stresses were mainly investigated by transgenic technologies. At the transcriptional level, the transcriptome analysis of sugar beet in response to salt, cold and biotic stresses were conducted by RNA-Seq or SSH methods. At the translational level, more than 800 differentially expressed proteins in response to salt, K+/Na+ ratio, iron deficiency and resupply and heavy metal (zinc) stress were identified by quantitative proteomics techniques. Understanding how sugar beet respond and tolerate biotic and abiotic stresses is important for boosting sugar beet productivity under these challenging conditions. In order to minimize the negative impact of these stresses, studying how the sugar beet has evolved stress coping mechanisms will provide new insights and lead to novel strategies for improving the breeding of stress-resistant sugar beet and other crops.
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Qi Y, Sun X, Zhang M, Wen Q, Qiu L, Shen J. Identification of up-regulated transcripts during Pleurotus ostreatus
primordium stage and characterization of PoALDH1. J Basic Microbiol 2018; 58:1071-1082. [DOI: 10.1002/jobm.201800123] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2018] [Revised: 07/29/2018] [Accepted: 07/31/2018] [Indexed: 11/09/2022]
Affiliation(s)
- Yuancheng Qi
- College of Life Science; Henan Agricultural University; Zhengzhou China
| | - Xiankai Sun
- College of Life Science; Henan Agricultural University; Zhengzhou China
| | - Mengke Zhang
- College of Life Science; Henan Agricultural University; Zhengzhou China
| | - Qing Wen
- College of Life Science; Henan Agricultural University; Zhengzhou China
| | - Liyou Qiu
- College of Life Science; Henan Agricultural University; Zhengzhou China
| | - Jinwen Shen
- College of Life Science; Henan Agricultural University; Zhengzhou China
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Sahebi M, Hanafi MM, Rafii MY, Mahmud TMM, Azizi P, Osman M, Abiri R, Taheri S, Kalhori N, Shabanimofrad M, Miah G, Atabaki N. Improvement of Drought Tolerance in Rice ( Oryza sativa L.): Genetics, Genomic Tools, and the WRKY Gene Family. BIOMED RESEARCH INTERNATIONAL 2018; 2018:3158474. [PMID: 30175125 PMCID: PMC6106855 DOI: 10.1155/2018/3158474] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 06/14/2018] [Accepted: 07/05/2018] [Indexed: 11/17/2022]
Abstract
Drought tolerance is an important quantitative trait with multipart phenotypes that are often further complicated by plant phenology. Different types of environmental stresses, such as high irradiance, high temperatures, nutrient deficiencies, and toxicities, may challenge crops simultaneously; therefore, breeding for drought tolerance is very complicated. Interdisciplinary researchers have been attempting to dissect and comprehend the mechanisms of plant tolerance to drought stress using various methods; however, the limited success of molecular breeding and physiological approaches suggests that we rethink our strategies. Recent genetic techniques and genomics tools coupled with advances in breeding methodologies and precise phenotyping will likely reveal candidate genes and metabolic pathways underlying drought tolerance in crops. The WRKY transcription factors are involved in different biological processes in plant development. This zinc (Zn) finger protein family, particularly members that respond to and mediate stress responses, is exclusively found in plants. A total of 89 WRKY genes in japonica and 97 WRKY genes in O. nivara (OnWRKY) have been identified and mapped onto individual chromosomes. To increase the drought tolerance of rice (Oryza sativa L.), research programs should address the problem using a multidisciplinary strategy, including the interaction of plant phenology and multiple stresses, and the combination of drought tolerance traits with different genetic and genomics approaches, such as microarrays, quantitative trait loci (QTLs), WRKY gene family members with roles in drought tolerance, and transgenic crops. This review discusses the newest advances in plant physiology for the exact phenotyping of plant responses to drought to update methods of analysing drought tolerance in rice. Finally, based on the physiological/morphological and molecular mechanisms found in resistant parent lines, a strategy is suggested to select a particular environment and adapt suitable germplasm to that environment.
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Affiliation(s)
- Mahbod Sahebi
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| | - Mohamed M. Hanafi
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
- Laboratory of Plantation Science and Technology, Institute of Plantation Studies, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
- Department of Land Management, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| | - M. Y. Rafii
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| | - T. M. M. Mahmud
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| | - Parisa Azizi
- Laboratory of Plantation Science and Technology, Institute of Plantation Studies, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| | - Mohamad Osman
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| | - Rambod Abiri
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| | - Sima Taheri
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| | - Nahid Kalhori
- Department of Biology, Faculty of Science, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| | - M. Shabanimofrad
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| | - Gous Miah
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| | - Narges Atabaki
- Iran Azad University of Tehran Science & Reserach Branch, Hesarak, Tehran 1477893855, Iran
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Wang M, Zou Z, Li Q, Xin H, Zhu X, Chen X, Li X. Heterologous expression of three Camellia sinensis small heat shock protein genes confers temperature stress tolerance in yeast and Arabidopsis thaliana. PLANT CELL REPORTS 2017; 36:1125-1135. [PMID: 28455764 DOI: 10.1007/s00299-017-2143-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Accepted: 04/13/2017] [Indexed: 05/24/2023]
Abstract
CsHSP17.7, CsHSP18.1, and CsHSP21.8 expressions are induced by heat and cold stresses, and CsHSP overexpression confers tolerance to heat and cold stresses in transgenic Pichia pastoris and Arabidopsis thaliana. Small heat shock proteins (sHSPs) are crucial for protecting plants against biotic and abiotic stresses, especially heat stress. However, knowledge concerning the functions of Camellia sinensis sHSP in heat and cold stresses remains poorly understood. In this study, three C. sinensis sHSP genes (i.e., CsHSP17.7, CsHSP18.1, and CsHSP21.8) were isolated and characterized using suppression subtractive hybridization (SSH) technology. The CsHSPs expression levels in C. sinensis leaves were significantly up-regulated by heat and cold stresses. Phylogenetic analyses revealed that CsHSP17.7, CsHSP18.1, and CsHSP21.8 belong to sHSP Classes I, II, and IV, respectively. Heterologous expression of the three CsHSP genes in Pichia pastoris cells enhanced heat and cold stress tolerance. When exposed to heat and cold treatments, transgenic Arabidopsis thaliana plants overexpressing CsHSP17.7, CsHSP18.1, and CsHSP21.8 had lower malondialdehyde contents, ion leakage, higher proline contents, and transcript levels of stress-related genes (e.g., AtPOD, AtAPX1, AtP5CS2, and AtProT1) compared with the control line. In addition, improved seed germination vigor was also observed in the CsHSP-overexpressing seeds under heat stress. Taken together, our results suggest that the three identified CsHSP genes play key roles in heat and cold tolerance.
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Affiliation(s)
- Mingle Wang
- Tea Research Institute, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhongwei Zou
- Department of Plant Science, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada
| | - Qinghui Li
- Tea Research Institute, Nanjing Agricultural University, Nanjing, 210095, China
| | - Huahong Xin
- Tea Research Institute, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xujun Zhu
- Tea Research Institute, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xuan Chen
- Department of Chinese Medicine, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Xinghui Li
- Tea Research Institute, Nanjing Agricultural University, Nanjing, 210095, China.
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Ammar MH, Khan AM, Migdadi HM, Abdelkhalek SM, Alghamdi SS. Faba bean drought responsive gene identification and validation. Saudi J Biol Sci 2017; 24:80-89. [PMID: 28053575 PMCID: PMC5199002 DOI: 10.1016/j.sjbs.2016.05.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 05/08/2016] [Accepted: 05/15/2016] [Indexed: 11/16/2022] Open
Abstract
This study was carried out to identify drought-responsive genes in a drought tolerant faba bean variety (Hassawi 2) using a suppressive subtraction hybridization approach (SSH). A total of 913 differentially expressed clones were sequenced from a differential cDNA library that resulted in a total of 225 differentially expressed ESTs. The genes of mitochondrial and chloroplast origin were removed, and the remaining 137 EST sequences were submitted to the gene bank EST database (LIBEST_028448). A sequence analysis identified 35 potentially drought stress-related ESTs that regulate ion channels, kinases, and energy production and utilization and transcription factors. Quantitative PCR on Hassawi 2 genotype confirmed that more than 65% of selected drought-responsive genes were drought-related. Among these induced genes, the expression levels of eight highly up-regulated unigenes were further analyzed across 38 selected faba bean genotypes that differ in their drought tolerance levels. These unigenes included ribulose 1,5-bisphosphate carboxylase (rbcL) gene, non-LTR retroelement reverse related, probable cyclic nucleotide-gated ion channel, polyubiquitin, potassium channel, calcium-dependent protein kinase and putative respiratory burst oxidase-like protein C and a novel unigene. The expression patterns of these unigenes were variable across 38 genotypes however, it was found to be very high in tolerant genotype. The up-regulation of these unigenes in majority of tolerant genotypes suggests their possible role in drought tolerance. The identification of possible drought responsive candidate genes in Vicia faba reported here is an important step toward the development of drought-tolerant genotypes that can cope with arid environments.
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Affiliation(s)
- Megahed H. Ammar
- Legume Research Group, Plant Production Department, Faculty of Food and Agricultural Sciences, King Saud University, P.O. Box 2460, Riyadh 11451, Saudi Arabia
- Rice Research and Training Center, Sakha, 33717 KafrEl-Sheikh, Egypt
| | - Altaf M. Khan
- Legume Research Group, Plant Production Department, Faculty of Food and Agricultural Sciences, King Saud University, P.O. Box 2460, Riyadh 11451, Saudi Arabia
| | - Hussein M. Migdadi
- Legume Research Group, Plant Production Department, Faculty of Food and Agricultural Sciences, King Saud University, P.O. Box 2460, Riyadh 11451, Saudi Arabia
| | - Samah M. Abdelkhalek
- Botany and Microbiology Department, College of Science, King Saud University, Saudi Arabia
- Rice Research and Training Center, Sakha, 33717 KafrEl-Sheikh, Egypt
| | - Salem S. Alghamdi
- Legume Research Group, Plant Production Department, Faculty of Food and Agricultural Sciences, King Saud University, P.O. Box 2460, Riyadh 11451, Saudi Arabia
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Zhang Y, Nan J, Yu B. OMICS Technologies and Applications in Sugar Beet. FRONTIERS IN PLANT SCIENCE 2016; 7:900. [PMID: 27446130 PMCID: PMC4916227 DOI: 10.3389/fpls.2016.00900] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 06/07/2016] [Indexed: 05/08/2023]
Abstract
Sugar beet is a species of the Chenopodiaceae family. It is an important sugar crop that supplies approximately 35% of the sugar in the world. Sugar beet M14 line is a unique germplasm that contains genetic materials from Beta vulgaris L. and Beta corolliflora Zoss. And exhibits tolerance to salt stress. In this review, we have summarized OMICS technologies and applications in sugar beet including M14 for identification of novel genes, proteins related to biotic and abiotic stresses, apomixes and metabolites related to energy and food. An OMICS overview for the discovery of novel genes, proteins and metabolites in sugar beet has helped us understand the complex mechanisms underlying many processes such as apomixes, tolerance to biotic and abiotic stresses. The knowledge gained is valuable for improving the tolerance of sugar beet and other crops to biotic and abiotic stresses as well as for enhancing the yield of sugar beet for energy and food production.
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Affiliation(s)
- Yongxue Zhang
- Key Laboratory of Molecular Biology of Heilongjiang Province, College of Life Sciences, Heilongjiang UniversityHarbin, China
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang UniversityHarbin, China
| | - Jingdong Nan
- Key Laboratory of Molecular Biology of Heilongjiang Province, College of Life Sciences, Heilongjiang UniversityHarbin, China
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang UniversityHarbin, China
| | - Bing Yu
- Key Laboratory of Molecular Biology of Heilongjiang Province, College of Life Sciences, Heilongjiang UniversityHarbin, China
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang UniversityHarbin, China
- *Correspondence: Bing Yu
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Ashkani S, Rafii MY, Shabanimofrad M, Miah G, Sahebi M, Azizi P, Tanweer FA, Akhtar MS, Nasehi A. Molecular Breeding Strategy and Challenges Towards Improvement of Blast Disease Resistance in Rice Crop. FRONTIERS IN PLANT SCIENCE 2015; 6:886. [PMID: 26635817 PMCID: PMC4644793 DOI: 10.3389/fpls.2015.00886] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 10/06/2015] [Indexed: 05/20/2023]
Abstract
Rice is a staple and most important security food crop consumed by almost half of the world's population. More rice production is needed due to the rapid population growth in the world. Rice blast caused by the fungus, Magnaporthe oryzae is one of the most destructive diseases of this crop in different part of the world. Breakdown of blast resistance is the major cause of yield instability in several rice growing areas. There is a need to develop strategies providing long-lasting disease resistance against a broad spectrum of pathogens, giving protection for a long time over a broad geographic area, promising for sustainable rice production in the future. So far, molecular breeding approaches involving DNA markers, such as QTL mapping, marker-aided selection, gene pyramiding, allele mining and genetic transformation have been used to develop new resistant rice cultivars. Such techniques now are used as a low-cost, high-throughput alternative to conventional methods allowing rapid introgression of disease resistance genes into susceptible varieties as well as the incorporation of multiple genes into individual lines for more durable blast resistance. The paper briefly reviewed the progress of studies on this aspect to provide the interest information for rice disease resistance breeding. This review includes examples of how advanced molecular method have been used in breeding programs for improving blast resistance. New information and knowledge gained from previous research on the recent strategy and challenges towards improvement of blast disease such as pyramiding disease resistance gene for creating new rice varieties with high resistance against multiple diseases will undoubtedly provide new insights into the rice disease control.
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Affiliation(s)
- Sadegh Ashkani
- Laboratory of Food Crops, Institute of Tropical Agriculture, Universiti Putra MalaysiaSerdang, Malaysia
- Department of Agronomy and Plant Breeding, Yadegar –e- Imam Khomeini RAH Shahre-Rey Branch, Islamic Azad UniversityTehran, Iran
| | - Mohd Y. Rafii
- Laboratory of Food Crops, Institute of Tropical Agriculture, Universiti Putra MalaysiaSerdang, Malaysia
| | | | - Gous Miah
- Laboratory of Food Crops, Institute of Tropical Agriculture, Universiti Putra MalaysiaSerdang, Malaysia
| | - Mahbod Sahebi
- Laboratory of Plantation Crops, Institute of Tropical Agriculture, Universiti Putra MalaysiaSerdang, Malaysia
| | - Parisa Azizi
- Laboratory of Food Crops, Institute of Tropical Agriculture, Universiti Putra MalaysiaSerdang, Malaysia
| | - Fatah A. Tanweer
- Department of Crop Science, Faculty of Agriculture, Universiti Putra MalaysiaSerdang, Malaysia
- Department of Plant Breeding and Genetics, Faculty of Crop Production, Sindh Agriculture University TandojamSindh, Pakistan
| | - Mohd Sayeed Akhtar
- Laboratory of Plantation Crops, Institute of Tropical Agriculture, Universiti Putra MalaysiaSerdang, Malaysia
- Department of Botany, Gandhi Faiz-e-Aam CollegeShahjahanpur, India
| | - Abbas Nasehi
- Department of Plant Protection, Faculty of Agriculture, Universiti Putra MalaysiaSerdang, Malaysia
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