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Avila-Victor CM, Ordaz-Chaparro VM, Arjona-Suárez EDJ, Iracheta-Donjuan L, Gómez-Merino FC, Robledo-Paz A. In Vitro Mass Propagation of Coffee Plants ( Coffea arabica L. var. Colombia) through Indirect Somatic Embryogenesis. PLANTS (BASEL, SWITZERLAND) 2023; 12:1237. [PMID: 36986925 PMCID: PMC10052142 DOI: 10.3390/plants12061237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 03/02/2023] [Accepted: 03/04/2023] [Indexed: 06/18/2023]
Abstract
Coffea arabica is one of the two most consumed coffee species in the world. Micropropagation through somatic embryogenesis has allowed the large-scale propagation of different coffee varieties. However, the regeneration of plants using this technique depends on the genotype. This study aimed to develop a protocol for the regeneration of C. arabica L. var. Colombia by somatic embryogenesis for its mass propagation. Foliar explants were cultured on Murashige and Skoog (MS) supplemented with different concentrations of 2,4-dichlorophenoxyacetic acid (2,4-D), 6-benzylaminopurine (BAP), and phytagel for inducing somatic embryogenesis. In total, 90% of the explants formed embryogenic calli with a culture medium containing 2 mg L-1 of 2,4-D, 0.2 mg L-1 BAP, and 2.3 g L-1 phytagel. The highest number of embryos per gram of callus (118.74) was obtained in a culture medium containing 0.5 mg L-1 2,4-D, 1.1 mg L-1 BAP, and 5.0 g L-1 phytagel. In total, 51% of the globular embryos reached the cotyledonary stage when they were cultured on the growth medium. This medium contained 0.25 mg L-1 BAP, 0.25 mg L-1 indoleacetic acid (IAA), and 5.0 g L-1 of phytagel. The mixture of vermiculite:perlite (3:1) allowed 21% of embryos to become plants.
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Affiliation(s)
- Consuelo Margarita Avila-Victor
- Colegio de Postgraduados, Campus Montecillo, Carretera México-Texcoco Km. 36.5, Montecillo, Texcoco C.P. 56264, Estado de México, Mexico
| | - Víctor Manuel Ordaz-Chaparro
- Colegio de Postgraduados, Campus Montecillo, Carretera México-Texcoco Km. 36.5, Montecillo, Texcoco C.P. 56264, Estado de México, Mexico
| | - Enrique de Jesús Arjona-Suárez
- Colegio de Postgraduados, Campus Montecillo, Carretera México-Texcoco Km. 36.5, Montecillo, Texcoco C.P. 56264, Estado de México, Mexico
| | - Leobardo Iracheta-Donjuan
- Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Campo Experimental Rosario Izapa, Carretera Tapachula-Cacahoatán Km. 18, Tuxtla Chico C.P. 30870, Chiapas, Mexico
| | - Fernando Carlos Gómez-Merino
- Colegio de Postgraduados, Campus Montecillo, Carretera México-Texcoco Km. 36.5, Montecillo, Texcoco C.P. 56264, Estado de México, Mexico
| | - Alejandrina Robledo-Paz
- Colegio de Postgraduados, Campus Montecillo, Carretera México-Texcoco Km. 36.5, Montecillo, Texcoco C.P. 56264, Estado de México, Mexico
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AL-Eitan L, Alnemri M. Biosafety and Biosecurity in the Era of Biotechnology: The Middle East Region. JOURNAL OF BIOSAFETY AND BIOSECURITY 2022. [DOI: 10.1016/j.jobb.2022.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Decoding herbal materials of TCM preparations with the multi-barcode sequencing approach. Sci Rep 2022; 12:5988. [PMID: 35397643 PMCID: PMC8994760 DOI: 10.1038/s41598-022-09979-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 03/29/2022] [Indexed: 12/22/2022] Open
Abstract
With the rapid development of high-throughput sequencing technology, approaches for assessing biological ingredients in Traditional Chinese Medicine (TCM) preparations have also advanced. Using a multi-barcode sequencing approach, all biological ingredients could be identified from TCM preparations in theory, as long as their DNA is present. The biological ingredients of several classical TCM preparations were analyzed successfully based on this approach in previous studies. However, the universality, sensitivity and reliability of this approach on a diverse set of TCM preparations remain unclear. In this study, we selected four representative TCM preparations, namely Bazhen Yimu Wan, Da Huoluo Wan, Niuhuang Jiangya Wan, and You Gui Wan, for concrete assessment of the multi-barcode sequencing approach. Based on ITS2 and trnL biomarkers, we have successfully detected the prescribed herbal materials (PHMs) in these representative TCM preparations (minimum sensitivity: 77.8%, maximum sensitivity: 100%). The results based on ITS2 have also shown higher reliability than trnL at species level, while their combination could provide higher sensitivity and reliability. The multi-barcode sequencing approach has shown good universality, sensitivity and reliability in decoding these four representative TCM preparations. In the omics big-data era, this work has undoubtedly made one step forward for applying multi-barcode sequencing approach in PHMs analysis of TCM preparation, towards better digitization and modernization of drug quality control.
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Omire A, Neondo J, Budambula NLM, Wangai L, Ogada S, Mweu C. Genetic Diversity and Population Structure of Doum Palm (Hyphaene compressa) Using Genotyping by Sequencing. Front Genet 2022; 13:762202. [PMID: 35186022 PMCID: PMC8854861 DOI: 10.3389/fgene.2022.762202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Accepted: 01/03/2022] [Indexed: 11/19/2022] Open
Abstract
Doum palm (Hyphaene compressa) is a perennial economic plant primarily growing in Kenya’s Arid and Semi-Arid Lands (ASALs). It is heavily relied upon for food, animal feed, construction materials and medicine, making it an ideal plant for resource sustainability. However, the limited information on its genetic resources has hindered its breeding and conservation studies. This study used the genotyping by sequencing approach to identify Single Nucleotide Polymorphisms. These SNPs were further used to assess the genetic diversity and population structure of 96 H. compressa accessions from Coastal, Northern and Eastern ASAL regions of Kenya using two approaches; reference-based and de novo-based assemblies. STRUCTURE analysis grouped the sampled accessions into two genetic clusters (Cluster 1 and Cluster 2). Cluster 1 included accessions from the Northern region, whereas Cluster 2 included all accessions from Eastern and Coastal regions. Accessions from Kwale (Coastal) had mixed ancestry from both Cluster 1 and Cluster 2. These STRUCTURE findings were further supported by principal components analysis, discriminant analysis of principal components and phylogenetic analysis. Analysis of molecular variance indicated greater genetic variation within populations (92.7%) than among populations (7.3%). An overall FST of 0.074 was observed, signifying moderate genetic differentiation among populations. The results of this study will provide information useful in breeding, marker-assisted selection and conservation management of H. compressa.
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Affiliation(s)
- Agnes Omire
- Department of Botany, School of Biological Sciences, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Johnstone Neondo
- Institute for Biotechnology Research (IBR), Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Nancy L. M. Budambula
- Department of Biological Sciences, School of Pure and Applied Sciences, University of Embu, Embu, Kenya
| | - Laura Wangai
- Department of Biomedical Sciences, School of Health Sciences, Kirinyaga University, Kerugoya, Kenya
| | - Stephen Ogada
- Institute for Biotechnology Research (IBR), Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Cecilia Mweu
- Institute for Biotechnology Research (IBR), Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
- *Correspondence: Cecilia Mweu,
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Abdel-Hameed UK, Elenazy HH, Abdel-Hamid AME. Morphological and molecular genetic variations of some taxa of genus Acacia and their taxonomic significance1. JOURNAL OF TAIBAH UNIVERSITY FOR SCIENCE 2021. [DOI: 10.1080/16583655.2021.2012389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Usama K. Abdel-Hameed
- Department of Biology, College of Science, Taibah University, Al Madinah, Kingdom of Saudi Arabia
- Department of Botany, Faculty of Science, Ain Shams University, Cairo, Egypt
| | - Hanaa H. Elenazy
- Department of Biology, College of Science, Taibah University, Al Madinah, Kingdom of Saudi Arabia
| | - Amal M. E. Abdel-Hamid
- Department of Biological and Geological Sciences, Faculty of Education, Ain Shams University, Cairo, Egypt
- Department of Biology, College of Sciences and Arts, Taibah University, Al Ula, Kingdom of Saudi Arabia
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Alzahrani D, Albokhari E, Abba A, Yaradua S. The first complete chloroplast genome sequences in Resedaceae: Genome structure and comparative analysis. Sci Prog 2021; 104:368504211059973. [PMID: 34870493 PMCID: PMC10450604 DOI: 10.1177/00368504211059973] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Caylusea hexagyna and Ochradenus baccatus are two species in the Resedaceae family. In this study, we analysed the complete plastid genomes of these two species using high-throughput sequencing technology and compared their genomic data. The length of the plastid genome of C. hexagyna was 154,390 bp while that of O. baccatus was 153,380 bp. The lengths of the inverted repeats (IR) regions were 26,526 bp and 26,558 bp, those of the large single copy (LSC) regions were 83,870 bp and 83,023 bp; and those of the small single copy (SSC) regions were 17,468 bp and 17,241 bp in C. hexagyna and O. baccatus, respectively. Both genomes consisted of 113 genes: 79 protein-coding genes, 30 tRNA genes and 4 rRNA genes. Repeat analysis showed that the plastid genome included all types of repeats, with more frequent occurrences of palindromic sequences. Comparative studies of SSR markers showed that there were 256 markers in C. hexagyna and 255 in O. baccatus; the majority of the SSRs in these plastid genomes were mononucleotide repeats (A/T). All the clusters in the phylogenetic tree had high support. This study reported the first complete plastid genomes of the genera Caylusea and Ochradenus and the first for the Resedaceae family.
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Affiliation(s)
- Dhafer Alzahrani
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Enas Albokhari
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Biological Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Abidina Abba
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Biological Sciences, Federal University Lokoja, Lokoja, Kogi State, Nigeria
| | - Samaila Yaradua
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
- Centre for Biodiversity and Conservation, Department of Biology, Umaru Musa Yaradua University, Katsina, Nigeria
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Yang Z, Bai Y, Alatalo JM, Huang Z, Yang F, Pu X, Wang R, Yang W, Guo X. Spatio-temporal variation in potential habitats for rare and endangered plants and habitat conservation based on the maximum entropy model. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 784:147080. [PMID: 33905926 DOI: 10.1016/j.scitotenv.2021.147080] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 03/24/2021] [Accepted: 04/07/2021] [Indexed: 06/12/2023]
Abstract
Rare and endangered plants (REPs) act as key indicators for species habitat priorities, and can thus be critical in global biodiversity protection work. Human activities and climate change pose great threats to REPs, so protection should be a top priority. In this study, we used the maximum entropy model (Maxent) to identify current and future (2050) potential habitats of REPs in the Xishuangbanna tropical area of China. We compared potential habitats with existing protected areas (PAs) in gap analysis, and used a transfer matrix to quantify changes in potential habitats. By comparing the potential distribution obtained with existing land use and land cover, we analyzed the impact of human-dominated land use changes on potential habitats of REPs and identified the main habitat patch types of REPs. The results showed that the current potential habitat area of hotspots is 2989.85 km2, which will be reduced to 247.93 km2 by 2050, accounting for 15.60% and 1.29% of the total research area, respectively. Analysis of land use and land cover showed that rubber plantation was the human-dominated land use posing the greatest threat to potential habitats of REPs, occupying 23.40% and 21.62% of current and future potential habitats, respectively. Monsoon evergreen broad-leaved forest was identified as the main habitat patch type for REPs in Xishuangbanna and occupied the highest proportion of potential habitat area. Gap analysis showed that only 35.85% of habitat hotspots are currently included in existing PAs and that this will decrease to 32.26% by 2050. This emphasizes the importance of protecting current and future potential habitats of REPs in a dynamic conservation approach that can adapt to changes in future climate and human activities.
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Affiliation(s)
- Zongbao Yang
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla 666303, Yunnan, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yang Bai
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla 666303, Yunnan, China; University of Chinese Academy of Sciences, Beijing 100049, China; Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Mengla 666303, China.
| | - Juha M Alatalo
- Environmental Science Center, Qatar University, P.O.Box: 2713, Doha, Qatar
| | - Zhongde Huang
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla 666303, Yunnan, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fen Yang
- Yuexi Federation of Trade Unions, Yuexi 616650, Sichuan, China
| | - Xiaoyan Pu
- University of Chinese Academy of Sciences, Beijing 100049, China; CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650223, China
| | - Ruibo Wang
- Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming 650500, China
| | - Wei Yang
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla 666303, Yunnan, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xueyan Guo
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla 666303, Yunnan, China; University of Chinese Academy of Sciences, Beijing 100049, China
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Phylogenetic relationships and DNA barcoding of nine endangered medicinal plant species endemic to Saint Katherine protectorate. Saudi J Biol Sci 2021; 28:1919-1930. [PMID: 33732078 PMCID: PMC7938155 DOI: 10.1016/j.sjbs.2020.12.043] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 12/20/2020] [Accepted: 12/23/2020] [Indexed: 11/21/2022] Open
Abstract
A high degree of endemism has been recorded for several plant groups collectively in Saint Katherine Protectorate (SKP) in the Sinai Peninsula. Nine endangered endemic plant species in SKP were selected to test the variable abilities of three different DNA barcodes; Riboluse-1,5- Biphosphate Carboxylase/Oxygenase Large subunit (rbcL), Internal Transcribed Spacer (ITS), and the two regions of the plastid gene (ycf1) as well as Start Codon Targeted (SCoT) Polymorphism to find the phylogenetic relationships among them. The three barcodes were generally more capable of finding the genetic relationships among the plant species under study, new barcodes were introduced to the National Centre for Biotechnology Information (NCBI) for the first time through our work. The barcode sequences were efficient in finding the genetic relationships between the nine species. However, SCoT polymorphism could only cluster plant species belonging to the same genus together in one group, but it could not cluster plant species belonging to the same families except for some primers solely. RbcL was the most easily amplified and identified barcode in eight out of the nine species at the species level and the ninth barcode to the genus level. ITS identified all the species to the genus level. Finally, ycf1 identified six out of the eight species, but it could not identify two of the eight species to the genus level.
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Al-Asmari AK, Abbasmanthiri R, Osman NMA, Al-Asmari BA. Endangered Saudi Arabian plants having ethnobotanical evidence as antidotes for scorpion envenoming. CLINICAL PHYTOSCIENCE 2020. [DOI: 10.1186/s40816-020-00196-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
AbstractScorpion sting envenoming in Saudi Arabia posed major public health problems. Conventional treatment with antivenom with its limitations and hazards called for the use of support remediation like prazosin therapy and phytotherapy as alternative solutions in systematic medicine and a trend of use in medicinal plants. The present study is aiming to procure the medicinal plants that exhibit antidotes of scorpion stings which, were scientifically ignored in Saudi Arabia. Current study data of 11 rare and endangered medicinal plants were collected identified up to the family level, in addition to the parts used. The Family Leguminosae was represented by 4 species. The families Acanthaceae, Amaranthaceae, Annonaceae, Euphorbiaceae, Myrtaceae, Plumbaginaceae, and Zygophyllaceae, were represented with a single species each. All of them have got medicinal ability of antidote potential against scorpion venoms. These commonly used herbs that belonged to 8 families were similar in the use of all parts in treatment. This review study may assist the researchers recruiting new natural herbs and their active products as therapeutic agents against scorpion envenoming. However, these medicinal plants are still requiring pharmacological and phytochemical investigations in order to be claimed as effective antidotes in scorpion envenoming syndrome.
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Louati M, Ucarli C, Arikan B, Ghada B, Hannachi AS, Turgut-Kara N. Genetic, Morphological, and Biochemical Diversity of Argan Tree ( Argania spinosa L.) (Sapotaceae) in Tunisia. PLANTS (BASEL, SWITZERLAND) 2019; 8:E319. [PMID: 31480514 PMCID: PMC6783864 DOI: 10.3390/plants8090319] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 07/29/2019] [Accepted: 08/23/2019] [Indexed: 01/06/2023]
Abstract
Argan trees are normally endemic to Morocco and Algeria, but hundreds of argan trees exist in Tunisia, some introduced from Morocco and some from unknown origins. The aim of the present study was to evaluate the genetic, morphological, and biochemical diversity of the argan trees in Tunisia. In this study, we used morphometric data collected from vegetative tissue, as well as pomological characteristics related to fruits, stones, and kernels. Genetic variation in 60 trees of Tunisian Argania spinosa L. was estimated using inter-simple sequence repeats (ISSRs). Mutation screening and genotyping by high-resolution melting (HRM) was performed to detect delta-6-desaturase (D6D) variants in the tested individuals, and finally fatty acid analysis of argan leaves with gas chromatography (GC) was performed. The plant materials used in this study originated from four different sites in Tunisia. Analysis of morphological characteristics showed large variability both within and between the studied collections. The analysis of ISSR polymorphisms gave information about the diversity within and between populations. HRM analysis showed that all 60 argan individuals were grouped into 10 different categories. The results of the gas chromatography analysis showed that the presence of omega-3 fatty acids EPA and DHA was noticeable in some argan leaves.
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Affiliation(s)
- Marwa Louati
- Université de Tunis El Manar, Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie, Faculté des Sciences de Tunis, Tunis 2092, Tunisia
| | - Cuneyt Ucarli
- Faculty of Science, Department of Molecular Biology and Genetics, Istanbul University, Istanbul 34134, Turkey
| | - Burcu Arikan
- Faculty of Science, Department of Molecular Biology and Genetics, Istanbul University, Istanbul 34134, Turkey
| | - Baraket Ghada
- Université de Tunis El Manar, Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie, Faculté des Sciences de Tunis, Tunis 2092, Tunisia
| | - Amel Salhi Hannachi
- Université de Tunis El Manar, Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie, Faculté des Sciences de Tunis, Tunis 2092, Tunisia
| | - Neslihan Turgut-Kara
- Faculty of Science, Department of Molecular Biology and Genetics, Istanbul University, Istanbul 34134, Turkey.
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Gairola S, Al Shaer KI, Al Harthi EK, Mosa KA. Strengthening desert plant biotechnology research in the United Arab Emirates: a viewpoint. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2018; 24:521-533. [PMID: 30042610 PMCID: PMC6041242 DOI: 10.1007/s12298-018-0551-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 02/19/2018] [Accepted: 05/08/2018] [Indexed: 05/09/2023]
Abstract
The biotechnology of desert plants is a vast subject. The main applications in this broad field of study comprises of plant tissue culture, genetic engineering, molecular markers and others. Biotechnology applications have the potential to address biodiversity conservation as well as agricultural, medicinal, and environmental issues. There is a need to increase our knowledge of the genetic diversity through the use of molecular genetics and biotechnological approaches in desert plants in the Arabian Gulf region including those in the United Arab Emirates (UAE). This article provides a prospective research for the study of UAE desert plant diversity through DNA fingerprinting as well as understanding the mechanisms of both abiotic stress resistance (including salinity, drought and heat stresses) and biotic stress resistance (including disease and insect resistance). Special attention is given to the desert halophytes and their utilization to alleviate the salinity stress, which is one of the major challenges in agriculture. In addition, symbioses with microorganisms are thought to be hypothesized as important components of desert plant survival under stressful environmental conditions. Thus, factors shaping the diversity and functionality of plant microbiomes in desert ecosystems are also emphasized in this article. It is important to establish a critical mass for biotechnology research and applications while strengthening the channels for collaboration among research/academic institutions in the area of desert plant biotechnology.
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Affiliation(s)
- Sanjay Gairola
- Sharjah Seed Bank and Herbarium, Sharjah Research Academy, University City, Sharjah, P. Box 60999, Sharjah, UAE
| | - Khawla I. Al Shaer
- Plant Molecular Biology and Biotechnology Laboratory, Sharjah Research Academy, University City, Sharjah, P. Box 60999, Sharjah, UAE
| | - Eman K. Al Harthi
- Plant Molecular Biology and Biotechnology Laboratory, Sharjah Research Academy, University City, Sharjah, P. Box 60999, Sharjah, UAE
| | - Kareem A. Mosa
- Department of Applied Biology, College of Sciences, University of Sharjah, P.O. Box 27272, Sharjah, UAE
- Department of Biotechnology, Faculty of Agriculture, Al-Azhar University, Cairo, Egypt
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Verma KS, ul Haq S, Kachhwaha S, Kothari SL. RAPD and ISSR marker assessment of genetic diversity in Citrullus colocynthis (L.) Schrad: a unique source of germplasm highly adapted to drought and high-temperature stress. 3 Biotech 2017; 7:288. [PMID: 28868215 PMCID: PMC5570720 DOI: 10.1007/s13205-017-0918-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 08/16/2017] [Indexed: 10/19/2022] Open
Abstract
Citrullus colocynthis (L.) Schrad. (Cucurbitaceae) shows high levels of variation in fruit color, fruit stripe pattern, seed coat color, and size. Thirty-eight accessions of C. colocynthis plants from different parts of semi-arid Rajasthan were collected and genetic diversity was assessed using random-amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR) markers. Out of 65 RAPD decamer primers, 50 primers produced 549 scorable bands of which 318 were polymorphic. Polymorphic banding patterns with the number of amplified fragments varied from 5 (OPA-08 and OPF-9) to 19 (OPT-20) in the molecular size range of 150-6000 bp. Percent polymorphism ranged from 22.2% (OPA-09) to 83.3% (OPE-12) with 55.14% polymorphism. Out of the 20 ISSR primers screened, 13 primers produced 166 amplification products, of which 99 were polymorphic. The number of bands amplified per primer varied between 9 (UBC-807, 802) and 16 (UBC-803, 812) with average band size between 250 and 4000 bp. Percent polymorphism ranged from 45.4% (UBC-815) to 73.3% (UBC-814) with 65.05% polymorphism. Dendrogram constructed on the basis of RAPD + ISSR polymorphism separated the accessions into four distinct clusters at 72% variation with Jaccard's similarity coefficient ranging from minimum 0.64 to 0.95. The matrices for RAPD and ISSR were also compared using Mantel's test and obtained correlation value (r = 0.7947). Discriminating power of RAPD and ISSR markers was assessed by calculating polymorphic information content, multiplex ratio, marker index, and resolving power. Approx. 50% RAPD and ISSR markers showed PIC value and heterozygosity (H) ≥ 0.50, indicating marker as informative. The primers that showed higher polymorphism had higher RP, MR, and MI values.
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Affiliation(s)
- Kumar Sambhav Verma
- Department of Botany, University of Rajasthan, Jaipur, India
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, 302006 India
| | - Shamshad ul Haq
- Department of Botany, University of Rajasthan, Jaipur, India
| | - Sumita Kachhwaha
- Department of Botany, University of Rajasthan, Jaipur, India
- Bioinformatics Infrastructure Facility (BIF), University of Rajasthan, Jaipur, India
| | - S. L. Kothari
- Department of Botany, University of Rajasthan, Jaipur, India
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, 302006 India
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Al-Qurainy F, Nadeem M, Khan S, Alansi S, Tarroum M, Al-Ameri AA, Gaafar ARZ, Alshameri A. Rapid plant regeneration, validation of genetic integrity by ISSR markers and conservation of Reseda pentagyna an endemic plant growing in Saudi Arabia. Saudi J Biol Sci 2017; 25:111-116. [PMID: 29379366 PMCID: PMC5775100 DOI: 10.1016/j.sjbs.2017.07.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2017] [Revised: 06/27/2017] [Accepted: 07/15/2017] [Indexed: 12/31/2022] Open
Abstract
Reseda pentagyna is the only endemic species among the seven species of the genera Reseda found in Saudi Arabia. Probably no information is available on regeneration by conventional method of regeneration through seeds or cuttings. Therefore, alternative method of tissue culture was attempted to regenerate and multiply the plant. High shoot regeneration (14.44 shoots/explant) was obtained after four weeks, when shoot cuttings cultured on MS containing BA at 1.0 µM. Other cytokinins e.g., Kn, 2iP and TDZ found to be less effective in bud induction and shoot multiplication. Individual shoots were rooted on MS medium supplemented with various auxins at 0.5–5.0 µM concentrations. The IBA (1.5 µM) supplemented MS media induced maximum (83.3%) rooting. The plantlets were acclimatized and hardened under greenhouse conditions in plastic pots containing soil and farm yard manure with 95.0% success. The protocol developed would help to multiply the plant as well as conserve them in natural habitat. This can also be utilized to obtain active constituents for pharmaceutics and genetic manipulations.
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Affiliation(s)
- Fahad Al-Qurainy
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Mohammad Nadeem
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Salim Khan
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Saleh Alansi
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Mohamed Tarroum
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Abdulhafed A Al-Ameri
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Abdel-Rhman Z Gaafar
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Aref Alshameri
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
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Assaeed AM, Al-Faifi SA, Migdadi HM, El-Bana MI, Al Qarawi AA, Khan MA. Evaluation of genetic diversity of Panicum turgidum Forssk from Saudi Arabia. Saudi J Biol Sci 2017; 25:123-129. [PMID: 29379368 PMCID: PMC5775083 DOI: 10.1016/j.sjbs.2017.04.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Revised: 03/18/2017] [Accepted: 04/10/2017] [Indexed: 11/28/2022] Open
Abstract
The genetic diversity of 177 accessions of Panicum turgidum Forssk, representing ten populations collected from four geographical regions in Saudi Arabia, was analyzed using amplified fragment length polymorphism (AFLP) markers. A set of four primer-pairs with two/three selective nucleotides scored 836 AFLP amplified fragments (putative loci/genome landmarks), all of which were polymorphic. Populations collected from the southern region of the country showed the highest genetic diversity parameters, whereas those collected from the central regions showed the lowest values. Analysis of molecular variance (AMOVA) revealed that 78% of the genetic variability was attributable to differences within populations. Pairwise values for population differentiation and genetic structure were statistically significant for all variances. The UPGMA dendrogram, validated by principal coordinate analysis-grouped accessions, corresponded to the geographical origin of the accessions. Mantel's test showed that there was a significant correlation between the genetic and geographical distances (r = 0.35, P < 0.04). In summary, the AFLP assay demonstrated the existence of substantial genetic variation in P. turgidum. The relationship between the genetic diversity and geographical source of P. turgidum populations of Saudi Arabia, as revealed through this comprehensive study, will enable effective resource management and restoration of new areas without compromising adaptation and genetic diversity.
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Affiliation(s)
- Abdulaziz M Assaeed
- Department of Plant Production, King Saud University, PO Box 2460, Riyadh 11451, Saudi Arabia
| | - Sulieman A Al-Faifi
- Department of Plant Production, King Saud University, PO Box 2460, Riyadh 11451, Saudi Arabia
| | - Hussein M Migdadi
- Department of Plant Production, King Saud University, PO Box 2460, Riyadh 11451, Saudi Arabia
| | - Magdy I El-Bana
- Department of Botany, Faculty of Science, Port Said University, Egypt
| | - Abdulaziz A Al Qarawi
- Department of Plant Production, King Saud University, PO Box 2460, Riyadh 11451, Saudi Arabia
| | - Mohammad Altaf Khan
- Department of Plant Production, King Saud University, PO Box 2460, Riyadh 11451, Saudi Arabia
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15
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Sadeq MA, Pathak MR, Salih AA, Abido M, Abahussain A. In Vitro Regeneration of Endangered Medicinal Plant Heliotropium kotschyi (Ramram). Methods Mol Biol 2016; 1391:103-112. [PMID: 27108312 DOI: 10.1007/978-1-4939-3332-7_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Heliotropium kotschyi (Ramram) is an important endangered medicinal plant distributed in the Kingdom of Bahrain. Plant tissue culture technique is applied for ex situ conservation study. Nodal stem segments are cultured in modified MS media supplemented with various combination and concentration of plant growth regulators (PGRs). Plants are regenerated via shoot organogenesis from the nodal meristems. Plants are regenerated in three different steps: initial shoot development, shoot multiplication, and rooting. After 4 weeks of culture, 100 % explants respond to shoot initiation on the medium containing 8.88 μM BAP and 5.71 μM IAA. The highest frequency of shoot regeneration is observed in the same media after second subculture of shoots. The highest rooting frequency is observed in the presence of 2.85 μM IAA. After root development, the plantlets are transferred to pots filled with soil and 60 % of plants survived after 45 days. This plant regeneration protocol is of great value for rapid desert plant propagation program.
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Affiliation(s)
- Manal Ahmed Sadeq
- Desert and Arid Zone Sciences Program, College of Graduate Studies, Arabian Gulf University, Manama, Kingdom of Bahrain
| | - Malabika Roy Pathak
- Department of Life Sciences, Agricultural Biotechnology Program, College of Graduate Studies, Arabian Gulf University, Manama, Kingdom of Bahrain.
| | - Ahmed Ali Salih
- Desert and Arid Zone Sciences Program, College of Graduate Studies, Arabian Gulf University, Manama, Kingdom of Bahrain
| | - Mohammed Abido
- Desert and Arid Zone Sciences Program, College of Graduate Studies, Arabian Gulf University, Manama, Kingdom of Bahrain
| | - Asma Abahussain
- Desert and Arid Zone Sciences Program, College of Graduate Studies, Arabian Gulf University, Manama, Kingdom of Bahrain
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16
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Phenology and reintroduction strategies for Dendrobium aqueum Lindley – An endemic, near threatened orchid. J Nat Conserv 2015. [DOI: 10.1016/j.jnc.2014.11.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Gaafar ARZ, Al-Qurainy F, Khan S. Assessment of genetic diversity in the endangered populations of Breonadia salicina (Rubiaceae) growing in the kingdom of Saudi Arabia using inter-simple sequence repeat markers. BMC Genet 2014; 15:109. [PMID: 25277598 PMCID: PMC4192337 DOI: 10.1186/s12863-014-0109-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2013] [Accepted: 09/29/2014] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Breonadia salicina (Rubiaceae) is a critically endangered plant at the local scale native to southwestern Saudi Arabia. To understand the levels and partitioning of genetic variation across populations and geographical regions of this species, we assessed its genetic diversity using inter-simple sequence repeat (ISSR) markers. RESULTS Fourteen ISSR primers selected from 43 primers gave rise to 211 amplified loci, of which 68 were polymorphic. The percentage of polymorphic loci (PPL) at the population level ranged from 17.1 to 23.7%, with an average of 21.3%. Nei's gene diversity (h) and Shannon's information index (I) were 0.086 and 0.125, respectively. At the species level, PPL was 32.2%, while h and I were 0.116 and 0.172, respectively. A hierarchical analysis of molecular variance revealed a high level of genetic differentiation among populations (17% of total variance, P = 0.001), consistent with the gene differentiation coefficient (G ST = 0.256). Nevertheless, the evaluated genetic diversity was very low within populations; while relatively high among populations, levels were insufficient for long-term survival. Saudi Arabian accessions were also compared to accessions of a population from Yemen, where the species is more widespread. The Yemeni population also showed low genetic diversity but clustered separately. CONCLUSIONS Breonadia salicina in Saudi Arabia is characterized by low within-population genetic diversity and high among-population genetic differentiation. Based on our findings, this locally endangered species is on the verge of local extinction. The species' survival depends on successful implementation of suggested strategies for its long-term conservation.
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Saurabh S, Vidyarthi AS, Prasad D. RNA interference: concept to reality in crop improvement. PLANTA 2014; 239:543-64. [PMID: 24402564 DOI: 10.1007/s00425-013-2019-5] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2013] [Accepted: 12/21/2013] [Indexed: 05/18/2023]
Abstract
The phenomenon of RNA interference (RNAi) is involved in sequence-specific gene regulation driven by the introduction of dsRNA resulting in inhibition of translation or transcriptional repression. Since the discovery of RNAi and its regulatory potentials, it has become evident that RNAi has immense potential in opening a new vista for crop improvement. RNAi technology is precise, efficient, stable and better than antisense technology. It has been employed successfully to alter the gene expression in plants for better quality traits. The impact of RNAi to improve the crop plants has proved to be a novel approach in combating the biotic and abiotic stresses and the nutritional improvement in terms of bio-fortification and bio-elimination. It has been employed successfully to bring about modifications of several desired traits in different plants. These modifications include nutritional improvements, reduced content of food allergens and toxic compounds, enhanced defence against biotic and abiotic stresses, alteration in morphology, crafting male sterility, enhanced secondary metabolite synthesis and seedless plant varieties. However, crop plants developed by RNAi strategy may create biosafety risks. So, there is a need for risk assessment of GM crops in order to make RNAi a better tool to develop crops with biosafety measures. This article is an attempt to review the RNAi, its biochemistry, and the achievements attributed to the application of RNAi in crop improvement.
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Affiliation(s)
- Satyajit Saurabh
- Department of Biotechnology, Birla Institute of Technology, Mesra, Ranchi, 835125, India
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Al-Qurainy F, Khan S, Nadeem M, Tarroum M, Alaklabi A. Assessment of phylogenetic relationship of rare plant species collected from Saudi Arabia using internal transcribed spacer sequences of nuclear ribosomal DNA. GENETICS AND MOLECULAR RESEARCH 2013; 12:723-30. [PMID: 23546955 DOI: 10.4238/2013.march.11.21] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The rare and endangered plants of any country are important genetic resources that often require urgent conservation measures. Assessment of phylogenetic relationships and evaluation of genetic diversity is very important prior to implementation of conservation strategies for saving rare and endangered plant species. We used internal transcribed spacer sequences of nuclear ribosomal DNA for the evaluation of sequence identity from the available taxa in the GenBank database by using the Basic Local Alignment Search Tool (BLAST). Two rare plant species viz, Heliotropium strigosum claded with H. pilosum (98% branch support) and Pancratium tortuosum claded with P. tenuifolium (61% branch support) clearly. However, some species, viz Scadoxus multiflorus, Commiphora myrrha and Senecio hadiensis showed close relationships with more than one species. We conclude that nuclear ribosomal internal transcribed spacer sequences are useful markers for phylogenetic study of these rare plant species in Saudi Arabia.
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Affiliation(s)
- F Al-Qurainy
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
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