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Pan H, Deng L, Zhu K, Shi D, Wang F, Cui G. Evaluation of genetic diversity and population structure of Annamocarya sinensis using SCoT markers. PLoS One 2024; 19:e0309283. [PMID: 39231174 PMCID: PMC11373820 DOI: 10.1371/journal.pone.0309283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Accepted: 08/09/2024] [Indexed: 09/06/2024] Open
Abstract
Annamocarya sinensis (Dode) Leroy, a relict plant from the Tertiary period, is a member of Annamocarya genus in the Juglandaceae family. Despite its wide distribution in Guangxi Province, the habitats of this species had become fragmented and isolated, causing it facing deterioration. For protecting this endangered species, it is crucial to understand its status in the wild and genetic diversity. In this study, 216 A. sinensis accessions from 18 populations in Guangxi were examined using Start Codon Target Polymorphism (SCoT) markers for PCR amplification, genetic diversity, and population structure analysis. Out of the 20 SCoT primers used, 222 sites were amplified, with 185 being polymorphic (PPB of 83.33%). Polymorphic information content values ranged from 0.4380 to 0.4999, Nei's genetic diversity index ranging from 0.1573 to 0.2503, and Shannon diversity index ranged from 0.1583 to 0.3812. Through AMOVA analysis, the total genetic diversity and genetic diversity within populations was calculated out as 0.3271 and 0.1542 respectively, the genetic differentiation coefficient between populations was 0.5286, with a gene flow 0.4458. Cluster analysis categorized A. sinensis germplasm into three groups, while population structure analysis divided all accessions into three ancestral sources with 19.91% showing mixed ancestral origins. No significant correlation was observed between genetic and geographical distance on the Mentel test (r = 0.07348, p = 0.7468). Overall, A. sinensis displays a relatively rich genetic diversity at the species level, albeit with a fairly uniform genetic background and high genetic differentiation. This study provides a crucial basis for the conservation and innovative use of A. sinensis germplasm resources.
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Affiliation(s)
- Hong Pan
- College of Nature Conservation, Beijing Forestry University, Beijing, China
- Fangcheng Golden Camellia National Nature Reserve Management Center, Fangchenggang, China
| | - Libao Deng
- Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Kaixian Zhu
- Scientific Research Academy of Guangxi Environmental Protection, Nanning, China
| | - Deju Shi
- Guangxi University, Nanning, China
| | - Feiyong Wang
- Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Guofa Cui
- College of Nature Conservation, Beijing Forestry University, Beijing, China
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Abdelhameed AA, Ali M, Darwish DBE, AlShaqhaa MA, Selim DAFH, Nagah A, Zayed M. Induced genetic diversity through mutagenesis in wheat gene pool and significant use of SCoT markers to underpin key agronomic traits. BMC PLANT BIOLOGY 2024; 24:673. [PMID: 39004709 PMCID: PMC11247860 DOI: 10.1186/s12870-024-05345-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 06/26/2024] [Indexed: 07/16/2024]
Abstract
BACKGROUND This research explores the efficacy of mutagenesis, specifically using sodium azide (SA) and hydrazine hydrate (HZ) treatments, to introduce genetic diversity and enhance traits in three wheat (Triticum aestivum L.) genotypes. The experiment entails subjecting the seeds to different doses of SA and HZ and cultivating them in the field for two consecutive generations: M1 (first generation) and M2 (second generation). We then employed selective breeding techniques with Start Codon Targeted (SCoT) markers to select traits within the wheat gene pool. Also, the correlation between SCoT markers and specific agronomic traits provides insights into the genetic mechanisms underlying mutagenesis-induced changes in wheat. RESULTS In the study, eleven genotypes were derived from parent varieties Sids1, Sids12, and Giza 168, and eight mutant genotypes were selected from the M1 generation and further cultivated to establish the M2 generation. The results revealed that various morphological and agronomical characteristics, such as plant height, spikes per plant, spike length, spikelet per spike, grains per spikelet, and 100-grain weight, showed increases in different genotypes from M1 to M2. SCoT markers were employed to assess genetic diversity among the eleven genotypes. The bioinformatics analysis identified a correlation between SCoT markers and the transcription factors ABSCISIC ACID INSENSITIVE3 (ABI3) and VIVIPAROUS1 (VP1), crucial for plant development, growth, and stress adaptation. A comprehensive examination of genetic distance and the function identification of gene-associated SCoT markers may provide valuable insights into the mechanisms by which SA and HZ act as mutagens, enhancing wheat agronomic qualities. CONCLUSIONS This study demonstrates the effective use of SA and HZ treatments to induce gene diversity through mutagenesis in the wheat gene pool, resulting in the enhancement of agronomic traits, as revealed by SCoT markers. The significant improvements in morphological and agronomical characteristics highlight the potential of mutagenesis techniques for crop improvement. These findings offer valuable information for breeders to develop effective breeding programs to enhance wheat quality and resilience through increased genetic diversity.
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Affiliation(s)
- Ahmed Ali Abdelhameed
- Agricultural Botany Department (Genetics), Faculty of Agriculture, Al-Azhar University, Assuit Branch, Assuit, 71524, Egypt
| | - Mohammed Ali
- Maryout Research Station, Genetic Resources Department, Desert Research Center, 1 Mathaf El-Matarya St., El-Matareya, Cairo, 11753, Egypt
| | | | | | - Dalia Abdel-Fattah H Selim
- Department of Agricultural Botany, Faculty of Agricultural, Menoufia University, Shebin El-Kom, 32511, Egypt
| | - Aziza Nagah
- Botany and Microbiology Department, Faculty of Science, Benha University, Benha, 13518, Egypt
| | - Muhammad Zayed
- Department of Botany and Microbiology, Faculty of Science, Menoufia University, Shebin El-Kom, 32511, Egypt.
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Alhaithloul HAS, Awad NS, Qari SH, El-Homosy RF, Qaoud ESM, Alqahtani MM, Ghanem KZ, Alasmari A, Alzuaibr FM, Ghazzawy HS, Abdein MA. Genetic diversity, chemical constituents and anatomical analysis of eight popular Olive (Olea europaea L.) cultivars in Al-Jouf region, Saudi Arabia. Sci Rep 2024; 14:14688. [PMID: 38918489 PMCID: PMC11199486 DOI: 10.1038/s41598-024-65542-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 06/20/2024] [Indexed: 06/27/2024] Open
Abstract
In light of the multitude of olive trees cultivated and the lack of the genetic diversity of available genotypes to select varieties and lines that are characterized by high diversity and better performance under the corresponding conditions, A comparison analysis of the genotyping and morphological characteristics of eight olive cultivars growing in Saudi Arabia's Al-Jouf region was conducted and analyzed. Morpho-anatomical and chemical characteristics along with both inter-simple-sequence repeats (ISSRs) and start-codon-targeted (SCoT) markers were used to evaluate the genetic diversity among eight olive varieties in Al-Jouf, Saudi Arabia. Analyses of 27 morphological, chemical, and anatomical characteristics concluded the existence of genetic differences among the studied varieties. Moreover, six ISSR and eight SCoT primer combinations produced a total of 48 loci, of which 18 (10 ISSR and 8 SCoT) were polymorphic. The average polymorphism information content (PIC values of 0.48 and 0.44, respectively) and marker index (MI of 0.79 and 0.48, respectively) detected for ISSR and SCoT markers revealed the prevalence of high genetic diversity among the studied olive varieties. Based on chemical and anatomical characteristics and the selected molecular markers, the eight olive cultivars were grouped into two distinct clusters. Clusters in the adjacent joint dendrogram produced using ISSR, SCoT and combined data were similar, and grouped all individuals into two groups. However, the dendrogram generated on the basis of SCoT separated individuals into subgroups containing at least two varieties. The findings showed that both methods were effective in assessing diversity, and that SCoT markers can be used as a reliable and informative method for assessing genetic diversity and relationships among olive varieties and can serve as a complementary tool to provide a more complete understanding of the genetic diversity available in Olea europaea populations in Saudi Arabia.
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Affiliation(s)
- Haifa A S Alhaithloul
- Biology Department, College of Science, Jouf University, 2014, Sakaka, Al-Jouf, Saudi Arabia
| | - Nabil S Awad
- Department of Genetics, Faculty of Agriculture and Natural Resources, Aswan University, Aswân, Egypt
- College of Biotechnology, Misr University for Science and Technology, Giza, Egypt
| | - Sameer H Qari
- Biology Department, Genetics and Molecular Biology Central Laboratory, Aljumum University College, Umm Al-Qura University, Mecca, Saudi Arabia
| | - Rania F El-Homosy
- Genetics Department, Faculty of Agriculture, Assiut University, Assiut, 71516, Egypt
| | - El-Sayed M Qaoud
- Horticultural Department, Faculty of Agriculture, Suez Canal University, Ismailia, 41522, Egypt
| | - Mesfer M Alqahtani
- Department of Biological Sciences, Faculty of Science and Humanities, Shaqra University, P. O. Box 1040, 11911, Ad-Dawadimi, Saudi Arabia
| | - Kholoud Z Ghanem
- Department of Biological Science, College of Science &Humanities, Shaqra University, 11961, Riyadh, Saudi Arabia
| | - Abdulrahman Alasmari
- Biology Department, College of Science, University of Tabuk, 47713, Tabuk, Saudi Arabia
| | - Fahad M Alzuaibr
- Biology Department, College of Science, University of Tabuk, 47713, Tabuk, Saudi Arabia
| | - Hesham S Ghazzawy
- Date Palm Research Center of Excellence, King Faisal University, 31982, Al-Ahsa, Saudi Arabia
- Central Laboratory for Date Palm Research and Development, Agriculture Research Center, Giza, 12511, Egypt
| | - Mohamed A Abdein
- Seeds Development Department, El-Nada Misr Scientific Research and Development Projects, Turrell, Mansoura, 35511, Egypt.
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Al-Yasi HM, Al-Qthanin R. Comparing genetic differentiation and variation using ISSR and SCoT among Juniper plant markers in Saudi Arabia. FRONTIERS IN PLANT SCIENCE 2024; 15:1356917. [PMID: 38638351 PMCID: PMC11025456 DOI: 10.3389/fpls.2024.1356917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Accepted: 03/04/2024] [Indexed: 04/20/2024]
Abstract
Juniperus, a genus of fragrant evergreen trees in the Cupressaceae family, encompasses up to 67 distinct species distributed globally. Among these, Juniperus procera, also known as the East African pencil cedar or African Juniper, stands out for its notable medicinal properties. Due to the well-recognized therapeutic benefits of Juniper species, assessing genetic diversity is essential for various breeding initiatives. Thus, in this work, six ISSR and six SCoT primers were utilized to evaluate the genetic diversity between 23 Juniper genotypes collected from different locations in Saudi Arabia. 29 out of 103 and 26 out of 105 amplified bands, respectively, were found to be polymorphic markers using the ISSR and SCoT studies. With the help of 120 genotype-specific markers, including 60 for ISSR and 60 for SCoT, several varieties of Juniper were discovered. In addition, the polymorphism information content (PIC) was computed to assess the effectiveness of the markers. The findings of this study highlight the importance of conserving the genetic diversity of Juniperus procera, as it holds immense potential for developing new medicinal products. Additionally, the results provide valuable insights into the genetic structure of Juniper populations in western Saudi Arabia, which can inform future conservation and management efforts. However, all of the techniques utilized to profile the genotypes of Juniper can be regarded as useful techniques for long-term fingerprinting and diagnostic markers.
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Affiliation(s)
- Hatim M. Al-Yasi
- Department of Biology, College of Science, Taif University, Taif, Saudi Arabia
| | - Rahmah Al-Qthanin
- Biology Department, College of Sciences, King Khalid University, Abha, Saudi Arabia
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Alzahrani OR, Alshehri MA, Alasmari A, Ibrahim SD, Oyouni AA, Siddiqui ZH. Evaluation of genetic diversity among Saudi Arabian and Egyptian cultivars of alfalfa ( Medicago sativa L.) using ISSR and SCoT markers. JOURNAL OF TAIBAH UNIVERSITY FOR SCIENCE 2023. [DOI: 10.1080/16583655.2023.2194187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2023]
Affiliation(s)
- Othman R. Alzahrani
- Department of Biology, Faculty of Science, University of Tabuk, Tabuk, Saudi Arabia
- Genome and Biotechnology Unit, Faculty of Science, University of Tabuk, Tabuk, Saudi Arabia
| | - M. Ali Alshehri
- Department of Biology, Faculty of Science, University of Tabuk, Tabuk, Saudi Arabia
- Genome and Biotechnology Unit, Faculty of Science, University of Tabuk, Tabuk, Saudi Arabia
| | - A. Alasmari
- Department of Biology, Faculty of Science, University of Tabuk, Tabuk, Saudi Arabia
- Genome and Biotechnology Unit, Faculty of Science, University of Tabuk, Tabuk, Saudi Arabia
| | - S. D. Ibrahim
- Agricultural Genetic Engineering Research Institute (AGERI), ARC, Giza, Egypt
| | - Atif A. Oyouni
- Department of Biology, Faculty of Science, University of Tabuk, Tabuk, Saudi Arabia
- Genome and Biotechnology Unit, Faculty of Science, University of Tabuk, Tabuk, Saudi Arabia
| | - Zahid H. Siddiqui
- Department of Biology, Faculty of Science, University of Tabuk, Tabuk, Saudi Arabia
- Genome and Biotechnology Unit, Faculty of Science, University of Tabuk, Tabuk, Saudi Arabia
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Mahdieh M, Talebi SM, Dehghan T, Tabaripour R, Matsyura A. Molecular genetics, seed morphology and fatty acids diversity in castor (Ricinus communis L., Euphorbiaceae) Iranian populations. Mol Biol Rep 2023; 50:9859-9873. [PMID: 37848759 DOI: 10.1007/s11033-023-08904-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Accepted: 10/06/2023] [Indexed: 10/19/2023]
Abstract
BACKGROUND Castor (Ricinus communis L.) seeds contain a large amount of oil that has several biological activities. In the current research, phytogeographic distribution, seed morphological characteristics, molecular genetic diversity and structure, and fatty acid composition were investigated in nine Iranian castor populations. METHODS AND RESULTS The cetyltrimethylammonium bromide (CTAB) protocol was used to extract the nuclear genomes. These were later amplified using 13 SCoT molecular primers. The phytogeographic distribution was determined based on the Zohary mapping, GC apparatus determined the fatty acid composition of the seeds. GenAlex, STRUCTURE, GenoDive, PopGene, and PopART software were used for the statistical analyzes. On phytogeographic mapping, the harvested populations belonged to different districts of the Euro-Siberian and Irano-Turanian regions (Holarctic kingdom). Most of the quantitative morphological traits of the seeds differed significantly (P ≤ 0.05) between the populations. The AMOVA test demonstrated a large proportion of significant genetic diversity assigned among populations, which were approved by some estimated parameters of genetic diversity such as Nm, Ht, Hs, and Gst. Nei's genetic distance and structure analysis confirmed the existence of two main genotype groups and some intermediates. However, there was no isolation by distance between the genotypes. Unsaturated fatty acids were detected as the main component of seed oil with linoleic and ricinoleic acids. Significant correlations were detected between the main fatty acids of seed oil with seed morphological traits, geographic distance and the geographic parameters of habitats. According to the composition of the seed fatty acids, four chemotypes groups were detected. CONCLUSIONS The classification patterns of the populations based on molecular genetic data, fatty acid composition, and phytogeographic mapping were not identical. These findings indicated that Iranian castor populations had unusual seed fatty acid composition which strongly depended on habitat geographic factors and seed morphological traits. However, the identified chemotypes and genotypes can be used in future breeding programs.
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Affiliation(s)
- Majid Mahdieh
- Department of Biology, Faculty of Sciences, Arak University, Arak, 38156-8-8349, Iran
| | - Seyed Mehdi Talebi
- Department of Biology, Faculty of Sciences, Arak University, Arak, 38156-8-8349, Iran.
| | - Tahereh Dehghan
- Department of Biology, Faculty of Sciences, Arak University, Arak, 38156-8-8349, Iran
| | - Raheleh Tabaripour
- Department of Plant Sciences, Faculty of Biological Sciences, Alzahra University, Tehran, Iran
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Bakry SM, Aboul Naser AF, El Negoumy SIM, Kassem MES, Meselhy MR, Abdel-Sattar E. Comparative LC-MS/MS-based molecular networking, DNA fingerprinting, and in vitro anti-Helicobacter pylori activity of three Egyptian Ficus cultivars. J Pharm Biomed Anal 2023; 235:115620. [PMID: 37557066 DOI: 10.1016/j.jpba.2023.115620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 07/30/2023] [Accepted: 07/30/2023] [Indexed: 08/11/2023]
Abstract
Ficus species (Moraceae) have been used for nutrition and traditional medicine, and plants from this family are phytochemically abundant and serve as a potential source of natural products. As a result of the inherent complexity of the plant metabolomes and the fact that these Ficus species chemical space has not yet been fully decoded, it is still difficult to characterize their phytochemistry. Therefore, this study, we suggest the use of the molecular networking to elucidate the chemical classes existing in leaves of three Ficus species (F. deltoidei Jack, F. drupacea Thunb and F. sycomorus L.) and highlight the importance of molecular networking in examining their chemotaxonomy . By using computational tools, 90 metabolites were annotated , including phenolic acids, flavonoids, furanocoumarins, fatty acids and terpenoids. Phenolic acids were detected as the main class present in the three studied species. Flavonoids-C-glycosides, flavonoids-O-glycosides and isoflavonoids were mainly present in F. drupacea and F. sycomorus, while furanocoumarins were proposed in F. sycomorus. Vomifoliol-based sesquiterpenes were proposed in F. deltoidei. The chemotaxonomic differentiation agreed with the DNA fingerprinting using SCOT and ISSR markers. F. deltoidei, in particular, had a divergent chemical fingerprint as well as a different genotype. Chemotype differentiation using chemical fingerprints, in conjunction with the proposed genetic markers, creates an effective identification tool for the quality control of the raw materials and products derived from those three Ficus species. As well, F. drupacea exploited the most potent inhibition of H. pylori with MIC of 7.81 µg/ mL compared with clarithromycin. Overall, molecular networking provides a promising approach for the exploration of the chemical space of plant metabolomes and the elucidation of chemotaxonomy.
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Affiliation(s)
- Sherien M Bakry
- Phytochemistry and Plant Systematics Department, National Research Centre (NRC), 33 El Bohouth St., Dokki, 12622 Giza, Egypt
| | - Asmaa F Aboul Naser
- Therapeutic Chemistry Department, National Research Centre (NRC), 33 El Bohouth St., Dokki, 12622 Giza, Egypt
| | - Sabry I M El Negoumy
- Phytochemistry and Plant Systematics Department, National Research Centre (NRC), 33 El Bohouth St., Dokki, 12622 Giza, Egypt
| | - Mona E S Kassem
- Phytochemistry and Plant Systematics Department, National Research Centre (NRC), 33 El Bohouth St., Dokki, 12622 Giza, Egypt
| | - Meselhy R Meselhy
- Pharmacognosy Department, Faculty of Pharmacy, Cairo University, 11562 Cairo, Egypt
| | - Essam Abdel-Sattar
- Pharmacognosy Department, Faculty of Pharmacy, Cairo University, 11562 Cairo, Egypt.
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Salama DM, Osman SA, Shaaban EA, Abd Elwahed MS, Abd El-Aziz ME. Effect of foliar application of phosphorus nanoparticles on the performance and sustainable agriculture of sweet corn. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 203:108058. [PMID: 37778115 DOI: 10.1016/j.plaphy.2023.108058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 09/09/2023] [Accepted: 09/25/2023] [Indexed: 10/03/2023]
Abstract
Traditional phosphorus fertilizers are necessary for plant growth but about 80-90% are lost into the surrounding environment via irrigation, therefore nano-fertilizers have been developed as slow-release fertilizers to achieve sustainable agriculture. This trial investigated the impact of the foliar application of hydroxyapatite nanoparticles (HA-NPs) as a source of nano-phosphorus (P-NPs) on two cultivars of sweet corn (yellow and white) throughout two seasons. The morphology and structure of the prepared HA-NPs were characterized via transmission electron microscopy (TEM) and X-ray diffractometry (XRD). In addition, agro-morphological criteria, chemical contents (i.e., photosynthetic pigments, phenols, indoles, minerals, etc.), and genomic template stability percentage (GTS%) were evaluated in the produced sweet corn. The application of 50 mg/l HA-NPs improved the growth characteristics, yield per hectare, leaf pigments, and chemical content of yellow sweet corn, whereas the application of 100 mg/l of HA-NPs to white sweet corn enhanced the vegetative characteristics, production, photosynthetic pigments, phenols, and indoles. The difference in results may be due to the presence of a +ve unique band with SCoT-4 and SCot-2 primers at 1250 and 470 bp in yellow and white corn treated with 50 and 100 mg/l, respectively. The minimum GTS% was recorded at a concentration of 75 mg/l for both white and yellow corn. The HA-NPs can be applied as a foliar source of P-NPs to achieve agricultural sustainability.
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Affiliation(s)
- Dina M Salama
- Vegetable Research Department, National Research Centre, 33 El Bohouth St., Dokki, Giza, P.O. 12622, Egypt.
| | - Samira A Osman
- Genetics and Cytology Department, National Research Centre, 33 El Bohouth St., Dokki, Giza, P.O. 12622, Egypt
| | - Essam A Shaaban
- Pomology Department, National Research Centre, 33 El Bohouth St., Dokki, Giza, P.O. 12622, Egypt
| | - M S Abd Elwahed
- Botany Department, National Research Centre, 33 El Bohouth St., Dokki, Giza, P.O. 12622, Egypt
| | - Mahmoud E Abd El-Aziz
- Polymers & Pigments Department, National Research Centre, 33 El Bohouth St., Dokki, Giza, P.O. 12622, Egypt.
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Aly AA, Safwat G, Eliwa NE, Eltawil AHM, Abd El-Aziz MH. Changes in morphological traits, anatomical and molecular alterations caused by gamma-rays and zinc oxide nanoparticles in spinach (Spinacia oleracea L.) plant. Biometals 2023; 36:1059-1079. [PMID: 37173538 PMCID: PMC10545649 DOI: 10.1007/s10534-023-00505-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 04/21/2023] [Indexed: 05/15/2023]
Abstract
Spinach seeds were irradiated with gamma-rays after that soaked in zinc oxide nanoparticles (ZnO-NPs) at 0.0, 50, 100 and 200 ppm for twenty-four hours at room temperature. Vegetative plant growth, photosynthetic pigments, and proline contents were investigated. Also, anatomical studies and the polymorphism by the SCoT technique were conducted. The present results revealed that the germination percentage was at the maximum values for the treatment of 100 ppm ZnO-NPs (92%), followed by 100 ppm ZnO-NPs + 60 Gy (90%). The application of ZnO-NPs resulted in an enhancement in the plant length. The maximum of chlorophylls and carotenoids content was recorded in the treatment, 100 ppm ZnO-NPs + 60 Gy. Meanwhile, the irradiation dose level (60 Gy) with all ZnO-NPs treatments increased proline content and reached its maximum increase to 1.069 mg/g FW for the treatment 60 Gy combined with 200 ppm ZnO-NPs. Also, the anatomical studies declared that there were variations between the treatments; un-irradiated and irradiated combined with ZnO-NPs plants which reveal that the leave epidermal tissue increased with 200 ppm ZnO-NPs in both the upper and lower epidermis. While irradiated plants with 60 Gy combined with 100 ppm ZnO-NPs gave more thickness of upper epidermis. As well as SCoT molecular marker technique effectively induced molecular alterations between the treatments. Where, SCoT primers targeted many new and missing amplicons that are expected to be associated with the lowly and highly expressed genes with 18.2 and 81.8%, respectively. Also, showed that the soaking in ZnO-NPs was helped for reducing molecular alteration rate, both spontaneous and induced by gamma irradiation. This nominates ZnO-NPs as potential nano-protective agents that can reduce irradiation-induced genetic damage.
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Affiliation(s)
- Amina A Aly
- Natural Products Department, National Center for Radiation Research and Technology, Egyptian Atomic Energy Authority (EAEA), Cairo, Egypt.
| | - Gehan Safwat
- Faculty of Biotechnology, October University for Modern Science and Arts (MSA), Giza, Egypt
| | - Noha E Eliwa
- Natural Products Department, National Center for Radiation Research and Technology, Egyptian Atomic Energy Authority (EAEA), Cairo, Egypt
| | - Ahmed H M Eltawil
- Faculty of Biotechnology, October University for Modern Science and Arts (MSA), Giza, Egypt
| | - M H Abd El-Aziz
- Genetic Department Faculty of Agriculture, Mansoura University, Mansoura, Egypt
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Palacıoğlu G, Alkan M, Derviş S, Bayraktar H, Özer G. Molecular phylogeny of plant pathogenic fungi based on start codon targeted (SCoT) polymorphism. Mol Biol Rep 2023; 50:8271-8279. [PMID: 37578578 DOI: 10.1007/s11033-023-08735-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 08/02/2023] [Indexed: 08/15/2023]
Abstract
BACKGROUND A number of molecular marker systems have been developed to assess genetic diversity, carry out phylogenetic analysis, and diagnose and discriminate plant pathogenic fungi. The start codon targeted (SCoT) markers system is a novel approach used here to investigate intra and interspecific polymorphisms of phytopathogenic fungi. MATERIALS AND METHODS This study assessed genetic variability between and within 96 isolates of ten fungal species associated with a variety of plant species using 36 SCoT primers. RESULTS The six primers generated 331 distinct and reproducible banding patterns, of which 322 were polymorphic (97.28%), resulting in 53.67 polymorphic bands per primer. All primers produced informative amplification profiles that distinguished all fungal species. With a resolving power of 10.65, SCoT primer 12 showed the highest polymorphism among species, followed by primer 33 and primer 29. Polymorphic loci (PPL), Nei's diversity index (h), and Shannon index (I) percentages were 6.25, 0.018, and 0.028, respectively. UPGMA analysis separated all isolates based on morphological classification and revealed significant genetic variation among fungal isolates at the intraspecific level. PCoA analysis strongly supported fungal species discrimination and genetic variation. The other parameters of evaluation proved that SCoT markers are at least as effective as other DNA markers. CONCLUSIONS SCoT markers were effective in identifying plant pathogenic fungi and were a powerful tool for estimating genetic variation and population structure of different fungi species.
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Affiliation(s)
- Gülsüm Palacıoğlu
- Department of Plant Protection, Faculty of Agriculture, Şırnak University, Şırnak, Turkey
| | - Mehtap Alkan
- Department of Plant Protection, Faculty of Agriculture, Bolu Abant Izzet Baysal University, Bolu, Turkey
| | - Sibel Derviş
- Department of Plant and Animal Production, Vocational School of Kızıltepe, Mardin Artuklu University, Mardin, Turkey
| | - Harun Bayraktar
- Department of Plant Protection, Faculty of Agriculture, Ankara University, Ankara, Turkey.
| | - Göksel Özer
- Department of Plant Protection, Faculty of Agriculture, Bolu Abant Izzet Baysal University, Bolu, Turkey
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Abdelghany FM, Abdel-Warith AWA, Younis EM, Davies SJ, Elnakeeb MA, El-Nawasany MM, El-Bahlol AA, Bauomi MA, Abu-Almaaty AH, Omer MY. Genetic Differentiation of Five Sea Cucumber Species from the Red Sea, Hurghada, Egypt. BRAZ J BIOL 2023; 83:e271983. [PMID: 37283337 DOI: 10.1590/1519-6984.271983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 04/16/2023] [Indexed: 06/08/2023] Open
Abstract
This study aimed to assess the genetic differentiation and relationship among five sea cucumber species from the Red Sea in Egypt, namely Holothuria atra, H. impatiens, H. leucospilota, Actinopyga crassa and A. mauritiana, using Inter Simple Sequence Repeated (ISSR) and Start Codon Targeted (SCoT) markers. A collection of 100 specimens, with 20 individuals per species, was gathered for the analysis. With ten ISSR primers, 135 amplified bands were detected, including 11 distinct species-specific bands, indicating high-level polymorphism among species. Using ten SCoT primers, 151 amplicons were generated, including 30 species-specific bands, with 52% polymorphic bands indicating high-level polymorphism among species. The degree of genetic similarity (GS) among the different genotypes of species was calculated based on ISSR bands analysis, which ranged from 93% between H. atra and H. impatiens to 86% between H. atra and A. crassa. The highest genetic similarity was observed between H. atra and H. impatiens (90%), while the lowest was identified between A. crassa and A. mauritiana (75%) using SCoT bands. Notably, the ISSR and SCoT-based DNA analysis revealed similar genetic relationships between H. atra and H. impatiens compared to other sea cucumber species studied. This study provides new insights into the genetic diversity and relationship among sea cucumber species in the Red Sea, which could have implications for their conservation and management.
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Affiliation(s)
- F M Abdelghany
- Al-Azhar University, Faculty of Agriculture, Fish Production Department, Nasr City, Cairo, Egypt
| | - A W A Abdel-Warith
- King Saud University, College of Science, Department of Zoology, Riyadh, Saudi Arabia
| | - E M Younis
- King Saud University, College of Science, Department of Zoology, Riyadh, Saudi Arabia
| | - S J Davies
- National University of Ireland Galway, School of Science and Engineering, Galway, Ireland
| | - M A Elnakeeb
- Al-Azhar University, Faculty of Agriculture, Fish Production Department, Nasr City, Cairo, Egypt
| | - M M El-Nawasany
- Al-Azhar University, Faculty of Agriculture, Fish Production Department, Nasr City, Cairo, Egypt
| | - A A El-Bahlol
- Al-Azhar University, Faculty of Agriculture, Fish Production Department, Nasr City, Cairo, Egypt
| | - M A Bauomi
- Al-Azhar University, Faculty of Agriculture, Fish Production Department, Nasr City, Cairo, Egypt
| | - A H Abu-Almaaty
- Port Said University, Faculty of Science, Zoology Department, Port Said, Egypt
| | - M Y Omer
- National Institute of Oceanography and Fisheries, Hurghada, Egypt
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12
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Elsherif DE, Abd-ElShafy E, Khalifa AM. Impacts of ZnO as a nanofertilizer on fenugreek: some biochemical parameters and SCoT analysis. J Genet Eng Biotechnol 2023; 21:52. [PMID: 37126122 PMCID: PMC10151287 DOI: 10.1186/s43141-023-00501-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 04/20/2023] [Indexed: 05/02/2023]
Abstract
BACKGROUND Zinc oxide nanoparticles (ZnO NPs) can be considered as nanofertilizer providing zinc as an essential micronutrient for plant growth and production at specific safe dose, however, above this dose; ZnO NPs induce oxidative stress. The present research aimed to evaluate some physiological and molecular effects of ZnO NPs on Trigonella foenum-graecum (fenugreek) plant. RESULTS The ZnO NPs were applied at five different concentrations (10, 20, 30, 40, and 50 mg/l) via soaking fenugreek seeds for 24 h. Fenugreek seedlings were harvested after 14 days for biomass and biochemical analyses. The results revealed that increasing ZnO NPs concentration led to a significant increase in all measured parameters until peaked at 30 mg/l; after that, a decline trend was detected. However, malondialdehyde (MDA) increased significantly just at higher concentrations of ZnO NPs (40 and 50 mg/l). In addition, genetic variation measure using start codon targeted (SCoT) markers revealed that ZnO NP treatments exhibited limited genetic variation. CONCLUSION Results showed that treatment with ZnO NPs at 30 mg/l can improve biomass, bioactive compounds, and antioxidant activity of fenugreek seedlings, besides being safe for DNA. So, this concentration could be a decent nanofertilizer for fenugreek plant.
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Affiliation(s)
- Doaa E Elsherif
- Botany Department, Faculty of Science, Tanta University, Tanta, 31527, Egypt.
| | - Eman Abd-ElShafy
- Botany and Microbiology Department, Faculty of Science, Al-Azhar University (Girls Branch), Cairo, Egypt
| | - Asmaa M Khalifa
- Botany and Microbiology Department, Faculty of Science, Al-Azhar University (Girls Branch), Cairo, Egypt
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13
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Analysis of Genetic Diversity and Population Structure in Yam (Dioscorea Species) Germplasm Using Start Codon Targeted (SCoT) Molecular Markers. INTERNATIONAL JOURNAL OF PLANT BIOLOGY 2023. [DOI: 10.3390/ijpb14010025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023] Open
Abstract
Yam (Dioscorea spp.) is an important food security crop with economic, nutritional, and medicinal value. It is a source of carbohydrates for millions of people in tropical and sub-tropical regions of Africa, Asia, South America, the Caribbean, and the South Pacific Islands. Determining the appropriate parents for breeding programs is the most important decision that plant breeders must make to maximize genetic variability and produce excellent recombinant varieties. However, adequate genetic diversity and the population structure of yam accessions in Kenya are not available to guide accurate selection of parents for breeding. In the present study, 25 start-codon-targeted (SCoT) molecular markers were used to determine the genetic diversity and population structure among 20 yam accessions grown in Kenya. A total of 294 fragments were amplified, of which 95% were polymorphic with an average of 11.16 polymorphic fragments per primer. The polymorphic information content (PIC) value and primer resolving power (Rp) of 0.58 and 5.91, respectively, revealed high genetic diversity among the accessions. A dendrogram based on the unweighted pair group method of arithmetic means (UPGMA) grouped the 20 yam accessions into two clusters at 0.61 genetic similarity coefficients. Bayesian structure analysis revealed the existence of three subpopulations and some admixed accessions. Analysis of molecular variance (AMOVA) revealed a variance of 60% within the subpopulations and 40% among the subpopulations. The high degree of genetic diversity in the yam accessions successfully exhibited by SCoT molecular markers may serve as a valuable aid to widen the genetic base in yam breeding programs. The selection and hybridization of parental lines from the different clusters and sub-clusters identified could provide a foundation and could be exploited for yam breeding and variety development.
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Amer WM, Al Shaye NA, Hassan MO, Khalaf MH. Heteroblastic Inflorescence of Lamium amplexicaule L. in Egyptian Flora. PLANTS (BASEL, SWITZERLAND) 2023; 12:1028. [PMID: 36903891 PMCID: PMC10005391 DOI: 10.3390/plants12051028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 02/16/2023] [Accepted: 02/19/2023] [Indexed: 06/18/2023]
Abstract
Lamium amplexicaule L. (Family: Lamiaceae) is a cosmopolitan weed whose eradication is challenging. The phenoplasticity of this species is related to its heteroblastic inflorescence, which has not received adequate research worldwide in its morphological and genetic aspects. This inflorescence hosts two flower types, a cleistogamous (CL: closed flower) and a chasmogamous (CH: opened flower). This species subjected to detailed investigation is a model species to clarify: (1) the existence of the CL and CH flowers in relation to the time and individual plants. (2) the predominant flower morphs in Egypt. (3) the morphological and genetic variability between these morphs. Among the novel data retrieved from this work is the Presence of this species in three distinct morphs coexisting during winter. These morphs showed remarkable phenoplasticity, particularly in flower organs. Significant differences were observed between the three morphs in pollen fertility, nutlets productivity and sculpture, flowering time, and seed viability. These differences were extended to the genetic profile of these three morphs assessed by the inter simple sequence repeats (ISSRs) and start codon targeted (SCoT). This work highlights the urgent need to study the heteroblastic inflorescence of crop weeds to facilitate its eradication.
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Affiliation(s)
- Wafaa M. Amer
- Department of Botany and Microbiology, Faculty of Science, Cairo University, Giza 12613, Egypt
| | - Najla A. Al Shaye
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
| | - Mahmoud O. Hassan
- Department of Botany and Microbiology, Faculty of Science, Beni-Suef University, Beni-Suef 62521, Egypt
| | - Maha H. Khalaf
- Department of Botany and Microbiology, Faculty of Science, Beni-Suef University, Beni-Suef 62521, Egypt
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Rai MK. Start codon targeted (SCoT) polymorphism marker in plant genome analysis: current status and prospects. PLANTA 2023; 257:34. [PMID: 36622439 DOI: 10.1007/s00425-023-04067-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 01/04/2023] [Indexed: 06/17/2023]
Abstract
The present review illustrates a comprehensive overview of the start codon targeted (SCoT) polymorphism marker and their utilization in various applications related to genetic and genomic studies. Start codon targeted (SCoT) polymorphism marker, a targeted fingerprinting marker technique, has gained considerable importance in plant genetics, genomics, and molecular breeding due to its many desirable features. SCoT marker targets the region flanking the start codon, a highly conserved region in plant genes. Therefore, it can distinguish genetic variations in a specific gene that link to a specific trait. It is a simple, novel, cost-effective, highly polymorphic, and reproducible molecular marker for which there is no need for prior sequence information. In the recent past, SCoT markers have been employed in many commercially important and underutilized plant species for a variety of applications, including genetic diversity analysis, interspecific/generic genetic relationships, cultivar/hybrid/species identification, sex determination, construction of linkage map, association mapping/analysis, differential gene expression, and genetic fidelity analysis of tissue culture-raised plants. The main aim of this review is to provide up-to-date information on SCoT markers and their application in many commercially important and underutilized plant species, mainly progress made in the last 8-10 years.
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Affiliation(s)
- Manoj K Rai
- Department of Environmental Science, Indira Gandhi National Tribal University, Amarkantak, MP, 484887, India.
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Hussein ZS, Hegazy AK, Mohamed NH, El-Desouky MA, Ibrahim SD, Safwat G. Eco-physiological response and genotoxicity induced by crude petroleum oil in the potential phytoremediator Vinca rosea L. J Genet Eng Biotechnol 2022; 20:135. [PMID: 36125630 PMCID: PMC9489826 DOI: 10.1186/s43141-022-00412-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 08/25/2022] [Indexed: 11/29/2022]
Abstract
Background Phytoremediation is determined as an emerging green technology suitable for the safe remediation and restoration of polluted terrestrial and aquatic environments. In this study, the assessment of an ornamental plant, Vinca rosea L., as a phytoremediator of crude oil in polluted soils was conducted. In an open greenhouse experiment, plants were raised in sandy-clayey soils treated with 1, 3, 5, and 7% oil by weight. The experiment was conducted over 5 months. Results Total petroleum hydrocarbon (TPH) degradation percentage by V. rosea after a 5-month growth period ranged from 86.83 ± 0.44% to 59.05% ± 0.45% in soil treated with 1 and 7%, respectively. Plants raised in polluted soils demonstrated a dramatic reduction in germination rates, in addition to growth inhibition outcomes shown from decreased plant height. An increase in branching was observed with an increase in oil pollution percentages. Moreover, the phytomass allocated to the leaves was higher, while the phytomass witnessed lower values for fine roots, flowering and fruiting when compared to the controls. Apart from the apparent morphological changes, there was a decrease in chlorophyll a/b ratio, which was inversely proportional to the oil pollution level. The contents of carotenoids, tannins, phenolics, flavonoids, and antioxidant capacity were elevated directly with an increase in oil pollution level. The start codon-targeted (SCoT) polymorphisms and inter-simple sequence repeat (ISSR) primers showed the molecular variations between the control and plants raised in polluted soils. The genetic similarity and genomic DNA stability were negatively affected by increased levels of crude oil pollution. Conclusions The ability of V. rosea to degrade TPH and balance the increased or decreased plant functional traits at the macro and micro levels of plant structure in response to crude oil pollution supports the use of the species for phytoremediation of crude oil-polluted sites. The genotoxic effects of crude oil on V. rosea still require further investigation. Further studies are required to demonstrate the mechanism of phenolic, flavonoid, and antioxidant compounds in the protection of plants against crude oil pollution stress. Testing different molecular markers and studying the differentially expressed genes will help understand the behavior of genetic polymorphism and stress-resistant genes in response to crude oil pollution. Supplementary Information The online version contains supplementary material available at 10.1186/s43141-022-00412-6.
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Affiliation(s)
- Zahra S Hussein
- Faculty of Biotechnology, October University for Modern Sciences and Arts (MSA), 6th of October, 12451, Egypt.
| | - Ahmad K Hegazy
- Botany and Microbiology Department, Faculty of Science, Cairo University, Giza, 12613, Egypt.
| | - Nermen H Mohamed
- Egyptian Petroleum Research Institute, Nasr City, Cairo, 11727, Egypt
| | - Mohamed A El-Desouky
- Chemistry Department, Biochemistry Division, Faculty of Science, Cairo University, Giza, 12613, Egypt
| | - Shafik D Ibrahim
- Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center, Giza, Egypt
| | - Gehan Safwat
- Faculty of Biotechnology, October University for Modern Sciences and Arts (MSA), 6th of October, 12451, Egypt
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Dissection of genetic diversity and population structure in oregano (Origanum acutidens L.) genotypes based on agro-morphological properties and start codon targeted (SCoT) markers. Biologia (Bratisl) 2022. [DOI: 10.1007/s11756-021-00989-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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18
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O Attia A, A Ismail I, S Dessoky ED, S Aljuaid B. Using of DNA-Barcoding, SCoT and SDS-PAGE Protein to Assess Soma-Clonal Variation in Micro-Propagated Fig ( Ficus carica L.) Plant. Pak J Biol Sci 2022; 25:415-425. [PMID: 35638512 DOI: 10.3923/pjbs.2022.415.425] [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: 06/15/2023]
Abstract
<b>Background and Objective:</b> <i>In vitro</i> propagation of fig (<i>Ficus carica</i> L.) is one of the possible approaches that may be used to maximize the diversity of plant species. The current work was carried out to evaluate genetic stability of micropropagated fig plantlets and to determine the effect of <i>in vitro </i>propagation on genomic content of Saudi fig. <b>Materials and Methods:</b> The start codon-targeted (SCoT), DNA-barcoding chloroplast gene RNA polymerase1 (<i>rpoC1</i> sequencing) and total protein profiling assays (SDS-PAGE) techniques were used to detect genetic stability in micropropagated fig plantlets. <b>Results:</b> The Scorable PCR bands were produced with 10 SCoT primers used, where the total number of bands was 135 bands. Twenty polymorphic bands were generated with 18.4% of a polymorphism percentage. According to the result, no visual unique bands were generated which confirmed the genetic homogeneity of micropropagated plantlets samples compared to the control sample (mother plant). Sequence analysis and phylogenetic tree generated using fig <i>rpoC1</i> sequence showed high similarity between control and plantlets samples of fig plant. The protein profiling results revealed no remarkable changes between micropropagated plantlets and the mother plant. <b>Conclusion:</b> The results indicate that using SCoT, DNA barcoding and protein profiling have demonstrated their utility to detect genetic homogeneity in micropropagated fig plantlets, which suggests using of micropropagation protocol of plants applied on the plantlets in the current study as a reliable protocol for <i>in vitro</i> culture and conservation of fig plant.
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Alotaibi MO, Abd-Elgawad ME. ISSR and SCoT for Evaluation of Hereditary Differences of 29 Wild Plants in Al Jubail Saudi Arabian. Saudi J Biol Sci 2022; 29:3223-3231. [PMID: 35844376 PMCID: PMC9280174 DOI: 10.1016/j.sjbs.2022.01.053] [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: 09/15/2021] [Revised: 01/19/2022] [Accepted: 01/23/2022] [Indexed: 11/26/2022] Open
Abstract
This survey is concerned with the hereditary differences of 29 wild plants collected from fifteen different regions in Al Jubail, Saudi Arabia using two molecular marker systems, viz. inter simple sequence repeat (ISSR) and start codon targeted (SCoT) molecular markers. Ten ISSR and ten SCoT primers amplified a total of 142 and 163 bands with a 87% and 84% polymorphism, respectively. The average number of polymorphic bands for each pair of ISSR and SCoT primers combinations was 12.4 and 13.7, respectively. The highest genetic similarity for ISSR (0.97) and SCoT (0.90) were recognized between Zygophyllum qatarense-22 and Juncus rigidus-23, and between Zygophyllum qatarense-28 and Zygophyllum qatarense-29, whereas the lowest was (0.59) differentiated between Zygophyllum qatarense-6 and Salsola imbricate-18 for ISSR and between Cyperus conglomeratus-7 and Halopeplis perfoliata-14 for SCoT. This considers confirmed the value of molecular techniques such as ISSR and SCoT to assess the hereditary differences among the selected 29 weeds for hereditary preservation and plant enhancement.
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20
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Traditional System Versus DNA Barcoding in Identification of Bamboo Species: A Systematic Review. Mol Biotechnol 2021; 63:651-675. [PMID: 34002354 DOI: 10.1007/s12033-021-00337-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 05/11/2021] [Indexed: 02/07/2023]
Abstract
Bamboo, a gramineous plant belonging to the family Poaceae, comprises of 1575 species from 116 genera across the globe. It has the ability to grow and evolve on degraded land and hence, can be utilized in the various applications as an alternative for plastic and wood. DNA barcoding, a long genomic sequence, identifies barcode region which shows species-specific nucleotide differences. This technology is considered as advanced molecular technique utilized for characterization and classification of the various species by applying distinctive molecular markers. Recent investigations revealed the potential application of various barcode regions such as matK, rbcL, rpoB, rpoC1, psbA-trnH, and ITS2, in identification of many bamboo species from different genus. In this review we comprehensively discussed the relevance of DNA barcoding as a tool in classification/identification of various bamboo species. We highlighted the methodology, how this advance technology overcomes the challenges associated with traditional methods along with prospects for future research.
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Differential UGT76G1 and start codon-based characterization of six stevia germlines in Egypt. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2021. [DOI: 10.1016/j.bcab.2021.101981] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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22
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Application of seismo-mechanical stress in attenuation of in vitro induced abnormalities in Scaevola taccada (Gaertn.) Roxb. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2020. [DOI: 10.1016/j.bcab.2020.101821] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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23
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Gogoi B, Wann SB, Saikia SP. Comparative assessment of ISSR, RAPD, and SCoT markers for genetic diversity in Clerodendrum species of North East India. Mol Biol Rep 2020; 47:7365-7377. [PMID: 32880835 DOI: 10.1007/s11033-020-05792-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 08/28/2020] [Indexed: 11/25/2022]
Abstract
Clerodendrum belonging to the family of Lamiaceae is used in indigenous systems of medicine to treat various life-threatening diseases. The genus has complex morphological variations which lead to limits in its precise taxonomic classifications. Genetic diversity study could enhance taxonomic authentication and evolutionary relationship among the species of Clerodendrum. In this study, nine species of Clerodendrum collected from different regions of North East India were screened using ISSR, RAPD, and SCoT molecular markers. The markers of ISSR, RAPD, and SCoT generated a total of 79, 126, and 145 amplicons with an average of 6.58, 7.86, and 8.53 amplicon per primer. The polymorphism information contents (PIC) for ISSR, RAPD, and SCoT ranged from 0.28 to 0.37, 0.39 to 0.69, and 0.30 to 0.62 with resolving power (Rp) varying from 5.26 to 11.11, 4.04 to 9.67, and 4.54 to 8.65, respectively. Unweighted Pair Group Method with Arithmetic Mean (UPGMA) based clustering methods grouped 94 genotypes into 6 clusters for ISSR and 3 clusters each for RAPD and SCoT markers. Similarly, population structure-based analysis divided 94 genotypes into 6 populations for ISSR and RAPD and 4 populations for SCoT markers. AMOVA analysis revealed that SCoT markers generated maximum genetic variations within and among genotypes, contrary to ISSR and RAPD markers. Results in this study, suggest that the competence of three markers was relatively the same in genotypes fingerprinting, but SCoT was more efficient in the detection of polymorphism for Clerodendrum species. Further, these results could be integrated in the exploration of diverse Clerodendrum species and germplasm utilization.
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Affiliation(s)
- Barbi Gogoi
- Medicinal Aromatic and Economic Plants Group, Biological Sciences & Technology Division (BSTD), CSIR-North East Institute of Science & Technology, Jorhat, 785006, Assam, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - S B Wann
- Biotechnology Group, Biological Sciences & Technology Division (BSTD), CSIR-North East Institute of Science & Technology, Jorhat, 785006, Assam, India
| | - S P Saikia
- Medicinal Aromatic and Economic Plants Group, Biological Sciences & Technology Division (BSTD), CSIR-North East Institute of Science & Technology, Jorhat, 785006, Assam, India.
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Hewedy OA, Abdel Lateif KS, Seleiman MF, Shami A, Albarakaty FM, M. El-Meihy R. Phylogenetic Diversity of Trichoderma Strains and Their Antagonistic Potential against Soil-Borne Pathogens under Stress Conditions. BIOLOGY 2020; 9:E189. [PMID: 32718102 PMCID: PMC7466124 DOI: 10.3390/biology9080189] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Revised: 07/15/2020] [Accepted: 07/17/2020] [Indexed: 12/19/2022]
Abstract
Trichoderma species are known as excellent biocontrol agents against soil-borne pathogens that cause considerable crop losses. Eight strains of Trichoderma were isolated from five Egyptian regions. They identified based on translation elongation factor-1α (TEF1) sequencing as four different Trichoderma species: Trichoderma asperellum, Trichoderma harzianum, Trichoderma viride, and Trichoderma longibrachiatum. Optimal growth conditions (temperature and media), and the phosphate solubilization capability of Trichoderma strains were evaluated in vitro. Further, the ability of these strains to antagonize Fusarium solani, Macrophomina phaseolina, and Fusarium graminearum was also evaluated. The results revealed that Trichoderma harzianum (Th6) exhibited the highest antagonistic ability against F. solani, M. phaseolina and F. graminearum with inhibition rates of 71.42%, 72.97%, and 84.61%, respectively. Trichoderma viride (Tv8) exhibited the lowest antagonism against the same pathogens with inhibition rates of 50%, 64% and 69.23%, respectively. Simple-sequence repeats (SSRs) and random amplified polymorphic DNA (RAPD) markers were used to evaluate the genetic variability of the Trichoderma strains. The results revealed that of 45 RAPD amplified bands, 36 bands (80%) were polymorphic and of SSRs amplified 36 bands, 31 bands (86.11%) were polymorphic. The amplification of calmodulin and β-1,3-endoglucanase was noted at 500 bp and 230 bp, respectively. Data indicated that T. viride (Tv8) had the highest phosphate solubilization index (10.0 mm), while T. harzianum (Th6) had the lowest phosphate solubilization index (4.0 mm). In conclusion, T. harzianum (Th6) had the highest antagonistic activity in dual culture assay along with the growth rate; while T. viride (Tv8) had the highest phosphate solubilization activity. There are still gaps in obtaining new formulations, selecting potent Trichoderma strains to confirm disease control in planta. For improving Trichoderma recommendation in the organic agricultural system and sustaining the fertility of the soil, the field application of highly antagonistic biocontrol agents in different types of soil and plant species will be the first approach toward bio-pesticide treatments along with bio-fertilizer inoculation. Furthermore, secondary metabolites will be investigated for the most promising strains with the combination of different pathogens and application timing.
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Affiliation(s)
- Omar A. Hewedy
- Department of Plant Agriculture, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada
- Department of Genetics, Faculty of Agriculture, Menoufia University, Shibin El-Kom 32514, Egypt;
| | - Khalid S. Abdel Lateif
- Department of Genetics, Faculty of Agriculture, Menoufia University, Shibin El-Kom 32514, Egypt;
- Department of Biotechnology, College of Science, Taif University, Taif 21944, Saudi Arabia
| | - Mahmoud F. Seleiman
- Plant Production Department, College of Food and Agriculture Sciences, King Saud University, P.O. Box 2460, Riyadh 11451, Saudi Arabia
- Department of Crop Sciences, Faculty of Agriculture, Menoufia University, Shibin El-kom 32514, Egypt
| | - Ashwag Shami
- Biology Department, College of Sciences, Princess Nourah bint Abdulrahman University, Riyadh 11617, Saudi Arabia; (A.S.); (F.M.A.)
| | - Fawziah M. Albarakaty
- Biology Department, College of Sciences, Princess Nourah bint Abdulrahman University, Riyadh 11617, Saudi Arabia; (A.S.); (F.M.A.)
- Department of Biology, College of Applied Sciences, Umm AlQura University, Makkah Al Moukarramh 21955, Saudi Arabia
| | - Rasha M. El-Meihy
- Department of Agricultural Microbiology, Faculty of Agriculture, Benha University, Moshtohor 13736, Egypt
- School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, Wuhan 430070, China
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Hewedy OA, Abdel-Lateif KS, Bakr RA. Genetic diversity and biocontrol efficacy of indigenous Trichoderma isolates against Fusarium wilt of pepper. J Basic Microbiol 2019; 60:126-135. [PMID: 31840846 DOI: 10.1002/jobm.201900493] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 10/11/2019] [Accepted: 11/11/2019] [Indexed: 11/09/2022]
Abstract
Trichoderma species are recognized as biocontrol agents with great potential in inhibiting fungal pathogens that cause significant crop losses. In this study, 15 Trichoderma isolates were collected from various Egyptian locations. Internal transcribed spacer sequencing revealed four different Trichoderma species; Trichoderma harzianum, Trichoderma asperellum, Trichoderma longibrachiatum, and Trichoderma viride. The antagonistic activity of Trichoderma isolates against Fusarium oxysporum f. sp. capsici was evaluated in vitro. The effect of Trichoderma isolates on pepper growth plants in the presence of F. oxysporum was studied in planta. The inhibition of pathogen mycelial growth in vitro ranged between 35.71% and 85.75%. The isolates Ta3 and Tl had the highest antagonistic ability in vitro against F. oxysporum f. sp. capsici. However, Th7 and Th6 of T. harzianum isolates showed the highest values of disease severity reduction under greenhouse conditions. The genetic diversity of the Trichoderma isolates (Ta1, Ta2, Th1, Th2, Th3, Th4, Th5, and Tv) was investigated on the basis of ISSR and SCoT markers. SCoT primers generated a total of 28 bands, out of which 14 (50%) were polymorphic. ISSR primers gave 32 bands, and 11 of these bands (34.37%) were polymorphic.
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Affiliation(s)
- Omar A Hewedy
- Department of Genetics, Faculty of Agriculture, Menoufia University, Shibin El-Kom, Egypt
| | - Khalid S Abdel-Lateif
- Department of Genetics, Faculty of Agriculture, Menoufia University, Shibin El-Kom, Egypt.,Department of Biotechnology, College of Science, Taif University, Taif, Saudi Arabia
| | - Ramadan A Bakr
- Department of Agricultural Botany, Faculty of Agriculture, Menoufia University, Shibin El-Kom, Egypt
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Ezzat A, Adly M, El-Fiki A. Morphological, agronomical and molecular characterization in irradiated Cowpea (Vignaunguiculata (L.) Walp.) and detection by start codon target markers. JOURNAL OF RADIATION RESEARCH AND APPLIED SCIENCES 2019. [DOI: 10.1080/16878507.2019.1686578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Asmaa Ezzat
- Horticulture Department, Faculty of Agriculture, Minia University, Minia, Egypt
| | - Mohamed Adly
- National Centre for Radiation Research and TechnologyAtomic Energy Authority, Cairo, Egypt
| | - Ayman El-Fiki
- National Centre for Radiation Research and TechnologyAtomic Energy Authority, Cairo, Egypt
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Genetic stability assessment of Taraxacum pieninicum plantlets after long-term slow growth storage using ISSR and SCoT markers. Biologia (Bratisl) 2019. [DOI: 10.2478/s11756-019-00377-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Igwe DO, Afiukwa CA, Acquaah G, Ude GN. Genetic diversity and structure of Capsicum annuum as revealed by start codon targeted and directed amplified minisatellite DNA markers. Hereditas 2019; 156:32. [PMID: 31641342 PMCID: PMC6796447 DOI: 10.1186/s41065-019-0108-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 09/24/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Identification of high resolving DNA-based markers is of paramount importance to unlock the potential of genetic diversity and selection of unique accessions of Capsicum annuum L., within Cross River and Ebonyi States of Nigeria, for breeding and conservation. Therefore, we comparatively explored the effectiveness of start codon targeted (SCoT) and directed amplified minisatellite DNA (DAMD) markers for diversity analysis of the accessions. Fifteen accessions were collected for DNA extraction and amplifications with the markers. RESULTS Dendrograms from SCoT and DAMD categorized the accessions into five and three genetic groups, respectively, while the principal component analysis identified five genetic clusters, each from the markers. The average values of allele, gene diversity and polymorphic information content detected with SCoT and DAMD demonstrate that the two markers were effective and efficient, especially, SCoT in genetic diversity study of the accessions of pepper. Number of polymorphic loci (NPL) and percentage polymorphic loci (PPL) from SCoT (NPL = 64, PPL = 80.00-95.73%) and DAMD (NPL = 56, PPL = 53.33-86.67%) were high, but higher in SCoT markers. Other effective genetic parameters (effective number of alleles, Nei's genetic diversity and Shannon's information indices) identified with the two marker systems elucidated the allelic richness, rich genetic diversity within the populations and informative nature of the markers, especially SCoT. The intraspecific genetic diversity, interspecific genetic diversity, and coefficient of differentiation obtained with SCoT and DAMD further exposed the genetic structure with more genetic divergence within than among the populations of the accessions. Estimate of gene flow from the SCoT markers was 3.8375 and 0.6.2042 for the DAMD markers. The estimate of gene flow values from the markers indicated extensiveness with SCoT (Nm = 3.8375) and extremely extensive with DAMD (Nm = 6.2042) among the populations. CONCLUSION This study shows that SCoT markers may be more useful and informative than DAMD in measuring genetic diversity and differentiation of the accessions of the genus Capsicum. Genetic parameters obtained with SCoT showed that the accessions from Cross River were more genetically diverse than the ones from Ebonyi State. Therefore, SCoT may be a preferred marker in evaluating genetic diversity for improvement and conservation of this spicy crop, C. capsicum.
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Affiliation(s)
- David O. Igwe
- Department of Biotechnology, Faculty of Science, Ebonyi State University, Abakaliki, 053 Nigeria
- Biotechnology and Research Development Centre, Ebonyi State University, Abakaliki, Ebonyi State 053 Nigeria
- Department of Natural Sciences, Bowie State University, 14000 Jericho Park Road, Bowie, Maryland 20715 USA
| | - Celestine A. Afiukwa
- Department of Biotechnology, Faculty of Science, Ebonyi State University, Abakaliki, 053 Nigeria
- Biotechnology and Research Development Centre, Ebonyi State University, Abakaliki, Ebonyi State 053 Nigeria
| | - George Acquaah
- Department of Natural Sciences, Bowie State University, 14000 Jericho Park Road, Bowie, Maryland 20715 USA
| | - George N. Ude
- Department of Natural Sciences, Bowie State University, 14000 Jericho Park Road, Bowie, Maryland 20715 USA
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Safari H, Zebarjadi A, Kahrizi D, Jafari AA. The study of inter-specific relationships of Bromus genus based on SCoT and ISSR molecular markers. Mol Biol Rep 2019; 46:5209-5223. [PMID: 31313131 DOI: 10.1007/s11033-019-04978-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 07/11/2019] [Indexed: 10/26/2022]
Abstract
The genus of Bromus is one of the most important collection of rangeland plants, which are distributed in a wide range of natural areas of Iran. Interspecific relationships were evaluated in 90 accessions of 18 Bromus species based on 15 ISSR and 15 SCoT primers. SCoT markers separated the accessions better than ISSR marker. In addition, there was a high interspecific diversity between surveying germplasm. The sections of Bromus genus completely separated based on DNA molecular markers. SCoT markers could separate the accessions in each species. The primers of SC5 and SC35 from SCoT marker and UBC861, UBC857 and UBC844 primers from ISSR marker were identified as the best primers in revealing of genetic diversity between accessions. The sections of Ceratochloa, Genea, Pnigma and Bromus were monophyletic and were placed in one cluster. The section Bromus had a direct relationship with section Genea. In other words, section Ceratochloa has a direct relationship with Pnigma. B. tectorum and B. sericeus. B. sterilis had the most distance with other species in section Genea. B. squarrosus and B. japonicus had the most similarity and B. briziformis with B. danthoniae and B. scoparius with B. rechingeri had a moderate relationship in section Bromus. B. tomentosus and B. persicus had the highest similarity and B. riparius with B. biebersteinii and B. tomentellus with B. inermis had a moderate similarity in section Pnigma.
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Affiliation(s)
- Hooshmand Safari
- Department of Agronomy and Plant Breeding, Faculty of Science and Agricultural Engineering, Razi University, Kermanshah, Iran.,Faculty Member of Research Department of Forests and Rangelands, Kermanshah Agricultural and Natural Resources Research and Education Center, AREEO, Kermanshah, Iran
| | - Alireza Zebarjadi
- Department of Agronomy and Plant Breeding, Faculty of Science and Agricultural Engineering, Razi University, Kermanshah, Iran.
| | - Danial Kahrizi
- Department of Agronomy and Plant Breeding, Faculty of Science and Agricultural Engineering, Razi University, Kermanshah, Iran
| | - Ali Ashraf Jafari
- Research Institute of Forests and Rangelands, Agricultural Research, Education and Extension Organization (AREEO), Tehran, Iran
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Gupta V, Jatav PK, Haq SU, Verma KS, Kaul VK, Kothari SL, Kachhwaha S. Translation initiation codon (ATG) or SCoT markers-based polymorphism study within and across various Capsicum accessions: insight from their amplification, cross-transferability and genetic diversity. J Genet 2019. [DOI: 10.1007/s12041-019-1095-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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31
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Sharma U, Rai MK, Shekhawat NS, Kataria V. Genetic homogeneity revealed in micropropagated Bauhinia racemosa Lam. using gene targeted markers CBDP and SCoT. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2019; 25:581-588. [PMID: 30956438 PMCID: PMC6419707 DOI: 10.1007/s12298-018-00639-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 09/20/2018] [Accepted: 12/26/2018] [Indexed: 05/20/2023]
Abstract
Two gene targeted markers i.e. CAAT box-derived polymorphism (CBDP) and start codon targeted (SCoT) polymorphism were applied to analyze the genetic stability of in vitro propagated plants of Bauhinia racemosa Lam. multiplied by enhanced axillary shoot proliferation of mature tree derived nodal explant. Nine randomly selected micropropagated plants of 1 year age were subjected to molecular analysis. The isolated genomic DNA samples were subjected to PCR amplification with a total of 61 primers (25 CBDP and 36 SCoT) out of which 39 primers (21 CBDP and 18 SCoT) produced scorable amplicons. A total of 97 and 88 clear, distinct and reproducible amplicons were produced by CBDP and SCoT primers, respectively. The monomorphic banding pattern obtained through all the tested primers corroborated the true to type nature of in vitro propagated plants of B. racemosa.
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Affiliation(s)
- Udit Sharma
- Biotechnology Unit, Department of Botany (UGC-Centre of Advanced Study), Jai Narain Vyas University, New Campus, Jodhpur, Rajasthan 342001 India
| | - Manoj K. Rai
- Biotechnology Unit, Department of Botany (UGC-Centre of Advanced Study), Jai Narain Vyas University, New Campus, Jodhpur, Rajasthan 342001 India
- Department of Environmental Science, Indira Gandhi National Tribal University, Amarkantak, M.P. 484887 India
| | - N. S. Shekhawat
- Biotechnology Unit, Department of Botany (UGC-Centre of Advanced Study), Jai Narain Vyas University, New Campus, Jodhpur, Rajasthan 342001 India
| | - Vinod Kataria
- Biotechnology Unit, Department of Botany (UGC-Centre of Advanced Study), Jai Narain Vyas University, New Campus, Jodhpur, Rajasthan 342001 India
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Xu YX, Shen SY, Chen W, Chen L. Analysis of Genetic Diversity and Development of a SCAR Marker for Green Tea (Camellia sinensis) Cultivars in Zhejiang Province: The Most Famous Green Tea-Producing Area in China. Biochem Genet 2019; 57:555-570. [PMID: 30734883 DOI: 10.1007/s10528-019-09909-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 01/28/2019] [Indexed: 11/24/2022]
Abstract
Camellia sinensis (L.) O. Kuntze is one of the most important non-alcoholic beverage crops in Asian and African countries. In recent years, many green tea cultivars have been released and played an important role in improving the production and quality of tea trees. The objectives of this study were to assess the genetic diversity of the eighteen main green tea cultivars in Zhejiang Province-the most famous green tea-producing area of China-using start codon-targeted (SCoT) markers and to develop a specific sequence-characterized amplified region (SCAR) marker for application in cultivar diagnosis. Thirty-one SCoT primers produced 264 loci, 226 of which were polymorphic. The genetic similarity coefficients among these green tea cultivars ranged from 0.587 to 0.814, indicating that a high level of genetic diversity was present. Both a UPGMA dendrogram and a PCoA plot grouped the tea cultivars into three groups. The partitioning of groups in the UPGMA and PCoA was similar, and much of the clustering was highly consistent with the classification of tea cultivars according to their genetic backgrounds. A unique SCoT band, SCoT4-1649, specific to the tea cultivar 'Yingshuang,' was transformed into a SCAR marker. This SCAR marker is highly useful for the identification and germplasm conservation of green tea cultivars.
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Affiliation(s)
- Yan-Xia Xu
- National Center for Tea Improvement, Tea Research Institute of the Chinese Academy of Agricultural Sciences/ Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, 9 South Meiling Road, Hangzhou, 310008, China
| | - Si-Yan Shen
- National Center for Tea Improvement, Tea Research Institute of the Chinese Academy of Agricultural Sciences/ Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, 9 South Meiling Road, Hangzhou, 310008, China
| | - Wei Chen
- National Center for Tea Improvement, Tea Research Institute of the Chinese Academy of Agricultural Sciences/ Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, 9 South Meiling Road, Hangzhou, 310008, China
| | - Liang Chen
- National Center for Tea Improvement, Tea Research Institute of the Chinese Academy of Agricultural Sciences/ Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, 9 South Meiling Road, Hangzhou, 310008, China.
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33
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Golkar P, Mokhtari N. Molecular diversity assessment of a world collection of safflower genotypes by SRAP and SCoT molecular markers. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2018; 24:1261-1271. [PMID: 30425439 PMCID: PMC6214440 DOI: 10.1007/s12298-018-0545-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Revised: 03/06/2018] [Accepted: 05/02/2018] [Indexed: 05/05/2023]
Abstract
Safflower (Carthamus tinctorius L.) is considered as an oil crop that is rich in medicinal and industrial properties. In this study, the genetic diversity of safflower was assessed using 12 polymorphic sequence-related amplified polymorphism (SRAPs) and 11 polymorphic start codon targeted (SCoT) markers in 100 genotypes of safflower gathered from different geographical regions of the world. The 23 primers generated a total of 227 polymorphism fragments with a mean of 68.2% within the range of 3 (SCoT 31 and SCoT 35) to 13 (SCoT 35) bands per primer. Polymorphism per primer ranged between 100% (in Me4-Em1) and 18.1% (in SCoT19), with an average of 36.76%. The polymorphism information contents of the SRAP and SCoT markers were 0.35 and 0.30, respectively, indicating that SRAP markers were more effective than SCoT markers for assessing the degree of genetic diversity of the safflower. The results of the analysis of molecular variance showed a significant difference across cultivated safflower genotypes possessing a high intra-population variation. The examined accessions were categorized into five clusters based on similarity centers: the Middle East containing Iran, Iraq, Turkey, and Tajikistan; the Far East, including India, Pakistan, and Korea; Europe; the American continent; and Africa, including Egypt, Sudan and Libya. The present study shows the effectiveness of employing the mixture of SRAP and SCoT markers in the identification of safflower genetic diversity that would be useful for conservation and population genetics of safflower improvement in further studies.
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Affiliation(s)
- Pooran Golkar
- Research Institute for Biotechnology and Bioengineering, Isfahan University of Technology, Isfahan, 84156 83111 Iran
| | - Niloofar Mokhtari
- Department of Agricultural Biotechnology, College of Agriculture, Isfahan University of Technology, Isfahan, 84156 83111 Iran
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Amer A, Taha H, Ammar N, Salama M, El-Alfy T. Applicability of Different Molecular Markers Techniques for Genetic Distinguish Between Two Genera <I>Cressa</I> Linn. and <I>Cuscuta</I> Yunck. Family Convolvulaceae. Pak J Biol Sci 2018; 21:179-186. [PMID: 30311474 DOI: 10.3923/pjbs.2018.179.186] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
BACKGROUND AND OBJECTIVE The DNA fingerprinting is used to determine the relationship between species in the same genus or between genera related to the same family. The aim of this study was to determine the relationships between two samples related to the same family Convolvulaceae, representing two genera, Cressa Linn. and Cuscuta Yunck. by RAPD, ISSR and SCoT molecular techniques (PCR based DNA fingerprint). MATERIALS AND METHODS The RAPD, ISSR and SCoT based DNA fingerprinting techniques were implemented to identify the fingerprint diversity between two genera, Cressa Linn. and Cuscuta Yunck-belonging to the family Convolvulaceae. RESULTS Applying of RAPD technique revealed that using OP-A02, OP-A09, OP-A10, OP-C04 and OP-M01 primers recorded 60, 83.33, 100, 50 and 70.66% polymorphism, respectively. On the other hand, ISSR technique recorded 40, 50, 100, 66.67, 33.33 and 37.5% polymorphism with 44B, HB-08, HB-09, HB-10, HB-11 and HB-12 primers, respectively. However, amplification of SCoT technique, SCoT 1, SCoT 2, SCoT 3, SCoT 4, SCoT 6, SCoT 8, SCoT 10 and SCoT 12 primers recorded 33.33, 28.57, 14.28, 66.66, 25, 40, 42.85 and 50%, respectively . The total polymorphism recorded 73.33, 54.58 and 37.7% for RAPD, ISSR and SCoT techniques, respectively. CONCLUSION The result of this study indicated that SCoT technique was more efficient and sustainable for distinguish between two genera under investigation.
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35
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Talebi R, Nosrati S, Etminan A, Naji AM. Genetic diversity and population structure analysis of landrace and improved safflower (Cartamus tinctorious L.) germplasm using arbitrary functional gene-based molecular markers. BIOTECHNOL BIOTEC EQ 2018. [DOI: 10.1080/13102818.2018.1499443] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
Affiliation(s)
- Reza Talebi
- Department of Plant Breeding, Sanandaj Branch, Islamic Azad University, Sanandaj, Iran
| | - Somayeh Nosrati
- Department of Plant Breeding, Kermanshah Branch, Islamic Azad University, Kermanshah, Iran
| | - Alireza Etminan
- Department of Plant Breeding, Kermanshah Branch, Islamic Azad University, Kermanshah, Iran
| | - Amir Mohammad Naji
- Department of Plant Breeding, Faculty of Agriculture, Shahed University, Tehran, Iran
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Rafizadeh A, Koohi-Dehkordi M, Sorkheh K. Molecular insights of genetic variation in milk thistle (Silybum marianum [L.] Gaertn.) populations collected from southwest Iran. Mol Biol Rep 2018; 45:601-609. [PMID: 29882084 DOI: 10.1007/s11033-018-4198-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 05/24/2018] [Indexed: 10/14/2022]
Abstract
Milk thistle (Silybum marianum) is among the world's popular medicinal plants. Start Codon Targeted (SCoT) marker system was utilized to investigate the genetic variability of 80 S. marianum genotypes from eight populations in Iran. SCoT marker produced 255 amplicons and 84.03% polymorphism was generated. The SCoT marker system's polymorphism information content value was 0.43. The primers' resolving power values were between 4.18 and 7.84. The percentage of polymorphic bands was between 33.3 and 100%. The Nei's gene diversity (h) was 0.19-1.30 with an average 0.72. The Shannon's index (I) ranged from 0.29 to 1.38 with an average value of 0.83. The average gene flow (0.37) demonstrated a high genetic variation among the studied populations. The variation of 42% was displayed by the molecular variance analysis among the populations while a recorded variation of 58% was made within the populations. Current investigation suggested that SCoT marker system could effectively evaluate milk thistle genotypes genetic diversity.
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Affiliation(s)
- Azam Rafizadeh
- Department of Agricultural Science, Payame-Noor University, P. O. Box 19395-3697, Tehran, Iran
| | - Mehrana Koohi-Dehkordi
- Department of Agricultural Science, Payame-Noor University, P. O. Box 19395-3697, Tehran, Iran.
| | - Karim Sorkheh
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, Shahid Chamran University of Ahvaz, P. O. Box 61355/144, Ahvaz, Iran
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Balážová Ž, Gálová Z, Vivodík M, Chňapek M, Hornyák Gregáňová R. Molecular analysis of buckwheat using gene specific markers. POTRAVINARSTVO 2018. [DOI: 10.5219/954] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Buckwheat (Fagopyrium esculentum) is a pseudo-cereal which has spread troughout the world and nowadays it represents cultural, economic and nutritionally important pseudocereal. It´s enviromentally friendly, characterized by high fiber, routine, protein and B vitamins, and is general-purpose. The goal of the present study was to analyze 17 genotypes of buckwheat by using 7 SCoT markers. In total, 52 fragments were detected, of which 38 were polymorphic. The average number of polymorphic fragments was 5.43. The most polymorphic fragments were detected in SCoT 26 and SCoT 29 markers, and the average percentage of polymorphism was 73.36 %. SCoT 29 reached the highest percentage of polymorphism (87.5 %) and SCoT 36 was lowest (60 %). The DI values ”‹”‹ranged from 0.625 (SCoT 36) to 0.887 (SCoT 26) and the average DI value was 0.749. The average PIC value was 0.729 with PIC values ranging from 0.386 (SCoT 36) to 0.831 (SCoT 26). To determine the genetic diversity of 17 genotypes of the buckwheat, a dendrogram was created using the hierarchical cluster analysis. The genotypes were divided into two major clusters (I and II). Cluster I was divided into three other subgroups. Sixteen genotypes were included in cluster I and the genotype of Madawaska (USA) was genetically the farthest in cluster II. Genetically the closest were the varieties of Ballada (Russia) and Bamby (Austria). Used SCoT markers were sufficiently polymorphic, were able identify and differentiate chosen set of buckwheat genotypes.
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Bhattacharyya P, van Staden J. Molecular insights into genetic diversity and population dynamics of five medicinal Eulophia species: a threatened orchid taxa of Africa. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2018; 24:631-641. [PMID: 30042618 PMCID: PMC6041235 DOI: 10.1007/s12298-018-0523-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 11/16/2017] [Accepted: 03/05/2018] [Indexed: 05/22/2023]
Abstract
Genetic diversity existing amongst five Eulophia orchid species were assessed using start codon targeted polymorphism (SCoT) and inter-retrotransposon amplified polymorphism (IRAP) markers. A total of 12 SCoT and 5 IRAP markers revealed an average of 63% genetic variability [SCoT = 63.87; IRAP = 64.95%] amongst the five Eulophia species investigated. The genetic similarities were assessed using both UPGMA and Bayesian approaches which indicated identical clustering patterns at a genetic similarity level of 50%. Analysis of molecular variance (AMOVA) revealed the presence of a significant degree of genetic variability, mostly compartmentalized within the species level. Amongst the five assessed Eulophia species, E. parviflora was the most genetically diverse representative whereas E. welwitschii was found to be least diverse based on a comparative assessment of various population genetic parameters like Nei's gene diversity (h) and Shannon's information index (I) with an overall gene flow value greater than 1. In order to evaluate the comparative marker efficiency, SCoT and IRAP marker data were subjected to various benchmark analyses like marker index, resolving power, polymorphic index content, multiplex ratio and effective multiplex ratio which revealed the robustness of both the marker techniques in assessment of genetic diversity. The present report provides the first molecular insights into the aspects of inter and intra specific genetic variability in medicinally as well as horticulturally important Eulophia species along with addressing their conservation concerns. In a nutshell, the present approach is simple, rapid and cost effective and can be extended for analysis of genetic diversity of other related plant species.
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Affiliation(s)
- Paromik Bhattacharyya
- Research Centre for Plant Growth and Development, School of Life Sciences, University of KwaZulu-Natal, Pietermaritzburg, Private Bag X01, Scottsville, 3209 South Africa
| | - Johannes van Staden
- Research Centre for Plant Growth and Development, School of Life Sciences, University of KwaZulu-Natal, Pietermaritzburg, Private Bag X01, Scottsville, 3209 South Africa
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Feng S, Zhu Y, Yu C, Jiao K, Jiang M, Lu J, Shen C, Ying Q, Wang H. Development of Species-Specific SCAR Markers, Based on a SCoT Analysis, to Authenticate Physalis (Solanaceae) Species. Front Genet 2018; 9:192. [PMID: 29910824 PMCID: PMC5992434 DOI: 10.3389/fgene.2018.00192] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 05/11/2018] [Indexed: 11/13/2022] Open
Abstract
Physalis is an important genus in the Solanaceae family. It includes many species of significant medicinal value, edible value, and ornamental value. However, many Physalis species are easily confused because of their similar morphological traits, which hinder the utilization and protection of Physalis resources. Therefore, it is necessary to create fast, sensitive, and reliable methods for the Physalis species authentication. Intended for that, in this study, species-specific sequence-characterized amplified region (SCAR) markers were developed for accurate identification of the closely related Physalis species P. angulata, P. minima, P. pubescens, and P. alkekengi var. franchetii, based on a simple and novel marker system, start codon targeted (SCoT) marker. A total of 34 selected SCoT primers yielded 289 reliable SCoT loci, of which 265 were polymorphic. Four species-specific SCoT fragments (SCoT3-1404, SCoT3-1589, SCoT5-550, and SCoT36-520) from Physalis species were successfully identified, cloned, and sequenced. Based on these selected specific DNA fragments, four SCAR primers pairs were developed and named ST3KZ, ST3MSJ, ST5SJ, and ST36XSJ. PCR analysis of each of these primer pairs clearly demonstrated a specific amplified band in all samples of the target Physalis species, but no amplification was observed in other Physalis species. Therefore, the species-specific SCAR primer pairs developed in this study could be used as powerful tools that can rapidly, effectively, and reliably identify and differentiate Physalis species.
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Affiliation(s)
- Shangguo Feng
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | - Yujia Zhu
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Chenliang Yu
- The Institute of Vegetable, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Kaili Jiao
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Mengying Jiang
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Jiangjie Lu
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Chenjia Shen
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Qicai Ying
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Huizhong Wang
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
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Genetic diversity in the endangered terrestrial orchid Cypripedium japonicum in East Asia: Insights into population history and implications for conservation. Sci Rep 2018; 8:6467. [PMID: 29691494 PMCID: PMC5915404 DOI: 10.1038/s41598-018-24912-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 04/05/2018] [Indexed: 11/08/2022] Open
Abstract
Little is known about levels and patterns of genetic diversity for the entire range of endangered orchids native to China, Korea, and Japan. In this study, we focus on Cypripedium japonicum and suggest three hypotheses: 1) that genetic drift has been a primary evolutionary force; 2) that populations in central and western China harbor higher levels of genetic variation relative to those from eastern China; and 3) that C. japonicum in China maintains the highest genetic variation among the three countries. Using ISSR and SCoT markers, we investigated genetic diversity in 17 populations to test the three hypotheses. As anticipated, we found low levels of genetic diversity at the species level with substantially high degree of genetic divergence, which can be mainly attributed to random genetic drift. Chinese populations harbor the highest within-population genetic variation, which tends to increase from east to west. We also found a close relationship between Korean populations and central/western Chinese populations. Historical rarity coupled with limited gene flow seems to be important factors for shaping genetic diversity and structure of C. japonicum. Our results indicate that the mountain areas in central and western China were likely refugia at the Last Glacial Maximum.
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Etminan A, Pour-Aboughadareh A, Noori A, Ahmadi-Rad A, Shooshtari L, Mahdavian Z, Yousefiazar-Khanian M. Genetic relationships and diversity among wild Salvia accessions revealed by ISSR and SCoT markers. BIOTECHNOL BIOTEC EQ 2018. [DOI: 10.1080/13102818.2018.1447397] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
Affiliation(s)
- Alireza Etminan
- Department of Plant Breeding, Kermanshah Branch, Islamic Azad University, Kermanshah, Iran
| | - Alireza Pour-Aboughadareh
- Department of Genetics and Plant Breeding, Faculty of Agricultural and Natural Resources, Imam Khomeini International University, Qazvin, Iran
| | - Afsaneh Noori
- Department of Plant Breeding, Kermanshah Branch, Islamic Azad University, Kermanshah, Iran
| | - Amin Ahmadi-Rad
- Young Researchers and Elite Club, Kermanshah Branch, Islamic Azad University, Kermanshah, Iran
| | - Lia Shooshtari
- Department of Plant Breeding, Kermanshah Branch, Islamic Azad University, Kermanshah, Iran
| | - Zahra Mahdavian
- Department of Plant Breeding, Kermanshah Branch, Islamic Azad University, Kermanshah, Iran
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Vivodík M, Saadaoui E, Balážová Ž, Gálová Z, Petrovičová L. Genetic diversity and population structure in tunisian castor genotypes (Ricinus communis L.) Detected using scot markers. POTRAVINARSTVO 2018. [DOI: 10.5219/873] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Due to the chemical and physical properties of castor oil (Ricinus communis L.) that make it a valuable raw material for numerous industrial applications, including the production of biofuel, interest to develop more and better varieties has been increased. In the present study, the representatives of the genus castor collected from 12 different parts of Tunisia were differentiated by the DNA fingerprinting patterns using 37 SCoT primers. PCR amplification of DNA using 37 primers for SCoT analysis produced 268 DNA fragments that could be scored in all 56 genotypes of Tunisian castor. The number of amplified fragments varied from 4 (SCoT 45, SCoT 31 and ScoT 17) to 10 (SCoT 3, SCoT 11, SCoT 14, SCoT 18 and SCoT 12). Of the 268 amplified bands 230 were polymorphic, with an average of 6.22 polymorphic bands per primer. To determine the level of polymorphism in the analysed group of Tunisian castor genotypes polymorphic information content (PIC) was calculated. The lowest values of polymorphic information content were recorded for SCoT 17 (0.411) and the the highest PIC values were detected for SCoT 14 (0.868) with an average of 0.751. A dendrogram was constructed from a genetic distance matrix based on profiles of the 37 SCoT primers using the unweighted pair-group method with the arithmetic average (UPGMA). According to analysis, the collection of 56 Tunisian castor genotypes were clustered into two main clusters (1 and 2). Of the 56 genotypes of Tunisian castor, 2 unique genotypes were separated (BA-5 and K-4). Genetically the closest were two genotypes from Tunisian region Souassi (S-2 and S-5) in subclaster 2bc. Results showed the utility of SCoT markers for estimation of genetic diversity of castor genotypes leading to genotype identification.
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Balážová Ž, Gálová Z, Vivodík M, Petrovičová L, Gregáňová RH. Molecular variability of oat based on gene specific markers. POTRAVINARSTVO 2017. [DOI: 10.5219/774] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Oat (Avena sativa L.) is a grass planted as a cereal crop. Cultivation of oat is increasing in the recent years because of its good nutrition value. The aim of our study was to analyze genetic variability of oat accessions based on SCoT markers. Eighteen primers were used to study polymorfism of 8 oat genotypes. All 18 primers produced polymorphic and reproducible data. Altogether 153 different fragments were amplified of which 67 were polymorphic with an average number of 3.72 polymorphic fragments per genotype. The number of polymorphic fragments ranged from one (SCoT9, SCoT62) to nine (SCoT40). The percentage of polymorphic bands ranged from 14.29% (SCoT9) to 60% (SCoT59) with an average of 41.62%. Genetic polymorphism was characterized based on diversity index (DI), probability of identity (PI) and polymorphic information content (PIC). The diversity index of the tested SCoT markers ranged from 0 (SCoT9, SCoT62) to 0.878 (SCoT40) with an average of 0.574. The polymorphic information content ranged from 0 (SCoT9, SCoT62) to 0.876 (SCoT40) with an average of 0.524. Dendrogram based on hierarchical cluster analysis using UPGMA algorithm grouped genotypes into two main clusters. Two genotypes, Taiko and Vok were genetically the closest. Results showed the utility of SCoT markers for estimation of genetic diversity of oat genotypes leading to genotype identification.
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Petrovičová L, Balážová Ž, Vivodík M, Gálová Z. Detection genetic variability of secale cereale L. by scot markers. POTRAVINARSTVO 2017. [DOI: 10.5219/726] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Rye (Secale cereale L.) is our traditional cereal used for baking. The genetic variability of grown rye has been reduced by modern agronomic practices, which subsequently prompted the importance of search for species that could be useful as a gene pool for the improving of flour quality for human consumption or for other industrial uses. Therefore, the aim of this study was to detect genetic variability among the set of 45 rye genotypes using 8 SCoT markers. Amplification of genomic DNA of 45 genotypes, using SCoT analysis, yielded 114 fragments, with an average of 14.25 polymorphic fragments per primer. The most polymorphic primer was SCoT 36, where 21 polymorphic amplification products were detected. In contract the lowest polymorphic primer was SCoT 45 with 5 polymorphic products. Genetic polymorphism was characterized based on diversity index (DI), probability of identity (PI) and polymorphic information content (PIC). The hierarchical cluster analysis showed that the rye genotypes were divided into 2 main clusters. One rye genotype Motto, origin from Poland formed a separate subcluster (1b). Subscluster 2a included only genotype Valtické (CSK). In this experiment, SCoT proved to be a rapid, reliable and practicable method for revealing of polymorphism in the rye cultivars.
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Chai X, Dong R, Liu W, Wang Y, Liu Z. Optimizing Sample Size to Assess the Genetic Diversity in Common Vetch (Vicia sativa L.) Populations Using Start Codon Targeted (SCoT) Markers. Molecules 2017; 22:molecules22040567. [PMID: 28362323 PMCID: PMC6154542 DOI: 10.3390/molecules22040567] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2017] [Revised: 03/28/2017] [Accepted: 03/29/2017] [Indexed: 11/16/2022] Open
Abstract
Common vetch (Vicia sativa subsp. sativa L.) is a self-pollinating annual forage legume with worldwide importance. Here, we investigate the optimal number of individuals that may represent the genetic diversity of a single population, using Start Codon Targeted (SCoT) markers. Two cultivated varieties and two wild accessions were evaluated using five SCoT primers, also testing different sampling sizes: 1, 2, 3, 5, 8, 10, 20, 30, 40, 50, and 60 individuals. The results showed that the number of alleles and the Polymorphism Information Content (PIC) were different among the four accessions. Cluster analysis by Unweighted Pair Group Method with Arithmetic Mean (UPGMA) and STRUCTURE placed the 240 individuals into four distinct clusters. The Expected Heterozygosity (HE) and PIC increased along with an increase in sampling size from 1 to 10 plants but did not change significantly when the sample sizes exceeded 10 individuals. At least 90% of the genetic variation in the four germplasms was represented when the sample size was 10. Finally, we concluded that 10 individuals could effectively represent the genetic diversity of one vetch population based on the SCoT markers. This study provides theoretical support for genetic diversity, cultivar identification, evolution, and marker-assisted selection breeding in common vetch.
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Affiliation(s)
- Xutian Chai
- The State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China.
| | - Rui Dong
- The State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China.
| | - Wenxian Liu
- The State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China.
| | - Yanrong Wang
- The State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China.
| | - Zhipeng Liu
- The State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China.
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Vishwakarma MK, Kale SM, Sriswathi M, Naresh T, Shasidhar Y, Garg V, Pandey MK, Varshney RK. Genome-Wide Discovery and Deployment of Insertions and Deletions Markers Provided Greater Insights on Species, Genomes, and Sections Relationships in the Genus Arachis. FRONTIERS IN PLANT SCIENCE 2017; 8:2064. [PMID: 29312366 PMCID: PMC5742254 DOI: 10.3389/fpls.2017.02064] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 11/17/2017] [Indexed: 05/04/2023]
Abstract
Small insertions and deletions (InDels) are the second most prevalent and the most abundant structural variations in plant genomes. In order to deploy these genetic variations for genetic analysis in genus Arachis, we conducted comparative analysis of the draft genome assemblies of both the diploid progenitor species of cultivated tetraploid groundnut (Arachis hypogaea L.) i.e., Arachis duranensis (A subgenome) and Arachis ipaënsis (B subgenome) and identified 515,223 InDels. These InDels include 269,973 insertions identified in A. ipaënsis against A. duranensis while 245,250 deletions in A. duranensis against A. ipaënsis. The majority of the InDels were of single bp (43.7%) and 2-10 bp (39.9%) while the remaining were >10 bp (16.4%). Phylogenetic analysis using genotyping data for 86 (40.19%) polymorphic markers grouped 96 diverse Arachis accessions into eight clusters mostly by the affinity of their genome. This study also provided evidence for the existence of "K" genome, although distinct from both the "A" and "B" genomes, but more similar to "B" genome. The complete homology between A. monticola and A. hypogaea tetraploid taxa showed a very similar genome composition. The above analysis has provided greater insights into the phylogenetic relationship among accessions, genomes, sub species and sections. These InDel markers are very useful resource for groundnut research community for genetic analysis and breeding applications.
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Affiliation(s)
| | - Sandip M. Kale
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
| | - Manda Sriswathi
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
| | - Talari Naresh
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
| | - Yaduru Shasidhar
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
| | - Vanika Garg
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
| | - Manish K. Pandey
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
- *Correspondence: Manish K. Pandey
| | - Rajeev K. Varshney
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
- The University of Western Australia, Crawley, WA, Australia
- Rajeev K. Varshney
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Thakur J, Dwivedi MD, Sourabh P, Uniyal PL, Pandey AK. Genetic Homogeneity Revealed Using SCoT, ISSR and RAPD Markers in Micropropagated Pittosporum eriocarpum Royle- An Endemic and Endangered Medicinal Plant. PLoS One 2016; 11:e0159050. [PMID: 27434060 PMCID: PMC4951010 DOI: 10.1371/journal.pone.0159050] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2015] [Accepted: 06/27/2016] [Indexed: 11/18/2022] Open
Abstract
Pittosporum eriocarpum Royle, a medicinally important taxon, is endemic to Uttarakhand region of Himalaya. It has become endangered due to over-collection and the loss of habitats. As raising plants through seeds in this plant is problematic, a reliable protocol for micropropagation using nodal explants has been developed. High shoot regeneration (95%) occurred in MS medium augmented with BA 0.4mg/l in combination IBA 0.6mg/l. In vitro regenerated shoots were rooted in MS medium supplemented with three auxins, of which 0.6 mg/l indole butyric acid proved to be the best for rooting (90%) with maximum number of roots per shoot. Thereafter, rooted plants were hardened and nearly 73% of rooted shoots were successfully acclimatized and established in the field. Start codon targeted (SCoT), inter simple sequence repeats (ISSR) and random amplified polymorphic DNA (RAPD) markers were used to validate the genetic homogeneity amongst nine in vitro raised plantlets with mother plant. DNA fingerprints of in vitro regenerated plantlets displayed monomorphic bands similar to mother plant, indicating homogeneity among the micropropagated plants with donor mother plant. The similarity values were calculated based on SCoT, ISSR and RAPD profiles which ranged from 0.89 to 1.00, 0.91 to 1.00 and 0.95 to 1.00 respectively. The dendrograms generated through Unweighted Pair Group Method with arithmetic mean (UPGMA) analysis revealed 97% similarity amongst micropropagated plants with donor mother plant, thus confirming genetic homogeneity of micropropagated clones. This is the first report on micropropagation and genetic homogeneity assessment of P. eriocarpum. The protocol would be useful for the conservation and large scale production of P. eriocarpum to meet the demand for medicinal formulations and also for the re-introduction of in vitro grown plants in the suitable natural habitats to restore the populations.
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Affiliation(s)
- Julie Thakur
- Department of Botany, University of Delhi, Delhi, India
| | | | | | | | - Arun K. Pandey
- Department of Botany, University of Delhi, Delhi, India
- * E-mail:
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Satya P, Banerjee R, Karan M, Mukhopadhyay E, Chaudhary B, Bera A, Maruthi R, Sarkar S. Insight into genetic relation and diversity of cultivated and semi-domesticated under-utilized Crotalaria species gained using start codon targeted (SCoT) markers. BIOCHEM SYST ECOL 2016. [DOI: 10.1016/j.bse.2016.02.032] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Wild Panax vietnamensis and Panax stipuleanatus markedly increase the genetic diversity of Panax notoginseng (Araliaceae) revealed by start codon targeted (SCoT) markers and ITS DNA barcode. BIOCHEM SYST ECOL 2016. [DOI: 10.1016/j.bse.2016.03.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Zhang Y, Yan H, Jiang X, Wang X, Huang L, Xu B, Zhang X, Zhang L. Genetic variation, population structure and linkage disequilibrium in Switchgrass with ISSR, SCoT and EST-SSR markers. Hereditas 2016; 153:4. [PMID: 28096766 PMCID: PMC5226102 DOI: 10.1186/s41065-016-0007-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 03/29/2016] [Indexed: 11/29/2022] Open
Abstract
Background To evaluate genetic variation, population structure, and the extent of linkage disequilibrium (LD), 134 switchgrass (Panicum virgatum L.) samples were analyzed with 51 markers, including 16 ISSRs, 20 SCoTs, and 15 EST-SSRs. Results In this study, a high level of genetic variation was observed in the switchgrass samples and they had an average Nei’s gene diversity index (H) of 0.311. A total of 793 bands were obtained, of which 708 (89.28 %) were polymorphic. Using a parameter marker index (MI), the efficiency of the three types of markers (ISSR, SCoT, and EST-SSR) in the study were compared and we found that SCoT had a higher marker efficiency than the other two markers. The 134 switchgrass samples could be divided into two sub-populations based on STRUCTURE, UPGMA clustering, and principal coordinate analyses (PCA), and upland and lowland ecotypes could be separated by UPGMA clustering and PCA analyses. Linkage disequilibrium analysis revealed an average r2 of 0.035 across all 51 markers, indicating a trend of higher LD in sub-population 2 than that in sub-population 1 (P < 0.01). Conclusions The population structure revealed in this study will guide the design of future association studies using these switchgrass samples.
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Affiliation(s)
- Yu Zhang
- Grassland Science Department, Sichuan Agricultural University, Chengdu, 611130 China.,IRTA. Centre de Recerca en Agrigenòmica (CSIC-IRTA-UAB), Campus UAB - Edifici CRAG, Bellaterra - Cerdanyola del Vallès, Barcelona, 08193 Spain
| | - Haidong Yan
- Grassland Science Department, Sichuan Agricultural University, Chengdu, 611130 China
| | - Xiaomei Jiang
- Grassland Science Department, Sichuan Agricultural University, Chengdu, 611130 China
| | - Xiaoli Wang
- Guizhou Institute of Prataculture, Guiyang, 550006 PR China
| | - Linkai Huang
- Grassland Science Department, Sichuan Agricultural University, Chengdu, 611130 China
| | - Bin Xu
- College of Grassland Science, Nanjing Agricultural University, Nanjing, 210095 China
| | - Xinquan Zhang
- Grassland Science Department, Sichuan Agricultural University, Chengdu, 611130 China
| | - Lexin Zhang
- Grassland Science Department, Sichuan Agricultural University, Chengdu, 611130 China
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