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Trieu LN, Bich TT, Van Ket N, Van Long N. Genetic diversity, variation, and structure of two populations of bigfin reef squid (Sepioteuthis lessoniana d'Orbigny) in Con Dao and Phu Quoc islands, Vietnam. J Genet Eng Biotechnol 2023; 21:116. [PMID: 37955754 PMCID: PMC10643773 DOI: 10.1186/s43141-023-00573-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Accepted: 10/26/2023] [Indexed: 11/14/2023]
Abstract
BACKGROUND Bigfin squid is one of the economically important seafood resources in Vietnam's fisheries and the waters around Con Dao and Phu Quoc islands are two major fishing grounds where this species has been actively exploited. The start codon targeted polymorphism (SCoT) and CAAT box-derived polymorphism (CBDP) techniques were used to generate DNA fingerprinting data to analyze the genetic diversity, variation, and structure of the two populations in the waters surrounding Phu Quoc and Con Dao islands together with mitochondrial cytochrome C oxidase subunit I (COI) gene sequence data. RESULTS Con Dao population possessed a higher diversity [expected heterozygosity (He) = 0.2254, Shannon index (I) = 0.3459, percentage of polymorphic bands (PPB) = 80.14%, nucleotide diversity (π) = 0.0336, haplotype diversity (h) = 0.910 with 16 haplotypes] than Phu Quoc population (He = 0.1854, I = 0.2873, PPB = 70.38%, π = 0.0246, h = 0.838 with 14 haplotypes). The genetic diversity at species level in the investigated region was at level of He = 0.2169, I = 0.3399, PPB = 86.41, π = 0.0289, and h = 0.892 with 24 haplotypes. Based on DNA fingerprinting data, the pairwise genetic similarity coefficients among individuals of the Con Dao population were lower (average of 0.7977) than the Phu Quoc population (average of 0.8316). Based on mitochondrial COI data, the pairwise genetic distances among individuals of the Con Dao population were higher (average of 0.0361) than the Phu Quoc population (average of 0.0263). Gene differentiation (GST) between two investigated populations was 0.0316 and 0.0310 leading to the genetic distance was 0.0573 and 0.0213 and the gene flow between them was Nm = 8.2209 and 11.4700 migrants per generation among populations based on DNA fingerprinting and based on COI gene sequence data, respectively. Genetic variation within individuals of both populations (WP) played the key role in total genetic variation at species level in surveyed region. CONCLUSIONS For the bigfin reef squid species in the surveyed region, the Con Dao population had the higher genetic diversity than the Phu Quoc population, between them existed a low to moderate genetic differentiation and a genetic exchange via gene flow. The DNA fingerprinting data better revealed the genetic differentiation between the two surveyed populations while the mitochondrial COI gene sequence data could show the phylogenetic relationship among the surveyed individuals and the other from the sea regions in Southeast Asia. Based on the results obtained, fisheries management strategies are suggested toward the conservation and sustainable exploitation of this species.
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Affiliation(s)
- Le Ngoc Trieu
- The Faculty of Biology, Dalat University (DLU), Lam Dong, Vietnam.
| | - Thai Thach Bich
- The Faculty of Biology, Dalat University (DLU), Lam Dong, Vietnam
| | - Nguyen Van Ket
- The Faculty of Biology, Dalat University (DLU), Lam Dong, Vietnam
| | - Nguyen Van Long
- Institute of Oceanography, Vietnam Academy of Science and Technology (VAST), Khanh Hoa, Vietnam
- Graduated University of Science and Technology (GUST), VAST, Ha Noi, Vietnam
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Ghonaim MM, Attya AM, Aly HG, Mohamed HI, Omran AAA. Agro-morphological, biochemical, and molecular markers of barley genotypes grown under salinity stress conditions. BMC Plant Biol 2023; 23:526. [PMID: 37899447 PMCID: PMC10614329 DOI: 10.1186/s12870-023-04550-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 10/19/2023] [Indexed: 10/31/2023]
Abstract
The aim of this study was to evaluate the impact of salt stress on morphological, yield, biochemical, and molecular attributes of different barley genotypes. Ten genotypes were cultivated at Fayoum Research Station, El-Fayoum Governorate, Egypt, during two seasons (2020-2021 and 2021-2022), and they were exposed to two different salt concentrations (tap water as a control and 8000 ppm). The results showed that genotypes and salt stress had a significant impact on all morphological and physiological parameters. The morphological parameters (plant height) and yield attributes (spike length, number of grains per spike, and grain yield per plant) of all barley genotypes were significantly decreased under salt stress as compared to control plants. Under salt stress, the total soluble sugars, proline, total phenol, total flavonoid, ascorbic acid, malondialdehyde, hydrogen peroxide, and sodium contents of the shoots of all barley genotypes significantly increased while the potassium content decreased. L1, which is considered a sensitive genotype was more affected by salinity stress than the tolerance genotypes L4, L6, L9, and Giza 138. SDS-PAGE of seed proteins demonstrated high levels of genetic variety with a polymorphism rate of 42.11%. All genotypes evaluated revealed significant variations in the seed protein biochemical markers, with new protein bands appearing and other protein bands disappearing in the protein patterns of genotypes cultivated under various conditions. Two molecular marker techniques (SCoT and ISSR primers) were used in this study. Ten Start Codon Targeted (SCoT) primers exhibited a total of 94 fragments with sizes ranging from 1800 base pairs to 100 base pairs; 29 of them were monomorphic, and 65 bands, with a polymorphism of 62.18%, were polymorphic. These bands contained 21 unique bands (9 positive specific markers and 12 negative specific markers). A total of 54 amplified bands with molecular sizes ranging from 2200 to 200 bp were produced using seven Inter Simple Sequence Repeat (ISSR) primers; 31 of them were monomorphic bands and 23 polymorphic bands had a 40.9% polymorphism. The techniques identified molecular genetic markers associated with salt tolerance in barley crop and successfully marked each genotype with distinct bands. The ten genotypes were sorted into two main groups by the unweighted pair group method of arithmetic averages (UPGMA) cluster analysis based on molecular markers and data at a genetic similarity coefficient level of 0.71.
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Affiliation(s)
- Marwa M Ghonaim
- Cell Study Research Department, Field Crops Research Institute, Agriculture Research Center, Giza, Egypt
| | - A M Attya
- Barley Research Department, Field Crops Research Institute, Agriculture Research Center, Giza, Egypt
| | - Heba G Aly
- Barley Research Department, Field Crops Research Institute, Agriculture Research Center, Giza, Egypt
| | - Heba I Mohamed
- Faculty of Education, Biological and Geological Sciences Department, Ain Shams University, El Makres St. Roxy, Cairo, 11341, Egypt.
| | - Ahmed A A Omran
- Faculty of Education, Biological and Geological Sciences Department, Ain Shams University, El Makres St. Roxy, Cairo, 11341, Egypt
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Soliman AA, Mousa MI, Mosalam AM, Ghareeb ZE, Ibrahim SD, Rehan M, Yu H, He Y. The Potential Genetic Effect for Yield and Foliar Disease Resistance in Faba Bean ( Vicia faba L.) Assessed via Morphological and SCoT Markers. Plants (Basel) 2023; 12:3645. [PMID: 37896108 PMCID: PMC10610329 DOI: 10.3390/plants12203645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Revised: 10/05/2023] [Accepted: 10/19/2023] [Indexed: 10/29/2023]
Abstract
Faba bean is considered one of the most prominent grain legumes, with high protein content for human food consumption and livestock feed. The present study evaluated the nature of gene action and determined the genetic diversity among different populations of three crosses for resistance to foliar diseases at the molecular level. Analysis of variance exposed significant differences among the generations for all measured traits. Both dominance and additive gene effects were essential, but dominance genes, for the most part, exhibited greater effects than additive ones. This indicates an essential role for dominant genes alongside the additives one in inheriting such traits. The third cross (Marina × Giza 40) gave desired significant and positive (additive × additive) values for the number of pods/plant, seeds/plant, and seed yield/plant, in addition to desirable negative values for chocolate spot and rust characteristics. Furthermore, assessing the lines under study using seven SCoT primers disclosed three bands with recorded molecular weights of 260, 207, and 178 bp, generated by SCoT-1, SCoT-4, and SCoT-7 primers, respectively. These bands exist in the resistant parent (Marina), which could be attributed to the high-disease-resistance phenotypes, and they are absent in the sensitive parent (Giza 40) and other putative sensitive lines. Based on the molecular profiles and the genetic similarity between parents and the selected lines, the highest similarity value (0.91) was detected between Marina genotype and BC1, revealing a high foliar disease resistance. Meanwhile, Giza 40 (susceptible to foliar diseases) exhibited the maximum value (0.93) with F2. Additionally, cluster analysis based on genetic relationships was performed, and a high level of correlation between the results of PCR-based SCoT analysis and the foliar disease reactions was observed in the field. Consequently, this study concluded that SCoT markers created reliable banding profiles for evaluating genetic polymorphism among faba bean lines, which could be a foundation for developing an efficient breeding program.
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Affiliation(s)
- Alaa A. Soliman
- Food Legumes Research Department, Field Crops Research Institute, Agricultural Research Center, Giza 12619, Egypt;
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming 650205, China;
| | - Manar I. Mousa
- Food Legumes Research Department, Field Crops Research Institute, Agricultural Research Center, Giza 12619, Egypt;
| | - Abeer M. Mosalam
- Department of Agronomy, Faculty of Agriculture, Damietta University, New Damietta 34511, Egypt;
| | - Zeinab E. Ghareeb
- Center Laboratory for Design and Statistical Analysis Research, Agricultural Research Center, Giza 12619, Egypt;
| | - Shafik D. Ibrahim
- Agricultural Genetic Engineering Research Institute, Agricultural Research Center, Giza 12619, Egypt;
| | - Medhat Rehan
- Department of Plant Production and Protection, College of Agriculture and Veterinary Medicine, Qassim University, Buraydah 51452, Saudi Arabia;
- Department of Genetics, Faculty of Agriculture, Kafrelsheikh University, Kafr El-Sheikh 33516, Egypt
| | - Haitian Yu
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming 650205, China;
| | - Yuhua He
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming 650205, China;
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Santra I, Ghosh B. Sustainable production of plumbagin via meta-topolin-mediated high frequency regeneration of genetically true-to-type Plumbago zeylanica L. 3 Biotech 2023; 13:225. [PMID: 37304405 PMCID: PMC10247922 DOI: 10.1007/s13205-023-03642-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Accepted: 05/21/2023] [Indexed: 06/13/2023] Open
Abstract
Plumbago zeylanica L. is commonly known as chitrak, consumed since long time owing to its potent medicinal benefits. It is a major source of the yellow crystalline naphthoquinone called plumbagin, which is highly acclaimed for its anticancerous activities on different cancers i.e. prostrate, breast, ovarian, etc. The growing urges for this compound make this plant extremely demanding in the global market; hence, the plant is indiscriminately harvested from its very natural habitat. Therefore, in vitro biomass production of this plant can be a sustainable alternative for plumbagin production. In this present study, it has been found that, compared to other cytokinins, biomass production was enhanced by using aromatic cytokinin meta-topolin (mT). The highest shoot buds produced by mT (1 mg/l) was 13.60 ± 1.14 after 14 d of culture establishment. After 84 d in the same medium, 129.8 ± 2.71 shoots were produced, and the fresh weight of the total biomass was 19.72 ± 0.65 g. The highest number of roots was induced (37.80 ± 0.84) with 1.0 mg/l Indole-3-butyric acid (IBA). The well rooted plantlets were acclimatized in field condition with 87%survival. The regenerated plants' genetic fidelity was accessed through molecular markers i.e. Inter simple sequence repeat (ISSR), Start codon targeted (SCoT) and cytology studies. The monomorphic bands amplified by the primers across in vivo and in vitro plants confer the genetic homogeneity of the regenerants. The plumbagin content from different parts of the in vitro grown plants in vivo mother plant was quantified through High-Performance Liquid Chromatography (HPLC), and found that they do not differ significantly. Even all parts of the in vitro plants produce plumbagin, roots contain the maximum amount (14.67 ± 0.24 mg/g dry weight basis).
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Affiliation(s)
- Indranil Santra
- Plant Biotechnology Laboratory, Department of Botany, Ramakrishna Mission Vivekananda Centenary College, Rahara, Kolkata, 700118 India
| | - Biswajit Ghosh
- Plant Biotechnology Laboratory, Department of Botany, Ramakrishna Mission Vivekananda Centenary College, Rahara, Kolkata, 700118 India
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Sykłowska-Baranek K, Gaweł M, Kuźma Ł, Wileńska B, Kawka M, Jeziorek M, Graikou K, Chinou I, Szyszko E, Stępień P, Zakrzewski P, Pietrosiuk A. Rindera graeca (A. DC.) Boiss. & Heldr. (Boraginaceae) In Vitro Cultures Targeting Lithospermic Acid B and Rosmarinic Acid Production. Molecules 2023; 28:4880. [PMID: 37375435 DOI: 10.3390/molecules28124880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 06/15/2023] [Accepted: 06/16/2023] [Indexed: 06/29/2023] Open
Abstract
The in vitro cultures of Rindera graeca, a rare endemic plant, were developed as a sustainable source of phenolic acids. Various shoot and root cultures were established and scaled up in a sprinkle bioreactor. A multiplication rate of 7.2 shoots per explant was achieved. HPLC-PDA-ESI-HRMS analysis revealed the presence of rosmarinic acid (RA) and lithospermic acid B (LAB) as the main secondary metabolites in both the shoot and root cultures. The maximum RA (30.0 ± 3.2 mg/g DW) and LAB (49.3 ± 15.5 mg/g DW) yields were determined in root-regenerated shoots. The strongest free radical scavenging activity (87.4 ± 1.1%), according to 2,2-diphenyl-1-picrylhydrazyl-hydrate assay, was noted for roots cultivated in a DCR medium. The highest reducing power (2.3 µM ± 0.4 TE/g DW), determined by the ferric-reducing antioxidant power assay, was noted for shoots cultivated on an SH medium containing 0.5 mg/L 6-benzylaminopurine. A genetic analysis performed using random amplified polymorphic DNA and start codon targeted markers revealed genetic variation of 62.8% to 96.5% among the investigated shoots and roots. This variability reflects the capacity of cultivated shoots and roots to produce phenolic compounds.
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Affiliation(s)
- Katarzyna Sykłowska-Baranek
- Department of Pharmaceutical Biology, Faculty of Pharmacy, Medical University of Warsaw, 1 Banacha St., 02-097 Warsaw, Poland
| | - Małgorzata Gaweł
- Department of Pharmaceutical Biology, Faculty of Pharmacy, Medical University of Warsaw, 1 Banacha St., 02-097 Warsaw, Poland
| | - Łukasz Kuźma
- Department of Biology and Pharmaceutical Botany, Faculty of Pharmacy, Medical University of Łódź, 1 Muszyńskiego, 90-151 Łódź, Poland
| | - Beata Wileńska
- Faculty of Chemistry, University of Warsaw, 1 Pasteura St., 02-093 Warsaw, Poland
- Biological and Chemical Research Centre, 101 Żwirki i Wigury St., 02-097 Warsaw, Poland
| | - Mateusz Kawka
- Department of Pharmaceutical Biology, Faculty of Pharmacy, Medical University of Warsaw, 1 Banacha St., 02-097 Warsaw, Poland
| | - Małgorzata Jeziorek
- Department of Pharmaceutical Biology, Faculty of Pharmacy, Medical University of Warsaw, 1 Banacha St., 02-097 Warsaw, Poland
| | - Konstantia Graikou
- Laboratory of Pharmacognosy and Chemistry of Natural Products, Faculty of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis, 15771 Athens, Greece
| | - Ioanna Chinou
- Laboratory of Pharmacognosy and Chemistry of Natural Products, Faculty of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis, 15771 Athens, Greece
| | - Ewa Szyszko
- Department of Pharmaceutical Biology, Faculty of Pharmacy, Medical University of Warsaw, 1 Banacha St., 02-097 Warsaw, Poland
| | - Piotr Stępień
- Department of Pharmaceutical Biology, Faculty of Pharmacy, Medical University of Warsaw, 1 Banacha St., 02-097 Warsaw, Poland
| | - Patryk Zakrzewski
- Department of Pharmaceutical Biology, Faculty of Pharmacy, Medical University of Warsaw, 1 Banacha St., 02-097 Warsaw, Poland
| | - Agnieszka Pietrosiuk
- Department of Pharmaceutical Biology, Faculty of Pharmacy, Medical University of Warsaw, 1 Banacha St., 02-097 Warsaw, Poland
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Buddhachat K, Thongphueak J, Changtor P, Nukool W, Saengthong M, Kamol P, Suyasunanont U, Kosavititkul P, Pradit W, Nganvongpanit K, Chomdej S. Herbal species authentication by melting fingerprint coupled with high resolution melting analysis (MF-HRM). Mol Biol Rep 2023; 50:2421-2433. [PMID: 36592289 DOI: 10.1007/s11033-022-08235-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 12/23/2022] [Indexed: 01/03/2023]
Abstract
BACKGROUND Herbal medicines have recently attracted increasing attention for use as food supplements with health benefits; however, species authentication can be difficult due to incomplete morphological characters. Here, a molecular tool was developed for the identification of species in the National List of Essential Medicinal Plants in Thailand. METHODS The identification process used DNA fingerprints including start codon targeted (SCoT) and inter simple sequence repeat (ISSR) polymorphisms, coupled with high resolution melting (HRM), to produce melting fingerprint (MF)-HRM. RESULTS Results indicated that MF-HRM, SCoT-HRM and ISSR-HRM could be used for DNA fingerprints as S34, S36, S9 and S8 of SCoT and UBC873, S25 and UBC841 of ISSR. The melting fingerprints obtained from S34 of SCoT exhibited the best primers for identification of herbal species with 87.5% accuracy and relatively high repeatability. The presence of intraspecific variation in a few species affected the shift of melting fingerprints within species. MF-HRM using S34 showed improved species prediction compared to DNA fingerprints. The concentration of DNA with 10 ng/µl was recommended to perform MF-HRM. MF-HRM enabled species authentication of herbal commercialized products at only 20% resulting from the low quality of DNA isolated, while admixture of multiple product species interfered with the MF process. CONCLUSION Findings suggested that MF-HRM showed promise as a molecular tool for the authentication of species in commercial herbal products with high specificity, moderate repeatability and rapidity without prior sequence information. This information will greatly improve quality control and traceability during the manufacturing process.
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Affiliation(s)
- Kittisak Buddhachat
- Department of Biology, Faculty of Science, Naresuan University, Phitsanulok, 65000, Thailand. .,Center of Excellence in Research for Agricultural Biotechnology, Department of Agricultural Science, Faculty of Agriculture, Natural Resources and Environment, Naresuan University, Phitsanulok, 65000, Thailand.
| | - Jinnaphat Thongphueak
- Department of Biology, Faculty of Science, Naresuan University, Phitsanulok, 65000, Thailand
| | - Phanupong Changtor
- Department of Biology, Faculty of Science, Naresuan University, Phitsanulok, 65000, Thailand
| | - Wanrachon Nukool
- Department of Biology, Faculty of Science, Naresuan University, Phitsanulok, 65000, Thailand
| | - Maturada Saengthong
- Department of Biology, Faculty of Science, Naresuan University, Phitsanulok, 65000, Thailand
| | - Puntitra Kamol
- Department of Biology, Faculty of Science, Naresuan University, Phitsanulok, 65000, Thailand
| | - Urasri Suyasunanont
- Department of Biology, Faculty of Science, Naresuan University, Phitsanulok, 65000, Thailand
| | - Prasuk Kosavititkul
- Department of Biology, Faculty of Science, Naresuan University, Phitsanulok, 65000, Thailand
| | - Waranee Pradit
- Research Center in Bioresources for Agriculture, Industry and Medicine, Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Korakot Nganvongpanit
- Department of Veterinary Biosciences and Public Health, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai, 50100, Thailand.,Excellence Center in Veterinary Bioscience, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Siriwadee Chomdej
- Research Center in Bioresources for Agriculture, Industry and Medicine, Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, 50200, Thailand.
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Safhi FA, ALshamrani SM, Jalal AS, El-Moneim DA, Alyamani AA, Ibrahim AA. Genetic Characterization of Some Saudi Arabia's Accessions from Commiphora gileadensis Using Physio-Biochemical Parameters, Molecular Markers, DNA Barcoding Analysis and Relative Gene Expression. Genes (Basel) 2022; 13:2099. [PMID: 36421774 PMCID: PMC9690626 DOI: 10.3390/genes13112099] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 10/29/2022] [Accepted: 11/07/2022] [Indexed: 09/02/2023] Open
Abstract
Commiphora gileadensis L. is a medicinal plant, known as balsam, with pharmaceutical potential for its phytochemical activities and chemical constituents. Genetic diversity is a genetic tool used in medicinal plant evolution and conservation. Three accessions from C. gileadensis were collected from three localities in Saudi Arabia (Jeddah, Jizan and Riyadh). Genetic characterization was carried out using physio-biochemical parameters, molecular markers (inter-simple sequence repeat (ISSR) and start codon targeted (SCoT)), DNA barcoding (18 S rRNA and ITS rDNA regions), relative gene expressions (phenylalanine ammonia-lyase 1 (PAL1), defensin (PR-12)) and pathogenesis-related protein (AFPRT). The results of this study showed that C. gileadensis accession C3, collected from Riyadh, had the highest content from the physio-biochemical parameters perspective, with values of 92.54 mg/g and 77.13 mg/g for total phenolic content (TPC) and total flavonoid content (TFC), respectively. Furthermore, the highest content of antioxidant enzyme activity was present in accession C3 with values of 16.87, 60.87, 35.76 and 27.98 U mg-1 for superoxide dismutase (SOD), peroxidase (POD), catalase (CAT) (mol/min/mg FW) and ascorbate peroxidase (APX) (U mg-1 protein), respectively. The highest total number of bands and number of unique bands were 138 and 59, respectively, for the SCoT marker. The SCoT marker was the most efficient for the genetic diversity of C. gileadensis by producing the highest polymorphism (75.63%). DNA barcoding using 18 S and ITS showed the nearby Commiphora genus and clustered C. gileadensis accessions from Jeddah and Jizan in one clade and the C. gileadensis accession from Ryiadh in a separate cluster. Moreover, relative gene expression of the PAL1, defensin (PR-12) and AFPRT (PR1) genes was upregulated in the C. gileadensis accession from Ryiadh. In conclusion, ecological and environmental conditions in each locality affect the genomic expression and genetic diversity, which can help the evolution of important medicinal plants and improve breeding and conservation systems.
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Affiliation(s)
- Fatmah Ahmed Safhi
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
| | | | - Areej Saud Jalal
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
| | - Diaa Abd El-Moneim
- Department of Plant Production(Genetic Branch), Faculty of Environmental and Agricultural Sciences, Arish University, El-Arish 45511, Egypt
| | - Amal A. Alyamani
- Department of Biotechnology, Faculty of Science, Taif University, Taif 21974, Saudi Arabia
| | - Amira A. Ibrahim
- Botany and Microbiology Department, Faculty of Science, Arish University, El-Arish 45511, Egypt
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Al-Khayri JM, Mahdy EMB, Taha HSA, Eldomiaty AS, Abd-Elfattah MA, Abdel Latef AAH, Rezk AA, Shehata WF, Almaghasla MI, Shalaby TA, Sattar MN, Ghazzawy HS, Awad MF, Alali KM, Jain SM, Hassanin AA. Genetic and Morphological Diversity Assessment of Five Kalanchoe Genotypes by SCoT, ISSR and RAPD-PCR Markers. Plants (Basel) 2022; 11:plants11131722. [PMID: 35807674 PMCID: PMC9268761 DOI: 10.3390/plants11131722] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 06/24/2022] [Accepted: 06/25/2022] [Indexed: 05/14/2023]
Abstract
Determining the appropriate parents for breeding programs is the most important decision that plant breeders must make to maximize the genetic variability and produce excellent recombinant genotypes. Several methods are used to identify genotypes with desirable phenotypic features for breeding experiments. In this study, five kalanchoe genotypes were morphologically characterized by assessing plant height, number of inflorescences, number of flowers, flower length, flower diameter and number of petals. The analysis showed the distinction of yellow kalanchoe in the plant height trait, while the orange kalanchoe was distinguished in the number of inflorescences, the number of flowers and flower length traits, whereas the violet kalanchoe possessed the largest flower diameter and the highest number of petals. The molecular profiling was performed by random amplified polymorphism DNA (RAPD), inter-simple sequence repeats (ISSR) and start codon targeted (SCoT)-polymerase chain reaction (PCR) tools. Genomic DNA was extracted from young leaves and the PCR reactions were performed using ten primers for each SCoT, ISSR and RAPD marker. Only four out of ten primers showed amplicon profiles in all PCR markers. A total of 70 bands were generated by SCoT, ISSR and RAPD-PCR with 35 polymorphic bands and 35 monomorphic bands. The total number of bands of RAPD, ISSR and SCoT was 15, 17 and 38, respectively. The polymorphism percentages achieved by RAPD, ISSR and SCoT were 60.25%, 15% and 57%, respectively. The cluster analysis based on morphological data revealed two clusters. Cluster I consisted of violet and orange kalanchoe, and cluster II comprised red, yellow and purple kalanchoe. Whereas the cluster analysis based on molecular data revealed three clusters. Cluster I included only yellow kalanchoe, cluster II comprised orange and violet kalanchoe while cluster III comprised red, and purple kalanchoe. The study concluded that orange, violet and yellow kalanchoe are distinguished parents for breeding economically valued traits in kalanchoe. Also, the study concluded that SCoT and RAPD markers reproduced reliable banding patterns to assess the genetic polymorphism among kalanchoe genotypes that consider the basis stone for genetic improvements in ornamental plants.
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Affiliation(s)
- Jameel M. Al-Khayri
- Department of Agricultural Biotechnology, College of Agriculture and Food Sciences, King Faisal University, Al-Ahsa 31982, Saudi Arabia; (A.A.R.); (W.F.S.); (K.M.A.)
- Correspondence: (J.M.A.-K.); (A.A.H.A.L.); (A.A.H.)
| | - Ehab M. B. Mahdy
- National Gene Bank (NGB), Agricultural Research Centre (ARC), Giza 12613, Egypt;
| | - Heba S. A. Taha
- Genetics Department, Faculty of Agriculture, Zagazig University, Zagazig 44511, Egypt; (H.S.A.T.); (A.S.E.)
| | - Ahmed S. Eldomiaty
- Genetics Department, Faculty of Agriculture, Zagazig University, Zagazig 44511, Egypt; (H.S.A.T.); (A.S.E.)
| | | | - Arafat Abdel Hamed Abdel Latef
- Department of Botany and Microbiology, Faculty of Science, South Valley University, Qena 83523, Egypt
- Correspondence: (J.M.A.-K.); (A.A.H.A.L.); (A.A.H.)
| | - Adel A. Rezk
- Department of Agricultural Biotechnology, College of Agriculture and Food Sciences, King Faisal University, Al-Ahsa 31982, Saudi Arabia; (A.A.R.); (W.F.S.); (K.M.A.)
| | - Wael F. Shehata
- Department of Agricultural Biotechnology, College of Agriculture and Food Sciences, King Faisal University, Al-Ahsa 31982, Saudi Arabia; (A.A.R.); (W.F.S.); (K.M.A.)
| | - Mustafa I. Almaghasla
- Department of Arid Land Agriculture, College of Agriculture and Food Sciences, King Faisal University, P.O. Box 420, Al-Ahsa 31982, Saudi Arabia; (M.I.A.); (T.A.S.)
- Plant Pests, and Diseases Unit, College of Agriculture and Food Sciences, King Faisal University, P.O. Box 420, Al-Ahsa 31982, Saudi Arabia
| | - Tarek A. Shalaby
- Department of Arid Land Agriculture, College of Agriculture and Food Sciences, King Faisal University, P.O. Box 420, Al-Ahsa 31982, Saudi Arabia; (M.I.A.); (T.A.S.)
- Horticulture Department, Faculty of Agriculture, Kafrelsheikh University, Kafr El-Sheikh 33516, Egypt
| | - Muhammad N. Sattar
- Central Laboratories, King Faisal University, P.O. Box 420, Al-Ahsa 31982, Saudi Arabia;
| | - Hesham S. Ghazzawy
- Date Palm Research Center of Excellence, King Faisal University, Al-Ahsa 31982, Saudi Arabia;
| | - Mohamed F. Awad
- Department of Biology, College of Science, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia;
| | - Khalid M. Alali
- Department of Agricultural Biotechnology, College of Agriculture and Food Sciences, King Faisal University, Al-Ahsa 31982, Saudi Arabia; (A.A.R.); (W.F.S.); (K.M.A.)
| | - Shri Mohan Jain
- Department of Agricultural Sciences, University of Helsinki, 00014 Helsinki, Finland;
| | - Abdallah A. Hassanin
- Genetics Department, Faculty of Agriculture, Zagazig University, Zagazig 44511, Egypt; (H.S.A.T.); (A.S.E.)
- Correspondence: (J.M.A.-K.); (A.A.H.A.L.); (A.A.H.)
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Samarina LS, Malyarovskaya VI, Rakhmangulov RS, Koninskaya NG, Matskiv AO, Shkhalakhova RM, Orlov YL, Tsaturyan GA, Shurkina ES, Gvasaliya MV, Kuleshov AS, Ryndin AV. Population Analysis of Diospyros lotus in the Northwestern Caucasus Based on Leaf Morphology and Multilocus DNA Markers. Int J Mol Sci 2022; 23:2192. [PMID: 35216308 DOI: 10.3390/ijms23042192] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/13/2022] [Accepted: 02/15/2022] [Indexed: 01/02/2023] Open
Abstract
Diospyros lotus is the one of the most frost-tolerant species in the Diospyros genera, used as a rootstock for colder regions. Natural populations of D. lotus have a fragmented character of distribution in the Northwestern Caucasus, one of the coldest regions of Diospyros cultivation. To predict the behavior of D. lotus populations in an extreme environment, it is necessary to investigate the intraspecific genetic diversity and phenotypic variability of populations in the colder regions. In this study, we analyzed five geographically distant populations of D. lotus according to 33 morphological leaf traits, and the most informative traits were established, namely, leaf length, leaf width, leaf index (leaf to length ratio) and the length of the fourth veins. Additionally, we evaluated the intraspecific genetic diversity of D. lotus using ISSR and SCoT markers and proposed a new parameter for the evaluation of genetic polymorphism among populations, in order to eliminate the effect of sample number. This new parameter is the relative genetic polymorphism, which is the ratio of polymorphism to the number of samples. Based on morphological and genetic data, the northernmost population from Shkhafit was phenotypically and genetically distant from the other populations. The correspondence between several morphological traits (leaf width, leaf length and first to fifth right vein angles) and several marker bands (SCoT5, SCoT7, SCoT30: 800–1500 bp; ISSR13, ISSR14, ISSR880: 500–1000 bp) were observed for the Shkhafit population. Unique SCoT and ISSR fragments can be used as markers for breeding purposes. The results provide a better understanding of adaptive mechanisms in D. lotus in extreme environments and will be important for the further expansion of the cultivation area for persimmon in colder regions.
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Talebi SM, Askary M, Samiei-Rad M, Tabaripour R, Matsyura A. Do we have infraspecific taxa of Salvia macrosiphon Boiss. (Lamiaceae) in Iran? Mol Biol Rep 2022; 49:1181-1189. [PMID: 34981338 DOI: 10.1007/s11033-021-06946-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Accepted: 09/23/2021] [Indexed: 11/29/2022]
Abstract
BACKGROUND Salvia macrosiphon is an aromatic perennial species of Lamiaceae family that grows naturally in different parts of Iran. This herb is widely used in folk and modern medicine. Although in Flora Iranica and Flora of Iran, no infraspecific taxonomic rank has been detected for S. macrosiphon, some infraspecific taxonomic ranks have been reported. In the current study, we evaluated the genetic diversity and structure of 11 populations of this species to detect inter and intrapopulation genetic diversity and to survey the possibility of infraspecific taxonomic ranks in this species. METHODS AND RESULTS We utilized the modified C-TAB protocol for DNA extraction and amplified the genomes using several SCoT molecular markers. We calculated of genetic diversity and polymorphism parameters using GenAlex 6.4, Geno-Dive ver.2, PopGene, PopART and Structure 2.3.4. The parameters of genetic polymorphism differed between the populations. Moreover, a low rate of gene flow supported a moderate level of population's genetic diversity and differentiation. According to haplotypes network (TCS) analysis, a high level of genetic mutation has occurred among the individuals of some populations leading to high intrapopulation diversity. On the basis of structure analysis and Nei's genetic distance, the examined populations were classified into four genotypes. CONCLUSIONS The clustering pattern of the populations in each group was not related to geographical distance or phytogeography. It seems that the wide geographic distribution, a small gene flow rate and the occurrence of a high level of genetic mutation lead to infraspecific genetic differentiation in the species and we suppose some infraspecific ranks exist for it.
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Affiliation(s)
- Seyed Mehdi Talebi
- Department of Biology, Faculty of Sciences, Arak University, Arāk, 38156-8-8349, Iran.
| | - Mehri Askary
- Department of Biology, Faculty of Sciences, Arak University, Arāk, 38156-8-8349, Iran
| | - Maryam Samiei-Rad
- Department of Biology, Faculty of Sciences, Arak University, Arāk, 38156-8-8349, Iran
| | - Raheleh Tabaripour
- Department of Plant Sciences, Faculty of Biological Sciences, Alzahra University, Tehran, Iran
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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] [What about the content of this article? (0)] [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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13
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Pinto GHT, Lopes AA, de Freitas Morel LJ, Crevelin EJ, Miranda CES, Contini SHT, de Castro França S, Bertoni BW, Pereira AMS. Genetic diversity among genotypes of Uncaria guianensis (Aubl.) J.F. Gmel. maintained in an in vitro germplasm bank. 3 Biotech 2022; 12:8. [PMID: 34956811 PMCID: PMC8651866 DOI: 10.1007/s13205-021-03016-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 10/05/2021] [Indexed: 01/03/2023] Open
Abstract
Phytotherapeutic preparations from Uncaria guianensis (Aubl.) J.F. Gmel. (Rubiaceae) are marketed worldwide and are mainly used for their anti-inflammatory activity. The species has not yet been domesticated and is threatened by deforestation and overexploitation. It is, therefore, important to preserve and manage this genetic resource in germplasm banks, so that the extractive provision of plant material can be replaced by cultivated production. The aim of this study was to evaluate the genetic diversity among 20 genotypes maintained under in vitro conditions using 9 primers start codon targeted (SCoT) polymorphism, and to determine the concentrations of the pentacyclic oxindole alkaloids (POAs); mitraphylline and isomitraphylline in methanolic extracts by high-performance liquid chromatography (HPLC). Plantlets were cultivated on woody plant medium supplemented with 20 g.L-1 sucrose and 4.4 μM benzylaminopurine and incubated under a 16 h photoperiod for 45 days. SCoT analysis separated the genotypes into four divergent clusters and confirmed significant genetic diversity with up to 70% dissimilarity. Moreover, HPLC revealed considerable chemical variability and allowed the separation of the tested genotypes into high, medium and low producers of mitraphylline/isomitraphylline. Genotypes with the highest concentrations of POAs originated from the state of Acre and Amapá, while those with the lowest levels were from the state of Pará. The results demonstrate that the genetic diversity within the in vitro germplasm bank is sufficient to support breeding studies, selection of elite genotypes and the large-scale multiplication of plants that could serve as feedstock for the industrial-scale production of phytomedicines. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-03016-y.
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14
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Abd El-Moneim D, ELsarag EIS, Aloufi S, El-Azraq AM, ALshamrani SM, Safhi FAA, Ibrahim AA. Quinoa ( Chenopodium quinoa Willd.): Genetic Diversity According to ISSR and SCoT Markers, Relative Gene Expression, and Morpho-Physiological Variation under Salinity Stress. Plants (Basel) 2021; 10:plants10122802. [PMID: 34961273 PMCID: PMC8707205 DOI: 10.3390/plants10122802] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 12/08/2021] [Accepted: 12/14/2021] [Indexed: 06/14/2023]
Abstract
Quinoa (Chenopodium quinoa Willd.) is a halophytic crop that can withstand a variety of abiotic stresses, including salt. The present research examined the mechanisms of salt tolerance in five different quinoa genotypes at four different salinity levels (control (60), 80, 120, and 160 mM NaCl). ISSR and SCoT analysis revealed high polymorphism percentages of 90.91% and 85.26%, respectively. Furthermore, ISSR 1 and SCoT 7 attained the greatest number of polymorphic amplicons (27 and 26), respectively. Notably, LINE-6 and M-28 genotypes demonstrated the greatest number of unique positive and negative amplicons (50 and 42) generated from ISSR and SCoT, respectively. Protein pattern analysis detected 11 bands with a polymorphism percentage 27.27% among the quinoa genotypes, with three unique bands distinguishable for the M-28 genotype. Similarity correlation indicated that the highest similarity was between S-10 and Regeolone-3 (0.657), while the lowest similarity was between M-28 and LINE-6 (0.44). Significant variations existed among the studied salinity treatments, genotypes, and the interactions between them. The highest and lowest values for all the studied morpho-physiological and biochemical traits were recorded at 60 and 160 mM NaCl concentrations, respectively, except for the Na and proline contents, which exhibited the opposite relationship. The M-28 genotype demonstrated the highest values for all studied characteristics, while the LINE-6 genotype represented the lowest in both seasons. On the other hand, mRNA transcript levels for CqSOS1 did not exhibit differential expression in roots and leaf tissues, while the expression of CqNHX1 was upregulated more in both tissues for the M-28 genotype than for the LINE-6 genotype, and its maximum induction was seen in the leaves. Overall, the genotypes M-28 and LINE-6 were identified as the most and least salinity-tolerant, respectively.
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Affiliation(s)
- Diaa Abd El-Moneim
- Department of Plant Production (Genetic Branch), Faculty of Environmental and Agricultural Sciences, Arish University, El-Arish 45511, Egypt
| | - Eman I. S. ELsarag
- Department of Plant Production (Agronomy Branch), Faculty of Environmental and Agricultural Sciences, Arish University, El-Arish 45511, Egypt; (E.I.S.E.); (A.M.E.-A.)
| | - Salman Aloufi
- Department of Biotechnology, Faculty of Science, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia;
| | - Asmaa M. El-Azraq
- Department of Plant Production (Agronomy Branch), Faculty of Environmental and Agricultural Sciences, Arish University, El-Arish 45511, Egypt; (E.I.S.E.); (A.M.E.-A.)
| | - Salha Mesfer ALshamrani
- Department of Biology, College of Science, University of Jeddah, Jeddah 21959, Saudi Arabia;
| | - Fatmah Ahmed Ahmed Safhi
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, Riyadh 11671, Saudi Arabia;
| | - Amira A. Ibrahim
- Plant Protection and Biomolecular Diagnosis Department, Arid Lands Cultivation Research Institute, City of Scientific Research and Technological Applications, New Borg El-Arab, Alexandria 21934, Egypt
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Youssef OA, Tammam AA, El-Bakatoushi RF, Alframawy AM, Emara MM, El-Sadek LM. Uptake of hematite nanoparticles in maize and their role in cell cycle dynamics, PCNA expression and mitigation of cadmium stress. Plant Biol (Stuttg) 2021; 23:1177-1189. [PMID: 34374200 DOI: 10.1111/plb.13315] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 04/24/2021] [Accepted: 06/14/2021] [Indexed: 06/13/2023]
Abstract
Cadmium toxicity is considered a major threat to several crops worldwide. Hematite nanoparticles (NPs), due to their small size and large specific surface area, could be applied as an adsorbent for toxic heavy metals in soil. Also, they serve as an efficient nano-fertilizer, promoting Fe availability and biomass production in plants, thus enabling Cd2+ -induced stress tolerance. The phytotoxicity of five different concentrations of hematite NPs, ranging from 500 to 8,000 mg·kg-1 , and Cd2+ concentrations (110 or 130 mg·kg-1 Cd2+ ) alone or combined with 500 mg·kg-1 NPs was evaluated in maize. The changes in fresh weight, element analysis, cell cycle regulation, DNA banding patterns and proliferating cell nuclear antigen (PCNA) expression were used as biomarkers. The results revealed that increased fresh weight and fewest polymorphic DNA bands were detectable after treatment with 500 mg·kg-1 NPs. However, at 8,000 mg·kg-1 NPs, PCNA expression increased significantly, which resulted in cell cycle arrest at the G1/S checkpoint in roots. Significant reductions in fresh weight, altered nutrient profiles and cell cycle perturbations are considered symptoms of Cd2+ toxicity in maize. Conversely, amending 500 mg·kg-1 NPs with 130 mg·kg-1 Cd2+ increased fresh weight, Fe concentration and genomic template stability, while reducing Cd2+ uptake and PCNA1 expression. Overall, 8,000 mg·kg-1 hematite NPs interfered with the cellular homeostatic balance of maize, resulting in a cascade of genotoxic events, leading to growth inhibition. Although 500 mg·kg-1 hematite NPs alleviated Cd2+ -induced DNA damage to a certain extent, their impact on cell cycle progression requires further verification.
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Affiliation(s)
- O A Youssef
- Botany and Microbiology Department, Faculty of Science, Alexandria University, Alexandria, Camp Caesar, 21525, Egypt
| | - A A Tammam
- Botany and Microbiology Department, Faculty of Science, Alexandria University, Alexandria, Camp Caesar, 21525, Egypt
| | - R F El-Bakatoushi
- Biology and Geology Sciences Department, Faculty of Education, Alexandria University, Alexandria, El-shatby, 526, Egypt
| | - A M Alframawy
- Nucleic Acids Research Department, Genetic Engineering & Biotechnology Research Institute (GEBRI), City for Scientific Research and Technological Applications, Alexandria, Borg El-Arab, 21933, Egypt
| | - M M Emara
- Chemistry Department, Faculty of Science, Alexandria University, Alexandria, Ibrahimia, 21321, Egypt
| | - L M El-Sadek
- Botany and Microbiology Department, Faculty of Science, Alexandria University, Alexandria, Camp Caesar, 21525, Egypt
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16
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Mostafavi AS, Omidi M, Azizinezhad R, Etminan A, Badi HN. Genetic diversity analysis in a mini core collection of Damask rose (Rosa damascena Mill.) germplasm from Iran using URP and SCoT markers. J Genet Eng Biotechnol 2021; 19:144. [PMID: 34591207 PMCID: PMC8484433 DOI: 10.1186/s43141-021-00247-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 09/14/2021] [Indexed: 11/10/2022]
Abstract
BACKGROUND Rosa damascena Mill is a well-known species of the rose family. It is famous for its essential oil content. The aim of the present study was to assess the genetic diversity and population structure of a mini core collection of the Iranian Damask rose germplasm. This involved the use of universal rice primers (URP) and start codon targeted (SCoT) molecular markers. RESULTS Fourteen URP and twelve SCoT primers amplified 268 and 216 loci, with an average of 19.21 and 18.18 polymorphic fragments per primer, respectively. The polymorphic information content for URR and SCoT primers ranged from 0.38 to 0.48 and 0.11 to 0.45, with the resolving power ranging from 8.75 to 13.05 and 9.9 to 14.59, respectively. Clustering was based on neighbor-joining (NJ). The mini core collection contained 40 accessions and was divided into three distinct clusters, centered on both markers and on the combination of data. CONCLUSION Cluster analysis and principal coordinate analysis were consistent with genetic relationships derived by STRUCTURE analysis. The findings showed that patterns of grouping did not correlate with geographical origin. Both molecular markers demonstrated that the accessions were not genetically diverse as expected, thereby highlighting the possibility that gene flow occurred between populations.
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Affiliation(s)
- Atefeh Sadat Mostafavi
- Department of Plant Breeding and Biotechnology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Mansour Omidi
- Department of Agronomy and Plant Breeding, Agricultural College, University of Tehran, Karaj, Iran
| | - Reza Azizinezhad
- Department of Plant Breeding and Biotechnology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Alireza Etminan
- Department of Plant breeding and Biotechnology, Kermanshah Branch, Islamic Azad University, Kermanshah, Iran
| | - Hassanali Naghdi Badi
- Department of Plant Breeding and Biotechnology, Science and Research Branch, Islamic Azad University, Tehran, Iran
- Medicinal Plants Research Center, Institute of Medicinal Plants, ACECR, Karaj, Iran
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Cieplak M, Okoń S, Werwińska K. Genetic Similarity of Avena sativa L. Varieties as an Example of a Narrow Genetic Pool of Contemporary Cereal Species. Plants (Basel) 2021; 10:1424. [PMID: 34371627 DOI: 10.3390/plants10071424] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 07/07/2021] [Accepted: 07/08/2021] [Indexed: 11/30/2022]
Abstract
The assessment of the genetic diversity of cultivated varieties is a very important element of breeding programs. This allows the determination of the level of genetic differentiation of cultivated varieties, their genetic distinctiveness, and is also of great importance in the selection of parental components for crossbreeding. The aim of the present study was to determine the level of genetic diversity of oat varieties currently grown in Central Europe based on two marker systems: ISSR and SCoT. The research conducted showed that both these types of markers were suitable for conducting analyses relating to the assessment of genetic diversity. The calculated coefficients showed that the analyzed cultivars were characterized by a high genetic similarity. However, the UPGMA and PCoA analyses clearly indicated the distinctiveness of the breeding programs conducted in Central European countries. The high genetic similarity of the analyzed forms allow us to conclude that it is necessary to expand the genetic pool of oat varieties. Numerous studies show that landraces may be the donor of genetic variation.
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Samarina LS, Malyarovskaya VI, Reim S, Yakushina LG, Koninskaya NG, Klemeshova KV, Shkhalakhova RM, Matskiv AO, Shurkina ES, Gabueva TY, Slepchenko NA, Ryndin AV. Transferability of ISSR, SCoT and SSR Markers for Chrysanthemum × Morifolium Ramat and Genetic Relationships Among Commercial Russian Cultivars. Plants (Basel) 2021; 10:1302. [PMID: 34199003 PMCID: PMC8309030 DOI: 10.3390/plants10071302] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 06/20/2021] [Accepted: 06/23/2021] [Indexed: 11/16/2022]
Abstract
Characterization of genetic diversity in germplasm collections requires an efficient set of molecular markers. We assessed the efficiency of 36 new SCoT markers, 10 new ISSR markers, and 5 microsatellites for the characterization of genetic diversity in chrysanthemum core collection of 95 accessions (Russian and foreign cultivars). Seven new SCoT (SCoT12, 20, 21, 23, 29, 31, 34) and six new ISSR markers ((GA)8T, (CT)8G, (CTTCA)3, (GGAGA)3, (TC)8C, (CT)8TG) were efficient for the genetic diversity analysis in Chrysanthemum × morifolium collection. After STRUCTURE analysis, most Russian cultivars showed 20-50% of genetic admixtures of the foreign cultivars. Neighbor joining analysis based on the combination of SSR, ISSR, and SCoT data showed the best accordance with phenotype and origin compared to the separate analysis by each marker type. The position of the accessions within the phylogenetic tree corresponded with the origin and with some important traits, namely, plant height, stem and peduncle thickness, inflorescence type, composite flower and floret types, flower color, and disc color. In addition, several SCoT markers were suitable to separate the groups distinctly by the phenotypical traits such as plant height (SCoT29, SCoT34), thickness of the stem and peduncle (SCoT31, SCoT34), and leaf size and the floret type (SCoT31). These results provide new findings for the selection of markers associated with important traits in Chrysanthemum for trait-oriented breeding and germplasm characterization.
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Affiliation(s)
- Lidia S. Samarina
- Federal Research Centre the Subtropical Scientific Centre of the Russian Academy of Sciences, 354002 Sochi, Russia; (V.I.M.); (L.G.Y.); (N.G.K.); (K.V.K.); (R.M.S.); (A.O.M.); (E.S.S.); (T.Y.G.); (N.A.S.); (A.V.R.)
| | - Valentina I. Malyarovskaya
- Federal Research Centre the Subtropical Scientific Centre of the Russian Academy of Sciences, 354002 Sochi, Russia; (V.I.M.); (L.G.Y.); (N.G.K.); (K.V.K.); (R.M.S.); (A.O.M.); (E.S.S.); (T.Y.G.); (N.A.S.); (A.V.R.)
| | - Stefanie Reim
- Institute for Breeding Research on Fruit Crops, Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, 01326 Dresden, Germany;
| | - Lyudmila G. Yakushina
- Federal Research Centre the Subtropical Scientific Centre of the Russian Academy of Sciences, 354002 Sochi, Russia; (V.I.M.); (L.G.Y.); (N.G.K.); (K.V.K.); (R.M.S.); (A.O.M.); (E.S.S.); (T.Y.G.); (N.A.S.); (A.V.R.)
| | - Natalia G. Koninskaya
- Federal Research Centre the Subtropical Scientific Centre of the Russian Academy of Sciences, 354002 Sochi, Russia; (V.I.M.); (L.G.Y.); (N.G.K.); (K.V.K.); (R.M.S.); (A.O.M.); (E.S.S.); (T.Y.G.); (N.A.S.); (A.V.R.)
| | - Kristina V. Klemeshova
- Federal Research Centre the Subtropical Scientific Centre of the Russian Academy of Sciences, 354002 Sochi, Russia; (V.I.M.); (L.G.Y.); (N.G.K.); (K.V.K.); (R.M.S.); (A.O.M.); (E.S.S.); (T.Y.G.); (N.A.S.); (A.V.R.)
| | - Ruset M. Shkhalakhova
- Federal Research Centre the Subtropical Scientific Centre of the Russian Academy of Sciences, 354002 Sochi, Russia; (V.I.M.); (L.G.Y.); (N.G.K.); (K.V.K.); (R.M.S.); (A.O.M.); (E.S.S.); (T.Y.G.); (N.A.S.); (A.V.R.)
| | - Alexandra O. Matskiv
- Federal Research Centre the Subtropical Scientific Centre of the Russian Academy of Sciences, 354002 Sochi, Russia; (V.I.M.); (L.G.Y.); (N.G.K.); (K.V.K.); (R.M.S.); (A.O.M.); (E.S.S.); (T.Y.G.); (N.A.S.); (A.V.R.)
| | - Ekaterina S. Shurkina
- Federal Research Centre the Subtropical Scientific Centre of the Russian Academy of Sciences, 354002 Sochi, Russia; (V.I.M.); (L.G.Y.); (N.G.K.); (K.V.K.); (R.M.S.); (A.O.M.); (E.S.S.); (T.Y.G.); (N.A.S.); (A.V.R.)
| | - Tatiana Y. Gabueva
- Federal Research Centre the Subtropical Scientific Centre of the Russian Academy of Sciences, 354002 Sochi, Russia; (V.I.M.); (L.G.Y.); (N.G.K.); (K.V.K.); (R.M.S.); (A.O.M.); (E.S.S.); (T.Y.G.); (N.A.S.); (A.V.R.)
| | - Natalia A. Slepchenko
- Federal Research Centre the Subtropical Scientific Centre of the Russian Academy of Sciences, 354002 Sochi, Russia; (V.I.M.); (L.G.Y.); (N.G.K.); (K.V.K.); (R.M.S.); (A.O.M.); (E.S.S.); (T.Y.G.); (N.A.S.); (A.V.R.)
| | - Alexey V. Ryndin
- Federal Research Centre the Subtropical Scientific Centre of the Russian Academy of Sciences, 354002 Sochi, Russia; (V.I.M.); (L.G.Y.); (N.G.K.); (K.V.K.); (R.M.S.); (A.O.M.); (E.S.S.); (T.Y.G.); (N.A.S.); (A.V.R.)
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Zheng K, Cai Y, Chen W, Gao Y, Jin J, Wang H, Feng S, Lu J. Development, Identification, and Application of a Germplasm Specific SCAR Marker for Dendrobium officinale Kimura et Migo. Front Plant Sci 2021; 12:669458. [PMID: 34054907 PMCID: PMC8160518 DOI: 10.3389/fpls.2021.669458] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 04/20/2021] [Indexed: 05/27/2023]
Abstract
The stems of Dendrobium officinale have been used as a rare and valuable Chinese tonic medicine, known as "Tiepi Fengdou", since the Qing dynasty. Because of the increased market demand and continued exploitation of this plant, the reserves of wild D. officinale resources have been depleted, and D. officinale products on the market are being increasingly adulterated. Such changes have strongly affected the sustainable utilization of this valuable medicinal plant resource and the development of related industries. In this study, a species-specific DNA marker was developed for the rapid and accurate authentication of D. officinale. In total, 36 start codon-targeted (SCoT) polymorphism primers were screened in 36 definite Dendrobium species, and a distinct species-specific DNA amplicon (SCoT13-215) for D. officinale was obtained. After the sequence was cloned and sequenced, a sequence-characterized amplified region marker was developed (named SHF/SHR) and validated through PCR amplification of all 38 Dendrobium samples. The marker's specificity for D. officinale was confirmed through the consistent amplification of a clear 197-bp band. This SCAR marker can be used to rapidly, effectively, and reliably identify D. officinale among various Dendrobium species and may play an important role in ensuring the quality of medicinal preparations and protecting the germplasm of this important medicinal species.
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Affiliation(s)
- Kaixin Zheng
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou, China
| | - Yuchen Cai
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou, China
| | - Weijie Chen
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Yadi Gao
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou, China
| | - Jingjing Jin
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Huizhong Wang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou, China
| | - Shangguo Feng
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou, China
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | - Jiangjie Lu
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou, China
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20
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Heylen OCG, Debortoli N, Marescaux J, Olofsson JK. A Revised Phylogeny of the Mentha spicata Clade Reveals Cryptic Species. Plants (Basel) 2021; 10:819. [PMID: 33924227 PMCID: PMC8074783 DOI: 10.3390/plants10040819] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 03/30/2021] [Accepted: 04/18/2021] [Indexed: 05/29/2023]
Abstract
The genus Mentha is taxonomically and phylogenetically challenging due to complex genomes, polyploidization and an extensive historical nomenclature, potentially hiding cryptic taxa. A straightforward interpretation of phylogenetic relationships within the section Mentha is further hindered by dominant but outdated concepts on historically identified hybrid taxa. Mentha spicata is traditionally considered to be of hybrid origin, but the evidence for this is weak. Here, we aim to understand the phylogenetic relationships within the section Mentha using large sample sizes and to revisit the hybrid status and identity of M. spicata. We show that two of three traditional species in the subsection Spicatae are polyphyletic, as is the subsection as a whole, while the real number of cryptic species was underestimated. Compared to previous studies we present a fundamentally different phylogeny, with a basal split between M. spicata s.s. and M. longifolia s.s. Cluster analyses of morphological and genotypic data demonstrate that there is a dissociation between morphologically and genotypically defined groups of samples. We did not find any evidence that M. spicata is of hybrid origin, and we conclude its taxonomic status should be revised. The combination of genetic and phenotypic information is essential when evaluating hyperdiverse taxonomic groups.
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Affiliation(s)
| | | | | | - Jill K. Olofsson
- Section for GeoGenetics, GLOBE Institute, University of Copenhagen, Øster Farimagsgade 5, bygning 7, DK-1353 Copenhagen, Denmark;
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21
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El Khodary YA, Ayoub IM, El-Ahmady SH, Ibrahim N. Molecular and phytochemical variability among genus Albizia: a phylogenetic prospect for future breeding. Mol Biol Rep 2021; 48:2619-28. [PMID: 33792827 DOI: 10.1007/s11033-021-06316-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Accepted: 03/24/2021] [Indexed: 10/21/2022]
Abstract
Fabaceae, the third-largest Angiosperm family, exhibits great morphological diversity with significantly high species diversification rate. Albizia, one of the largest genera of the legume family, possesses high ecological, economical and medicinal application prospects and displays a global distribution. The taxonomic classification among Albizia remains, however, unclear and has been subjected to changes. The resolution of phylogenetic relationships among members of genus Albizia is a priority. Nine Albizia species cultivated in Egypt; Albizia lebbeck, A. julibrissin, A. odoratissima, A. procera, A. anthelmintica, A. guachapele, A. myriophylla, A. richardiana and A. lucida were subjected to molecular classification via DNA fingerprinting techniques viz. Inter Simple Sequence Repeat (ISSR) and Start Codon Targeted polymorphism (SCoT) using ten primers, five for each technique. The total number of bands produced by ISSR and SCoT primers was 28 and 40, respectively. The percentage of polymorphism varied from 64.28% in ISSR to 67.50% in SCoT analysis. Additionally, chemotaxonomic analysis was implemented based on UV spectroscopic profiling and total phenolic content coupled to unsupervised chemometric tools; Principal Component Analysis (PCA) and Hierarchical Cluster Analysis (HCA). Interspecific relationships were confirmed via molecular and phytochemical analyses between A. procera and A. guachapele; A. lebbeck and A. odoratissima; and A. julibrissin and A. lucida. The study reveals that chemotaxonomic data can reflect phylogenetic relationships among examined Albizia species and provides insights to the significance of utilizing the strengths of both molecular taxonomy and chemotaxonomy to resolve phylogenetic relationship among this genus which offers baseline for breeding programs. Future strategies to enrich taxonomic classification among Albizia includes extensive morphological characterization, DNA barcoding techniques and metabolomic profiling.
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Gholami S, Vafaee Y, Nazari F, Ghorbani A. Exploring genetic variations in threatened medicinal orchids using start codon targeted ( SCoT) polymorphism and marker-association with seed morphometric traits. Physiol Mol Biol Plants 2021; 27:769-785. [PMID: 33967461 PMCID: PMC8055808 DOI: 10.1007/s12298-021-00978-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 03/03/2021] [Accepted: 03/12/2021] [Indexed: 05/05/2023]
Abstract
We aimed to study the genetic diversity and population structure of eight Iranian terrestrial orchid species, including Anacamptis coriophora (L.) R. M. Bateman, Pridgeon and M. W. Chase, Dactylorhiza umbrosa (Kar. & Kir.) Nevski, Himantoglossum affine (Boiss.) Schltr., Orchis collina Banks and Solander, Orchis mascula (L.) L., Orchis simia Lam., Ophrys schulzei Bornm. and Fleischm., and Ophrys straussii H. Fleischm. and Bornm. using start target codon markers (SCoT) and finding markers associated with seed morphometric traits. A total of 254 reproducible SCoT fragments were generated, of which 248 fragments were polymorphic (average polymorphism of 96.18%). The SCoT markers showed a narrow range of polymorphism information content (PIC) varied from 0.397 for S9 primer to 0.499 for S11 and S20 primers. Based on the population analysis results, the Orchis simia accessions collected from Paveh region (Os.P) represented the lowest observed number of alleles (Na) (1.13) and effective number of alleles (Ne) (1.09). At the same time, the highest Na (1.29) and Ne (1.18) values were obtained in O. schulzei collected from Javanrood (Oyst.JA). Shannon's information index (I) was ranged from 0.03 for D. umbrosa accessions collected from Marivan (Du.M population) to 0.263 for Ha.Ja population (H. affine accessions collected from Javanrood). The UPGMA dendrogram obtained with the Jaccard similarity coefficient (r = 0.97295) divided 97 studied terrestrial orchid accessions into eight groups mainly based on species type and geographical origin. Based on the Bayesian statistical index, the highest probability of the data was achieved when accessions were divided into eight groups (K = 8). Multiple association analysis (MRA) revealed significant associations between some of SCoT bands with seed morphometric traits. Our findings can be useful for germplasm characterization, conservation, and improvement of Iranian terrestrial orchid species. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-021-00978-4.
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Affiliation(s)
- Soheila Gholami
- Department of Horticultural Science and Engineering, Faculty of Agriculture, University of Kurdistan, 66177-15175 Sanandaj, Iran
| | - Yavar Vafaee
- Department of Horticultural Science and Engineering, Faculty of Agriculture, University of Kurdistan, 66177-15175 Sanandaj, Iran
- Medicinal Plants Breeding and Development Research Institute, University of Kurdistan, 66177-15175 Sanandaj, Iran
| | - Farzad Nazari
- Department of Horticultural Science and Engineering, Faculty of Agriculture, University of Kurdistan, 66177-15175 Sanandaj, Iran
| | - Abdolbaset Ghorbani
- Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Norbyvagen 18D, SE-75236 Uppsala, Sweden
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Sherif NA, Senthil Kumar T, Rao MV. DNA barcoding and genetic fidelity assessment of micropropagated Aenhenrya rotundifolia (Blatt.) C.S. Kumar and F.N. Rasm.: a critically endangered jewel orchid. Physiol Mol Biol Plants 2020; 26:2391-2405. [PMID: 33424154 PMCID: PMC7772124 DOI: 10.1007/s12298-020-00917-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 11/26/2020] [Accepted: 12/06/2020] [Indexed: 05/03/2023]
Abstract
Aenhenrya rotundifolia is a critically endangered terrestrial jewel orchid. It is monotypic and endemic to evergreen forests of southern western ghats of India. In the present study, identification of this plant species is validated with DNA barcoding using matK and rbcL chloroplast markers. Further, germ-free juvenile axillary bud explants were cultured on Mitra medium supplemented with different kinds of cytokinins like 6-benzyladenine, 6-furfurylaminopurine, N6-(Δ2-isopentyl) adenine, thidiazuron, zeatin and meta-topolin as well as auxins such as α-naphthaleneacetic acid, indole-3-acetic acid and indole-3-butyric acid at different concentrations and combinations for successful proliferation and establishment in vitro. After 12 weeks of culture, axillary bud explants produced an average of 30.12 ± 0.71 shoots per explant, 3.87 ± 0.06 cm shoot length, 1671 ± 2.82 mg fresh mass of proliferated shoots with a proliferation frequency of 100% on Mitra medium supplemented with 6.20 µM meta-topolin and 2.25 µM thidiazuron. No root formation was observed in in vitro proliferated microshoots. However, tiny hair like projections were observed in some elongated shoots on Mitra medium pertaining to 5.37 µM NAA. The tiny hair like structure bearing plantlets were hardened and acclimatized with 100% survival rate in the polytunnel chamber. After 8-10 months of establishment ex vitro, flowering was observed. Additionally, the genetic fidelity of in vitro derived plants was tested with ISSR and SCoT marker profiling. The test results revealed that the plants derived from the protocol has 99% genetic similarity to that of the donor mother plant. This study can be applied in forensic interventions of this species, describes the maintenance of germplasm in vitro and establishment of new viable population in its original habitats by restoring existing sites of this critically endangered jewel orchid.
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Affiliation(s)
- N. Ahamed Sherif
- PG and Research Department of Botany, Jamal Mohamed College (Autonomous), Affiliated to Bharathidasan University, Tiruchirappalli, 620020 Tamil Nadu India
- Department of Botany, School of Life Sciences, Bharathidasan University, Tiruchirappalli, 620024 Tamil Nadu India
| | - T. Senthil Kumar
- Department of Botany, School of Life Sciences, Bharathidasan University, Tiruchirappalli, 620024 Tamil Nadu India
| | - M. V. Rao
- Department of Botany, School of Life Sciences, Bharathidasan University, Tiruchirappalli, 620024 Tamil Nadu India
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Amom T, Tikendra L, Apana N, Goutam M, Sonia P, Koijam AS, Potshangbam AM, Rahaman H, Nongdam P. Efficiency of RAPD, ISSR, iPBS, SCoT and phytochemical markers in the genetic relationship study of five native and economical important bamboos of North-East India. Phytochemistry 2020; 174:112330. [PMID: 32146386 DOI: 10.1016/j.phytochem.2020.112330] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Revised: 02/21/2020] [Accepted: 02/24/2020] [Indexed: 05/26/2023]
Abstract
10 primers each of random amplified polymorphic DNA (RAPD), inter-simple sequence repeats (ISSR), inter primer binding site (iPBS) and start codon targeted (SCoT) were used to analyze genetic polymorphism and relationship between 50 genotypes of 5 economical important native bamboos (Bambusa cacharensis, B. mizorameana, Dendrocalamus manipureanus, D. hamiltonii and D. sikkimensis) of North-East India. The 40 different primers generated 111, 115, 116 and 138 polymorphic bands for RAPD, ISSR, iPBS and SCoT markers respectively. The comparative analysis of 4 marker systems based on polymorphic information content (PIC), effective multiplex ratio (EMR) and marker index (MI) values showed SCoT to be more informative with higher discriminating power than the other three markers. The correlation value (r) as determined by the Mantel test ranged from 0.60 (SCoT and RAPD) to 0.83 (iPBS and ISSR) indicating a high positive correlation between the markers. The close correspondence between the genetic matrices of RAPD, ISSR, iPBS and SCoT markers revealed the effectiveness of each marker system in determining the genetic relationship between bamboos. UPGMA (Unweighted Pair Group Arithmetic Mean Method) dendrograms generated from DNA marker analysis demonstrated species-specific clustering of different bamboo genotypes. Except for RAPD, the dendrograms of ISSR, iPBS and SCoT markers also showed a close association of bamboo genotypes based on geographical origin. Principal coordinate analysis (PCoA) revealed the distribution of different bamboo genotypes in accordance with the cluster analysis. The cluster grouping based on phytochemical study not only discriminated the different bamboo species but also illustrated a location-specific grouping of the genotypes. The bamboo clustering pattern derived from phytochemical analysis matched closely with the dendrograms generated by the DNA markers. The present investigation established the possibility of using a combined molecular and phytochemical marker approach to determine the genetic relationship between 5 native bamboos of North-East India with high precision.
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Affiliation(s)
- Thoungamba Amom
- Department of Biotechnology, Manipur University, Canchipur, Imphal, 795003, Manipur, India
| | - Leimapokpam Tikendra
- Department of Biotechnology, Manipur University, Canchipur, Imphal, 795003, Manipur, India
| | - Nandeibam Apana
- Department of Biotechnology, Manipur University, Canchipur, Imphal, 795003, Manipur, India
| | - Moirangthem Goutam
- Department of Biotechnology, Manipur University, Canchipur, Imphal, 795003, Manipur, India
| | - Paonam Sonia
- Department of Biotechnology, Manipur University, Canchipur, Imphal, 795003, Manipur, India
| | - Arunkumar Singh Koijam
- Department of Biotechnology, Manipur University, Canchipur, Imphal, 795003, Manipur, India
| | | | - Hamidur Rahaman
- Department of Biotechnology, Manipur University, Canchipur, Imphal, 795003, Manipur, India
| | - Potshangbam Nongdam
- Department of Biotechnology, Manipur University, Canchipur, Imphal, 795003, Manipur, India.
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Kulus D. Shoot Tip Cryopreservation of Lamprocapnos spectabilis (L.) Fukuhara Using Different Approaches and Evaluation of Stability on the Molecular, Biochemical, and Plant Architecture Levels. Int J Mol Sci 2020; 21:E3901. [PMID: 32486149 DOI: 10.3390/ijms21113901] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 05/22/2020] [Accepted: 05/29/2020] [Indexed: 01/22/2023] Open
Abstract
The aim of this study is to optimize and evaluate the effectiveness of vitrification, droplet-vitrification, and encapsulation-vitrification techniques in the cryopreservation of Lamprocapnos spectabilis (L.) Fukuhara ‘Gold Heart’, a popular medicinal and ornamental plant species. In vitro-derived shoot tips were used in the experiments. All three techniques were based on explant dehydration with plant vitrification solution 3 (PVS3; 50% glycerol and 50% sucrose) for 0, 30, 60, 90, 120, 150, or 180 min. The recovered microshoots were subjected to morphometric, biochemical, and molecular analyses (RAPD, ISSR, SCoT). The highest recovery level was reported with the encapsulation-vitrification protocol based on 150 min dehydration (73.1%), while the vitrification technique was the least effective (maximum 25.8% recovery). Explants cryopreserved with the encapsulation-vitrification technique produced the highest mean number of shoots (4.9); moreover, this technique was optimal in terms of rooting efficiency. The highest fresh weight of shoots, on the other hand, was found with the vitrification protocol based on a 30-min PVS3 treatment. The concentrations of chlorophyll a and b were lower in all cryopreservation-derived plants, compared to the untreated control. On the other hand, short dehydration and cryopreservation of non-encapsulated explants stimulated the synthesis of anthocyanins. A small genetic variation in 5% of all samples analyzed was detected by RAPD and ISSR marker systems. Only plants recovered from the encapsulation-vitrification protocol had no DNA sequence alternations.
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Abouseadaa HH, Atia MAM, Younis IY, Issa MY, Ashour HA, Saleh I, Osman GH, Arif IA, Mohsen E. Gene-targeted molecular phylogeny, phytochemical profiling, and antioxidant activity of nine species belonging to family Cactaceae. Saudi J Biol Sci 2020; 27:1649-1658. [PMID: 32489307 PMCID: PMC7253903 DOI: 10.1016/j.sjbs.2020.03.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 03/02/2020] [Accepted: 03/04/2020] [Indexed: 12/21/2022] Open
Abstract
Cactaceae plant family comprises over 130 genera and 2000 species of succulent flowering plants. The genera Mammillaria and Notocactus (Parodia), which have medicinal and nutritional applications as well as aesthetic appeal, are considered to be among the major genera of the family. Several species of both genera show morphological and chemical similarities and diversities according to environmental conditions and genotypes. Here, we assessed the genetic relationships of nine species belonging to two major genera Mammillaria and Notocactus under the family Cactaceae, using two modern gene-targeting marker techniques, the Start Codon Targeted (SCoT) Polymorphism and the Conserved DNA-Derived Polymorphism (CDDP). Besides, we screened the various phytochemicals and evaluated the antioxidant activities of the nine species of cacti. Five out of the 10 SCoT and eight CDDP primers used to screen genetic variations within the nine species yielded species-specific reproducible bands. The entire 156 loci were detected, of which 107 were polymorphic, 26 were monomorphic, and 23 were unique loci. The nine species were categorized into two groups based on the dendrogram and similarity matrix. Phytochemical profiling revealed that sterols, triterpenes, flavonoids, and tannins were found in all the tested species. Additionally, two Notocactus species (N. shlosserii and N. roseoluteus) and one Mammillaria species (M. spinosissima) revealed a considerable antioxidant activity. Our results demonstrated that gene-targeting marker techniques were highly powerful tools for the classification and characterization of the nine investigated species, despite displaying high similarities at both morphological and phytochemical levels.
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Affiliation(s)
| | - Mohamed A M Atia
- Molecular Genetics and Genome Mapping Lab., Agriculture Genetic Engineering Research Institute (AGERI), Agriculture Research Center (ARC), Egypt
| | - Inas Y Younis
- Pharmacognosy Department, Faculty of Pharmacy, Cairo University, Egypt
| | - Marwa Y Issa
- Pharmacognosy Department, Faculty of Pharmacy, Cairo University, Egypt
| | - Haraz A Ashour
- Pharmacy Department, King Abdullah medical complex, Jeddah, Saudi Arabia
| | - Ibrahim Saleh
- Prince Sultan Research Chair for Environment and Wildlife, Department of Botany & Microbiology, College of Sciences, King Saud University (KSU), Riyadh, Saudi Arabia
| | - Gamal H Osman
- Department of Biology, Faculty of Applied Science, Umm Al-Qura University, Makkah, Saudi Arabia.,Research Laboratories Center, Faculty of Applied Science, Umm Al-Qura University, Makkah, Saudi Arabia.,Microbial Genetics Department, Agricultural Genetic Engineering Research Institute (AGERI), ARC, Giza, Egypt
| | - Ibrahim A Arif
- Prince Sultan Research Chair for Environment and Wildlife, Department of Botany & Microbiology, College of Sciences, King Saud University (KSU), Riyadh, Saudi Arabia
| | - Engy Mohsen
- Pharmacognosy Department, Faculty of Pharmacy, Cairo University, Egypt
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Tyagi R, Sharma V, Sureja AK, Das Munshi A, Arya L, Saha D, Verma M. Genetic diversity and population structure detection in sponge gourd ( Luffa cylindrica) using ISSR, SCoT and morphological markers. Physiol Mol Biol Plants 2020; 26:119-131. [PMID: 32158125 PMCID: PMC7036400 DOI: 10.1007/s12298-019-00723-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 09/05/2019] [Accepted: 10/16/2019] [Indexed: 06/01/2023]
Abstract
Investigation of genetic diversity is essential for the selection of parents for crop breeding and conservation of genetic resources. To estimate the genetic variability and population structure in the midst of 45 accessions of sponge gourd brought together from different geographical areas of India, morphological traits and two molecular markers, ISSR and SCoT markers were compared. Principal components analysis of 20 morphological traits showed 72.70% variability and significant positive correlations between fruit traits. All three marker techniques clustered all accessions into two groups with few outgroups. High level of polymorphism was observed among ISSR (74.6%) and SCoT (71.5%) primers. The Bayesian model revealed the hidden grouping and showed admixture type of population. The diversity pattern is influenced by genetic marker used, as different molecular markers have different polymorphism evaluation efficiency. This study can be helpful in amplifying the genetic base and selection of specific traits for breeding. Thus, ISSR and SCoT markers are potential marker for identification in sponge gourd and provide valuable data on its genetic correlation and structure.
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Affiliation(s)
- Ruchi Tyagi
- Department of Bioscience and Biotechnology, Banasthali University, Banasthali, Rajasthan 304022 India
| | - Vinay Sharma
- Department of Bioscience and Biotechnology, Banasthali University, Banasthali, Rajasthan 304022 India
| | - Amish Kumar Sureja
- Division of Vegetable Science, Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Anilabh Das Munshi
- Division of Vegetable Science, Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Lalit Arya
- Division of Genomic Resources, ICAR-NBPGR, New Delhi, 110012 India
| | - Dipnarayan Saha
- Present Address: ICAR-Central Research Institute for Jute and Allied Fibres (ICAR), Barrackpore, India
| | - Manjusha Verma
- Division of Genomic Resources, ICAR-NBPGR, New Delhi, 110012 India
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Nasrollahi S, Badakhshan H, Sadeghi A. Analyzing Sunn pest resistance in bread wheat genotypes using phenotypic characteristics and molecular markers. Physiol Mol Biol Plants 2019; 25:765-778. [PMID: 31168238 PMCID: PMC6522623 DOI: 10.1007/s12298-019-00662-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 03/12/2019] [Accepted: 03/28/2019] [Indexed: 06/09/2023]
Abstract
Sunn pest is one of the most destructive insects in the western and central parts of Asia causing severe reductions of wheat yield and flour quality. Therefore, an effort was undertaken to find effective resistance by analyzing genetic variation among 25 wheat genotypes artificially infested in field-cages as well as using start codon targeted (SCoT) polymorphism and inter- retrotransposon amplified polymorphism (IRAP) markers. High variation was revealed amongst genotypes with Sunn pest resistance characteristics including Bayat, Bezostaya, Sayson, Line93, Line120, Rashagol, Golsepi and AarasGolsoor, which were classified as resistant to moderately resistant. SCoTs and IRAPs were determined as efficient markers for studying genetic diversity. The non-parametric Kruskal-Wallis test was conducted to evaluate the effect of specific SCoT and IRAP amplicons on Sunn pest resistance characteristics for wheat genotypes. The stepwise regression analysis exhibited seven informative SCoTs and IRAPs explaining the highest resistance characteristics variation ranging from 25.7-50.1 to 17.6-40.1, respectively. The relationship between resistance of genotypes and informative SCoT and IRAP amplicons was found based on canonical discriminant analysis showing the capacity of informative markers for functional marker selection method and screening the wheat germplasms for Sunn pest resistance characteristics.
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Affiliation(s)
- Shilan Nasrollahi
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, University of Kurdistan, Sanandaj, Iran
| | - Hedieh Badakhshan
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, University of Kurdistan, Sanandaj, Iran
| | - Amin Sadeghi
- Department of Plant Protection, College of Agriculture, University of Kurdistan, Sanandaj, Iran
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30
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Guo Y, Zhai L, Long H, Chen N, Gao C, Ding Z, Jin B. Genetic diversity of Bletilla striata assessed by SCoT and IRAP markers. Hereditas 2018; 155:35. [PMID: 30459533 PMCID: PMC6233545 DOI: 10.1186/s41065-018-0074-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Accepted: 10/28/2018] [Indexed: 11/20/2022] Open
Abstract
Background Bletilla striata is a well-known traditional Chinese herb with varieties of functions. In China, the natural resources of Bletilla striata have been severely damaged because of the excessive exploitation and destruction of natural habitats. The aim of present study was to provide a reference for fully exploiting and utilizing the germplasm resources of Bletilla striata. Results The genetic diversity of 50 varieties of Bletilla striata from different area in China was analyzed by SCoT and IRAP molecular marker technique. A total of 209 bands were amplified by 20 groups of SCoT primers, of which 201 (96.17%) were polymorphic, and 47 polymorphic bands (94%) were observed in 50 bands amplified by 8 groups of IRAP primers. The 50 populations of Bletilla striata were divided into two major groups by SCoT and IRAP at the genetic similarity coefficient value of 0.60 and 0.68 individually. The partition of clusters in the unweighted pair group method with arithmetic mean dendrogram and principal coordinate analysis plot based on the SCoT and IRAP markers was similar. Conclusions Results indicated the abundant genetic diversity of Bletilla striata among different areas. Our results will provide useful information for resource protection.
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Affiliation(s)
- Yan Guo
- 1College of Life Science, Zhejiang Chinese Medical University, Hangzhou, 310053 China
| | - Lina Zhai
- 1College of Life Science, Zhejiang Chinese Medical University, Hangzhou, 310053 China
| | - Hao Long
- 1College of Life Science, Zhejiang Chinese Medical University, Hangzhou, 310053 China
| | - Nipi Chen
- 1College of Life Science, Zhejiang Chinese Medical University, Hangzhou, 310053 China
| | - Chengxian Gao
- 1College of Life Science, Zhejiang Chinese Medical University, Hangzhou, 310053 China
| | - Zhishan Ding
- 2College of Medical Technology, Zhejiang Chinese Medical University, Hangzhou, 310053 China
| | - Bo Jin
- 1College of Life Science, Zhejiang Chinese Medical University, Hangzhou, 310053 China
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Tajbakht P, Talebi M, Rahimmalek M. Genetic diversity among and within Ferula asafoetida H. Karst. populations using molecular and phytochemical markers. Phytochemistry 2018; 155:19-29. [PMID: 30056277 DOI: 10.1016/j.phytochem.2018.07.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Revised: 07/13/2018] [Accepted: 07/16/2018] [Indexed: 06/08/2023]
Abstract
Ferula asafoetida is an herbaceous, perennial and monocarpic species of the Apiaceae family with medicinal properties. In this study, the genetic diversity of F. asafetida populations was assessed using SCoT and SRAP molecular markers. Nine SCoT and nine SRAP primer combinations amplified 211 and 194 bands, showing 96.07% and 92.87% of polymorphism, respectively. The dendrograms generated from Jaccard's similarity matrix and the UPGMA method revealed that genetic relationships among the F. asafoetida genotypes were not related to their geographical regions. The analysis also revealed a relatively acceptable differentiation in allele frequencies, illustrating the high genetic diversity and gene flows among the populations. The high percent of diversity among the populations indicated a rich resource of germplasm for breeding programs. Moreover, STRUCTURE analysis showed the high admixture of the studied accessions. According to AMOVA analysis, higher genetic variation occurred within the populations. Total phenolic content was also assessed using the folin-ciocalteu method, observing a relatively extent variety (0.163-0.938 mg TA/g DW) among the populations. In addition, HPLC analysis defined eleven compounds in which p-coumaric and 1,3- caffeoylquinic acids were the most abundant phenolic acids. Finally, Feragheh population possessed the highest TPC (total phenolic content) and gene diversity. Karaj population also exhibited the highest amount of flavonoids and phenolic acids such as kaempferol and p-coumaric acids.
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Affiliation(s)
- Pooneh Tajbakht
- Department of Agricultural Biotechnology, College of Agriculture, Isfahan University of Technology, Isfahan, 8415683111, Iran
| | - Majid Talebi
- Department of Agricultural Biotechnology, College of Agriculture, Isfahan University of Technology, Isfahan, 8415683111, Iran
| | - Mehdi Rahimmalek
- Department of Agronomy and Plant breeding, College of Agriculture, Isfahan University of Technology, Isfahan, 8415683111, Iran.
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Golkar P, Mokhtari N. Molecular diversity assessment of a world collection of safflower genotypes by SRAP and SCoT molecular markers. Physiol Mol Biol Plants 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] [What about the content of this article? (0)] [Affiliation(s)] [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] [What about the content of this article? (0)] [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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Chen DX, Wang Y, Zhang X, Pan Y, Li LY. [Analysis on genetic diversity and genetic relationship of medicinal species in Coptis by SCoT]. Zhongguo Zhong Yao Za Zhi 2018; 42:473-477. [PMID: 28952251 DOI: 10.19540/j.cnki.cjcmm.20170103.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Indexed: 11/18/2022]
Abstract
The genetic diversity and genetic relationship among four medicinal species of Coptis were detected by the approach of sequence-related amplified polymorphism (SCoT). The associated genetic parameters were calculated by POPGENE1.31. The systematic diagram of genetic relationship were clustered by TREECONW. The results showed that a total of 434 bands were produced by using 28 primers, of which 430 were polymorphic loci. There was a high level of genetic diversity among species (PPB=99.1%,Na=1.990 6,Ne=1.329 3,H=0.212 2,I=0.337 8). However, genetic diversity was lower within species, the average of genetic parameters wasPPB=16.8%,Na=1.168 2, Ne=1.073 0,H=0.043 7,I=0.067 7. The Nei's genetic differentiation coefficient was 0.794 0, that indicated that most of the genetic variation existed among species. By clustering analysis, different individuals gathered in the same group. The results confirmed that SCoT marker can be used as one of the effective methods to reveal the genetic diversity and relationship among medicinal species of Coptis.
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Affiliation(s)
- Da-Xia Chen
- Chongqing Academy of Chinese Materia Medica, Chongqing 400065, China.,Chongqing Engineering Research Center for Fine Variety Breeding Techniques of Chinese Materia Medica Chongqing 400065, China.,Chongqing Key Laboratory of Chinese Medicine Resources, Chongqing 400065, China.,Chongqing Sub-center of National Resource, Center for Chinese Materia Medica, China Academy of Chinese Medical Science, Chongqing 400065, China
| | - Yu Wang
- Chongqing Academy of Chinese Materia Medica, Chongqing 400065, China.,Chongqing Engineering Research Center for Fine Variety Breeding Techniques of Chinese Materia Medica Chongqing 400065, China.,Chongqing Key Laboratory of Chinese Medicine Resources, Chongqing 400065, China.,Chongqing Sub-center of National Resource, Center for Chinese Materia Medica, China Academy of Chinese Medical Science, Chongqing 400065, China
| | - Xue Zhang
- Chongqing Academy of Chinese Materia Medica, Chongqing 400065, China.,Chongqing Engineering Research Center for Fine Variety Breeding Techniques of Chinese Materia Medica Chongqing 400065, China.,Chongqing Key Laboratory of Chinese Medicine Resources, Chongqing 400065, China.,Chongqing Sub-center of National Resource, Center for Chinese Materia Medica, China Academy of Chinese Medical Science, Chongqing 400065, China
| | - Yuan Pan
- Chongqing Academy of Chinese Materia Medica, Chongqing 400065, China.,Chongqing Engineering Research Center for Fine Variety Breeding Techniques of Chinese Materia Medica Chongqing 400065, China.,Chongqing Key Laboratory of Chinese Medicine Resources, Chongqing 400065, China.,Chongqing Sub-center of National Resource, Center for Chinese Materia Medica, China Academy of Chinese Medical Science, Chongqing 400065, China
| | - Long-Yun Li
- Chongqing Academy of Chinese Materia Medica, Chongqing 400065, China.,Chongqing Engineering Research Center for Fine Variety Breeding Techniques of Chinese Materia Medica Chongqing 400065, China.,Chongqing Key Laboratory of Chinese Medicine Resources, Chongqing 400065, China.,Chongqing Sub-center of National Resource, Center for Chinese Materia Medica, China Academy of Chinese Medical Science, Chongqing 400065, China
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Atia MAM, Sakr MM, Mokhtar MM, Adawy SS. Development of Sex-Specific PCR-Based Markers in Date Palm. Methods Mol Biol 2017; 1638:227-44. [PMID: 28755227 DOI: 10.1007/978-1-4939-7159-6_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Molecular markers are used efficiently in the development and identification of gender-specific PCR-based markers in date palm. There is mounting evidence that different marker systems vary in their mechanisms of detecting polymorphism and genome coverage. Therefore, they could complement each other to generate accurate sex-specific markers in date palm. This chapter describes the uses of PCR-based molecular markers to develop and identify the gender in different date palm genotypes; these are amplified fragment length polymorphism (AFLP), start codon targeted polymorphism (SCoT), conserved DNA-derived polymorphism (CDDP), intron-targeted amplified polymorphism (ITAP), and random amplified polymorphic DNA (RAPD). Also described is how to characterize the identified markers by Sanger sequencing and to explore their functions through alignment of their sequences with the Genbank databases.
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Abstract
Molecular marker technologies which rely on DNA analysis provide powerful tools to assess biodiversity at different levels, i.e., among and within species. A range of different molecular marker techniques have been developed and extensively applied for detecting variability in date palm at the DNA level. Recently, the employment of gene-targeting molecular marker approaches to study biodiversity and genetic variations in many plant species has increased the attention of researchers interested in date palm to carry out phylogenetic studies using these novel marker systems. Molecular markers are good indicators of genetic distances among accessions, because DNA-based markers are neutral in the face of selection. Here we describe the employment of multidisciplinary molecular marker approaches: amplified fragment length polymorphism (AFLP), start codon targeted (SCoT) polymorphism, conserved DNA-derived polymorphism (CDDP), intron-targeted amplified polymorphism (ITAP), simple sequence repeats (SSR), and random amplified polymorphic DNA (RAPD) to assess genetic diversity in date palm.
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Affiliation(s)
- Mohamed A M Atia
- Molecular Genetics and Genome Mapping Laboratory (MGGM), Agricultural Genetic Engineering Research Institute (AGERI), ARC, Giza, P.O. Box 12619, Egypt.
| | - Mahmoud M Sakr
- Plant Biotechnology Department, National Research Center, Dokki, Giza, Egypt
| | - Sami S Adawy
- Molecular Genetics and Genome Mapping Laboratory (MGGM), Agricultural Genetic Engineering Research Institute (AGERI), ARC, Giza, P.O. Box 12619, Egypt
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Sorkheh K, Amirbakhtiar N, Ercisli S. Potential Start Codon Targeted ( SCoT) and Inter-retrotransposon Amplified Polymorphism (IRAP) Markers for Evaluation of Genetic Diversity and Conservation of Wild Pistacia Species Population. Biochem Genet 2016; 54:368-387. [PMID: 27056191 DOI: 10.1007/s10528-016-9725-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 03/10/2016] [Indexed: 10/22/2022]
Abstract
Wild pistachio species is important species in forests regions Iran and provide protection wind and soil erosion. Even though cultivation and utilization of Pistacia are fully exploited, the evolutionary history of the Pistacia genus and the relationships among the species and accessions is still not well understood. Two molecular marker strategies, SCoT and IRAP markers were analyzed for assessment of 50 accessions of this species accumulated from diverse geographical areas of Iran. A thorough of 115 bands were amplified using eight IRAP primers, of which 104 (90.4 %) have been polymorphic, and 246 polymorphic bands (68.7 %) had been located in 358 bands amplified by way of forty-four SCoT primers. Average PIC for IRAP and SCoT markers became 0.32 and 0.48, respectively. This is exposed that SCoT markers have been extra informative than IRAP for the assessment of variety among pistachio accessions. Primarily based on the two extraordinary molecular markers, cluster evaluation revealed that the 50 accessions taken for the evaluation may be divided into three distinct clusters. Those results recommend that the performance of SCoT and IRAP markers was highly the equal in fingerprinting of accessions. The results affirmed a low genetic differentiation among populations, indicating the opportunity of gene drift most of the studied populations. These findings might render striking information in breeding management strategies for genetic conservation and cultivar improvement.
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Affiliation(s)
- Karim Sorkheh
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, Shahid Chamran University of Ahvaz, P.O.Box 61355/144, Ahvaz, Iran.
| | - Nazanin Amirbakhtiar
- Department of seed and Plant improvement, Agricultural & Natural Resources Research and Education Center, P.O.Box 61333-3341, Ahvaz, Iran
| | - Sezai Ercisli
- Department of Horticulture, Agricultural Faculty, Ataturk University, 25240, Erzurum, Turkey
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Yan H, Zhang Y, Zeng B, Yin G, Zhang X, Ji Y, Huang L, Jiang X, Liu X, Peng Y, Ma X, Yan Y. Genetic Diversity and Association of EST-SSR and SCoT Markers with Rust Traits in Orchardgrass (Dactylis glomerata L.). Molecules 2016; 21:66. [PMID: 26760988 PMCID: PMC6273750 DOI: 10.3390/molecules21010066] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Revised: 12/24/2015] [Accepted: 12/29/2015] [Indexed: 11/16/2022] Open
Abstract
Orchardgrass (Dactylis glomerata L.), is a well-known perennial forage species; however, rust diseases have caused a noticeable reduction in the quality and production of orchardgrass. In this study, genetic diversity was assessed and the marker-trait associations for rust were examined using 18 EST-SSR and 21 SCoT markers in 75 orchardgrass accessions. A high level of genetic diversity was detected in orchardgrass with an average genetic diversity index of 0.369. For the EST-SSR and SCoT markers, 164 and 289 total bands were obtained, of which 148 (90.24%) and 272 (94.12%) were polymorphic, respectively. Results from an AMOVA analysis showed that more genetic variance existed within populations (87.57%) than among populations (12.43%). Using a parameter marker index, the efficiencies of the EST-SSR and SCoT markers were compared to show that SCoTs have higher marker efficiency (8.07) than EST-SSRs (4.82). The results of a UPGMA cluster analysis and a STRUCTURE analysis were both correlated with the geographic distribution of the orchardgrass accessions. Linkage disequilibrium analysis revealed an average r2 of 0.1627 across all band pairs, indicating a high extent of linkage disequilibrium in the material. An association analysis between the rust trait and 410 bands from the EST-SSR and SCoT markers using TASSEL software revealed 20 band panels were associated with the rust trait in both 2011 and 2012. The 20 bands obtained from association analysis could be used in breeding programs for lineage selection to prevent great losses of orchardgrass caused by rust, and provide valuable information for further association mapping using this collection of orchardgrass.
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Affiliation(s)
- Haidong Yan
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu 611130, China.
| | - Yu Zhang
- Institute of Agrifood Research and Technology (IRTA), Centre de Recerca en Agrigenòmica (CSIC-IRTA-UAB), Campus UAB-Edifici CRAG, Bellaterra, Cerdanyola del Vallès, Barcelona 08193, Spain.
| | - Bing Zeng
- Department of Animal Science, Southwest University, Rongchang, Chongqing 402460, China.
| | - Guohua Yin
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR 72704, USA.
| | - Xinquan Zhang
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu 611130, China.
| | - Yang Ji
- Department of Grassland Science, Sichuan Animal Science Academy, Chengdu 610066, China.
| | - Linkai Huang
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu 611130, China.
| | - Xiaomei Jiang
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu 611130, China.
| | - Xinchun Liu
- Agricultural College, Sichuan Agricultural University, Chengdu 611130, China.
| | - Yan Peng
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu 611130, China.
| | - Xiao Ma
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu 611130, China.
| | - Yanhong Yan
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu 611130, China.
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Rajesh MK, Sabana AA, Rachana KE, Rahman S, Jerard BA, Karun A. Genetic relationship and diversity among coconut (Cocos nucifera L.) accessions revealed through SCoT analysis. 3 Biotech 2015; 5:999-1006. [PMID: 28324407 PMCID: PMC4624129 DOI: 10.1007/s13205-015-0304-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Accepted: 04/24/2015] [Indexed: 11/22/2022] Open
Abstract
Coconut (Cocos nucifera L.) is one of the important palms grown both as a homestead and plantation crop in countries and most island territories of tropical regions. Different DNA-based marker systems have been utilized to assess the extent of genetic diversity in coconut. Advances in genomics research have resulted in the development of novel gene-targeted markers. In the present study, we have used a simple and novel marker system, start codon targeted polymorphism (SCoT), for its evaluation as a potential marker system in coconut. SCoT markers were utilized for assessment of genetic diversity in 23 coconut accessions (10 talls and 13 dwarfs), representing different geographical regions. Out of 25 SCoT primers screened, 15 primers were selected for this study based on their consistent amplification patterns. A total of 102 scorable bands were produced by the 15 primers, 88 % of which were polymorphic. The scored data were used to construct a similarity matrix. The similarity coefficient values ranged between 0.37 and 0.91. These coefficients were utilized to construct a dendrogram using the unweighted pair group of arithmetic means (UPGMA). The extent of genetic diversity observed based on SCoT analysis of coconut accessions was comparable to earlier findings using other marker systems. Tall and dwarf coconut accessions were clearly demarcated, and in general, coconut accessions from the same geographical region clustered together. The results indicate the potential of SCoT markers to be utilized as molecular markers to detect DNA polymorphism in coconut accessions.
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Hajibarat Z, Saidi A, Hajibarat Z, Talebi R. Characterization of genetic diversity in chickpea using SSR markers, Start Codon Targeted Polymorphism ( SCoT) and Conserved DNA-Derived Polymorphism (CDDP). Physiol Mol Biol Plants 2015; 21:365-73. [PMID: 26261401 PMCID: PMC4524857 DOI: 10.1007/s12298-015-0306-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Revised: 06/11/2015] [Accepted: 06/16/2015] [Indexed: 05/13/2023]
Abstract
To evaluate the genetic diversity among 48 genotypes of chickpea comprising cultivars, landraces and internationally developed improved lines genetic distances were evaluated using three different molecular marker techniques: Simple Sequence Repeat (SSR); Start Codon Targeted (SCoT) and Conserved DNA-derived Polymorphism (CDDP). Average polymorphism information content (PIC) for SSR, SCoT and CDDP markers was 0.47, 0.45 and 0.45, respectively, and this revealed that three different marker types were equal for the assessment of diversity amongst genotypes. Cluster analysis for SSR and SCoT divided the genotypes in to three distinct clusters and using CDDP markers data, genotypes grouped in to five clusters. There were positive significant correlation (r = 0.43, P < 0.01) between similarity matrix obtained by SCoT and CDDP. Three different marker techniques showed relatively same pattern of diversity across genotypes and using each marker technique it's obvious that diversity pattern and polymorphism for varieties were higher than that of genotypes, and CDDP had superiority over SCoT and SSR markers. These results suggest that efficiency of SSR, SCOT and CDDP markers was relatively the same in fingerprinting of chickpea genotypes. To our knowledge, this is the first detailed report of using targeted DNA region molecular marker (CDDP) for genetic diversity analysis in chickpea in comparison with SCoT and SSR markers. Overall, our results are able to prove the suitability of SCoT and CDDP markers for genetic diversity analysis in chickpea for their high rates of polymorphism and their potential for genome diversity and germplasm conservation.
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Affiliation(s)
- Zahra Hajibarat
- />Department of Biotechnology, College of New Technologies and Energy Engineering, Shahid Beheshti University, GC., Tehran, Iran
| | - Abbas Saidi
- />Department of Biotechnology, College of New Technologies and Energy Engineering, Shahid Beheshti University, GC., Tehran, Iran
| | - Zohreh Hajibarat
- />Department of Biotechnology, College of New Technologies and Energy Engineering, Shahid Beheshti University, GC., Tehran, Iran
| | - Reza Talebi
- />Department of Agronomy and Plant Breeding, Sanandaj Branch, Islamic Azad University, P.O.Box:618, Sanandaj, Iran
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Satya P, Karan M, Jana S, Mitra S, Sharma A, Karmakar P, Ray D. Start codon targeted (SCoT) polymorphism reveals genetic diversity in wild and domesticated populations of ramie (Boehmeria nivea L. Gaudich.), a premium textile fiber producing species. Meta Gene 2015; 3:62-70. [PMID: 25750860 PMCID: PMC4349193 DOI: 10.1016/j.mgene.2015.01.003] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2014] [Revised: 01/06/2015] [Accepted: 01/09/2015] [Indexed: 11/18/2022] Open
Abstract
Twenty-four start codon targeted (SCoT) markers were used to assess genetic diversity and population structure of indigenous, introduced and domesticated ramie (Boehmeria nivea L. Gaudich.). A total of 155 genotypes from five populations were investigated for SCoT polymorphism, which produced 136 amplicons with 87.5% polymorphism. Polymorphism information content and resolving power of the SCoT markers were 0.69 and 3.22, respectively. The Indian ramie populations exhibited high SCoT polymorphism (> 50%), high genetic differentiation (GST = 0.27) and moderate gene flow (Nm = 1.34). Analysis of molecular variance identified significant differences for genetic polymorphism among the populations explaining 13.1% of the total variation. The domesticated population exhibited higher genetic polymorphism and heterozygosity compared to natural populations. Cluster analysis supported population genetic analysis and suggested close association between introduced and domesticated genotypes. The present study shows effectiveness of employing SCoT markers in a cross pollinated heterozygous species like Boehmeria, and would be useful for further studies in population genetics, conservation genetics and cultivar improvement. Genetic diversity and population structure of ramie (Boehmeria nivea) were assessed by SCoT markers. SCoT markers revealed high polymorphism and resolving ability in Boehmeria nivea. The wild ramie showed moderate heterozygosity and gene flow with high genetic variation, suggesting unidirectional gene flow. The domesticated population exhibited highest heterozygosity and close association with introduced population.
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Affiliation(s)
- Pratik Satya
- ICAR-Central Research Institute for Jute and Allied Fibres, Barrackpore, Kolkata 700120, India
- Corresponding author.
| | - Maya Karan
- ICAR-Central Research Institute for Jute and Allied Fibres, Barrackpore, Kolkata 700120, India
| | - Sourav Jana
- ICAR-Central Research Institute for Jute and Allied Fibres, Barrackpore, Kolkata 700120, India
| | - Sabyasachi Mitra
- ICAR-Central Research Institute for Jute and Allied Fibres, Barrackpore, Kolkata 700120, India
| | - Amit Sharma
- ICAR-Central Research Institute for Jute and Allied Fibres, Barrackpore, Kolkata 700120, India
| | - P.G. Karmakar
- ICAR-Central Research Institute for Jute and Allied Fibres, Barrackpore, Kolkata 700120, India
| | - D.P. Ray
- ICAR-National Institute of Research on Jute and Allied Fibre Technology, Kolkata 700040, India
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Bhattacharyya P, Kumaria S, Diengdoh R, Tandon P. Genetic stability and phytochemical analysis of the in vitro regenerated plants of Dendrobium nobile Lindl., an endangered medicinal orchid. Meta Gene 2014; 2:489-504. [PMID: 25606433 PMCID: PMC4287867 DOI: 10.1016/j.mgene.2014.06.003] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Revised: 06/19/2014] [Accepted: 06/19/2014] [Indexed: 01/05/2023] Open
Abstract
An efficient genetically stable regeneration protocol with increased phytochemical production has been established for Dendrobium nobile, a highly prized orchid for its economic and medicinal importance. Protocorm like bodies (PLBs) were induced from the pseudostem segments using thidiazuron (TDZ; 1.5 mg/l), by-passing the conventional auxin-cytokinin complement approach for plant regeneration. Although, PLB induction was observed at higher concentrations of TDZ, plantlet regeneration from those PLBs was affected adversely. The best rooting (5.41 roots/shoot) was achieved in MS medium with 1.5 mg/l TDZ and 0.25% activated charcoal. Plantlets were successfully transferred to a greenhouse with a survival rate of 84.3%, exhibiting normal development. Genetic stability of the regenerated plants was investigated using randomly amplified polymorphic DNA (RAPD) and start codon targeted (SCoT) polymorphism markers which detected 97% of genetic fidelity among the regenerants. The PIC values of RAPD and SCoT primers were recorded to be 0.92 and 0.76 and their Rp values ranged between 3.66 and 10, and 4 and 12 respectively. The amplification products of the regenerated plants showed similar banding patterns to that of the mother plant thus demonstrating the homogeneity of the micropropagated plants. A comparative phytochemical analysis among the mother and the micropropagated plants showed a higher yield of secondary metabolites. The regeneration protocol developed in this study provides a basis for ex-situ germplasm conservation and also harnesses the various secondary metabolite compounds of medicinal importance present in D. nobile.
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Affiliation(s)
| | - Suman Kumaria
- Plant Biotechnology Laboratory, Department of Botany, Centre for Advanced Studies, North-Eastern Hill University, Shillong 793022, Meghalaya, India
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Pakseresht F, Talebi R, Karami E. Comparative assessment of ISSR, DAMD and SCoT markers for evaluation of genetic diversity and conservation of landrace chickpea (Cicer arietinum L.) genotypes collected from north-west of Iran. Physiol Mol Biol Plants 2013; 19:563-74. [PMID: 24431526 PMCID: PMC3781274 DOI: 10.1007/s12298-013-0181-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Morphological traits and three molecular markers techniques: start codon targeted (SCoT), inter-simple sequence repeat (ISSR) and directly amplified minisatellite DNA (DAMD) markers were compared for fingerprinting of 40 landraces chickpea genotypes collected from different geographical locations of north-west of Iran. Variance analysis of ten measured morphological traits showed significant differences existed between genotypes. Cluster analysis based on morphological traits, divided genotypes in three distinct clusters. Average polymorphism information content (PIC) for ISSR, DAMD and SCoT markers was 0.216, 0.232 and 0.232, respectively, and this revealed that SCoT markers were more informative, followed by ISSRs marker, than other markers for the assessment of diversity amongst genotypes. Cluster analysis for three different molecular types revealed that genotypes taken for the analysis can be divided in three and four distinct clusters. Accessions from same geographical regions mostly showed more genetic similarities than those from origins far isolated apart. These results suggest that efficiency of SCOT, DAMD and ISSR markers was relatively the same in fingerprinting of genotypes but SCOT and DAMD analysis are more effective in fingerprinting of chickpea genotypes. To our knowledge, this is the first detailed report of a comparison of performance among two targeted DNA region molecular markers (SCoT and DAMD) and the ISSR technique on a set of samples of chickpea. Overall, our results indicate that SCOT, ISSR and DAMD fingerprinting could be used to detect polymorphism for genotypes of chickpea.
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Affiliation(s)
- Fatemeh Pakseresht
- />Department of Agronomy & Plant Breeding, Kermanshah Branch, Islamic Azad University, Kermanshah, Iran
| | - Reza Talebi
- />College of Agriculture, Sanandaj Branch, Islamic Azad University, Sanandaj, Iran P.O. Box: 618
| | - Ezzat Karami
- />College of Agriculture, Sanandaj Branch, Islamic Azad University, Sanandaj, Iran P.O. Box: 618
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Bhattacharyya P, Kumaria S, Kumar S, Tandon P. Start Codon Targeted ( SCoT) marker reveals genetic diversity of Dendrobium nobile Lindl., an endangered medicinal orchid species. Gene 2013; 529:21-6. [PMID: 23939470 DOI: 10.1016/j.gene.2013.07.096] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Revised: 07/18/2013] [Accepted: 07/25/2013] [Indexed: 11/30/2022]
Abstract
Genetic variability in the wild genotypes of Dendrobium nobile Lindl. collected from different parts of Northeast India, was analyzed using a Start Codon Targeted (SCoT) marker system. A total of sixty individuals comprising of six natural populations were investigated for the existing natural genetic diversity. One hundred and thirty two (132) amplicons were produced by SCoT marker generating 96.21% polymorphism. The PIC value of the SCoT marker system was 0.78 and the Rp values of the primers ranged between 4.43 and 7.50. The percentage of polymorphic loci (Pp) ranging from 25% to 56.82%, Nei's gene diversity (h) from 0.08 to 0.15 with mean Nei's gene diversity of 0.28, and Shannon's information index (I) values ranging from 0.13 to 0.24 with an average value of 0.43 were recorded. The gene flow value (0.37) and the diversity among populations (0.57) demonstrated higher genetic variation among the populations. Analysis of molecular variance (AMOVA) showed 43.37% of variation within the populations, whereas 56.63% variation was recorded among the populations. Cluster analysis also reveals high genetic variation among the genotypes. Present investigation suggests the effectiveness of SCoT marker system to estimate the genetic diversity of D. nobile and that it can be seen as a preliminary point for future research on the population and evolutionary genetics of this endangered orchid species of medicinal importance.
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Affiliation(s)
- Paromik Bhattacharyya
- Plant Biotechnology Laboratory, Department of Botany, Centre for Advanced Studies, North-Eastern Hill University, Shillong 793022, Meghalaya, India
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