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Chavan J, Patil P, Patil A, Deshmukh A, Panari P, Mohite A, Lawand P, Yadav P, Bodhe M, Kadam A, Namdas D, Pawar B, Jadhav A, Shekhawat M, Santa-Catarina C. Salacia spp.: recent insights on biotechnological interventions and future perspectives. Appl Microbiol Biotechnol 2024; 108:200. [PMID: 38326604 PMCID: PMC10850189 DOI: 10.1007/s00253-023-12998-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 10/13/2023] [Accepted: 12/27/2023] [Indexed: 02/09/2024]
Abstract
The plants of the genus Salacia L. are the storehouse of several bioactive compounds, and are involved in treating human diseases and disorders. Hitherto, a number of reports have been published on in vitro biotechnology as well as microbial involvement in the improvement of Salacia spp. The present review provides comprehensive insights into biotechnological interventions such as tissue culture for plant propagation, in vitro cultures, and endophytic microbes for up-scaling the secondary metabolites and biological potential of Salacia spp. Other biotechnological interventions such as molecular markers and bio-nanomaterials for up-grading the prospective of Salacia spp. are also considered. The in vitro biotechnology of Salacia spp. is largely focused on plant regeneration, callus culture, cell suspension culture, somatic embryogenesis, and subsequent ex vitro establishment of the in vitro-raised plantlets. The compiled information on tissue cultural strategies, involvement of endophytes, molecular markers, and nanomaterials will assist the advanced research related to in vitro manipulation, domestication, and commercial cultivation of elite clones of Salacia spp. Moreover, the genetic diversity and other molecular-marker based assessments will aid in designing conservation policies as well as support upgrading and breeding initiatives for Salacia spp. KEY POINTS: • Salacia spp. plays a multifaceted role in human health and disease management. • Critical and updated assessment of tissue culture, endophytic microbes, metabolites, molecular markers, and bio-nanomaterials of Salacia spp. • Key shortcomings and future research directions for Salacia biotechnology.
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Affiliation(s)
- Jaykumar Chavan
- Department of Botany, Yashavantrao Chavan Institute of Science (Autonomous), Lead College of Karmaveer Bhaurao Patil University, Satara, 415001, India.
| | - Priyanka Patil
- Department of Botany, Yashavantrao Chavan Institute of Science (Autonomous), Lead College of Karmaveer Bhaurao Patil University, Satara, 415001, India
| | - Avdhoot Patil
- Department of Botany, Yashavantrao Chavan Institute of Science (Autonomous), Lead College of Karmaveer Bhaurao Patil University, Satara, 415001, India
| | - Akshay Deshmukh
- Department of Botany, Yashavantrao Chavan Institute of Science (Autonomous), Lead College of Karmaveer Bhaurao Patil University, Satara, 415001, India
| | - Pallavi Panari
- Department of Botany, Yashavantrao Chavan Institute of Science (Autonomous), Lead College of Karmaveer Bhaurao Patil University, Satara, 415001, India
| | - Ashwini Mohite
- Department of Botany, Yashavantrao Chavan Institute of Science (Autonomous), Lead College of Karmaveer Bhaurao Patil University, Satara, 415001, India
| | - Pramod Lawand
- Department of Botany, Yashavantrao Chavan Institute of Science (Autonomous), Lead College of Karmaveer Bhaurao Patil University, Satara, 415001, India
| | - Pradnya Yadav
- Department of Botany, Yashavantrao Chavan Institute of Science (Autonomous), Lead College of Karmaveer Bhaurao Patil University, Satara, 415001, India
| | - Minal Bodhe
- Department of Botany, Yashavantrao Chavan Institute of Science (Autonomous), Lead College of Karmaveer Bhaurao Patil University, Satara, 415001, India
| | - Abhijit Kadam
- Department of Botany, Yashavantrao Chavan Institute of Science (Autonomous), Lead College of Karmaveer Bhaurao Patil University, Satara, 415001, India
| | - Dada Namdas
- Department of Botany, Yashavantrao Chavan Institute of Science (Autonomous), Lead College of Karmaveer Bhaurao Patil University, Satara, 415001, India
| | - Bandu Pawar
- Department of Microbiology, Yashavantrao Chavan Institute of Science (Autonomous), Lead College of Karmaveer Bhaurao Patil University, Satara, 415001, India
| | - Amol Jadhav
- Department of Microbiology, Yashavantrao Chavan Institute of Science (Autonomous), Lead College of Karmaveer Bhaurao Patil University, Satara, 415001, India
| | - Mahipal Shekhawat
- Plant Biotechnology Unit, Kanchi Mamunivar Government Institute for Postgraduate Studies and Research, Puducherry, 605008, India
| | - Claudette Santa-Catarina
- Laboratório de Biologia Celular E Tecidual (LBCT), Centro de Biociências E Biotecnologia (CBB), Universidade Estadual Do Norte Fluminense Darcy Ribeiro (UENF), Av. Alberto Lamego 2000, Campos Dos Goytacazes, RJ, 28013-602, Brazil
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Palacıoğlu G, Alkan M, Derviş S, Bayraktar H, Özer G. Molecular phylogeny of plant pathogenic fungi based on start codon targeted (SCoT) polymorphism. Mol Biol Rep 2023; 50:8271-8279. [PMID: 37578578 DOI: 10.1007/s11033-023-08735-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 08/02/2023] [Indexed: 08/15/2023]
Abstract
BACKGROUND A number of molecular marker systems have been developed to assess genetic diversity, carry out phylogenetic analysis, and diagnose and discriminate plant pathogenic fungi. The start codon targeted (SCoT) markers system is a novel approach used here to investigate intra and interspecific polymorphisms of phytopathogenic fungi. MATERIALS AND METHODS This study assessed genetic variability between and within 96 isolates of ten fungal species associated with a variety of plant species using 36 SCoT primers. RESULTS The six primers generated 331 distinct and reproducible banding patterns, of which 322 were polymorphic (97.28%), resulting in 53.67 polymorphic bands per primer. All primers produced informative amplification profiles that distinguished all fungal species. With a resolving power of 10.65, SCoT primer 12 showed the highest polymorphism among species, followed by primer 33 and primer 29. Polymorphic loci (PPL), Nei's diversity index (h), and Shannon index (I) percentages were 6.25, 0.018, and 0.028, respectively. UPGMA analysis separated all isolates based on morphological classification and revealed significant genetic variation among fungal isolates at the intraspecific level. PCoA analysis strongly supported fungal species discrimination and genetic variation. The other parameters of evaluation proved that SCoT markers are at least as effective as other DNA markers. CONCLUSIONS SCoT markers were effective in identifying plant pathogenic fungi and were a powerful tool for estimating genetic variation and population structure of different fungi species.
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Affiliation(s)
- Gülsüm Palacıoğlu
- Department of Plant Protection, Faculty of Agriculture, Şırnak University, Şırnak, Turkey
| | - Mehtap Alkan
- Department of Plant Protection, Faculty of Agriculture, Bolu Abant Izzet Baysal University, Bolu, Turkey
| | - Sibel Derviş
- Department of Plant and Animal Production, Vocational School of Kızıltepe, Mardin Artuklu University, Mardin, Turkey
| | - Harun Bayraktar
- Department of Plant Protection, Faculty of Agriculture, Ankara University, Ankara, Turkey.
| | - Göksel Özer
- Department of Plant Protection, Faculty of Agriculture, Bolu Abant Izzet Baysal University, Bolu, Turkey
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Abdelghany FM, Abdel-Warith AWA, Younis EM, Davies SJ, Elnakeeb MA, El-Nawasany MM, El-Bahlol AA, Bauomi MA, Abu-Almaaty AH, Omer MY. Genetic Differentiation of Five Sea Cucumber Species from the Red Sea, Hurghada, Egypt. BRAZ J BIOL 2023; 83:e271983. [PMID: 37283337 DOI: 10.1590/1519-6984.271983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 04/16/2023] [Indexed: 06/08/2023] Open
Abstract
This study aimed to assess the genetic differentiation and relationship among five sea cucumber species from the Red Sea in Egypt, namely Holothuria atra, H. impatiens, H. leucospilota, Actinopyga crassa and A. mauritiana, using Inter Simple Sequence Repeated (ISSR) and Start Codon Targeted (SCoT) markers. A collection of 100 specimens, with 20 individuals per species, was gathered for the analysis. With ten ISSR primers, 135 amplified bands were detected, including 11 distinct species-specific bands, indicating high-level polymorphism among species. Using ten SCoT primers, 151 amplicons were generated, including 30 species-specific bands, with 52% polymorphic bands indicating high-level polymorphism among species. The degree of genetic similarity (GS) among the different genotypes of species was calculated based on ISSR bands analysis, which ranged from 93% between H. atra and H. impatiens to 86% between H. atra and A. crassa. The highest genetic similarity was observed between H. atra and H. impatiens (90%), while the lowest was identified between A. crassa and A. mauritiana (75%) using SCoT bands. Notably, the ISSR and SCoT-based DNA analysis revealed similar genetic relationships between H. atra and H. impatiens compared to other sea cucumber species studied. This study provides new insights into the genetic diversity and relationship among sea cucumber species in the Red Sea, which could have implications for their conservation and management.
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Affiliation(s)
- F M Abdelghany
- Al-Azhar University, Faculty of Agriculture, Fish Production Department, Nasr City, Cairo, Egypt
| | - A W A Abdel-Warith
- King Saud University, College of Science, Department of Zoology, Riyadh, Saudi Arabia
| | - E M Younis
- King Saud University, College of Science, Department of Zoology, Riyadh, Saudi Arabia
| | - S J Davies
- National University of Ireland Galway, School of Science and Engineering, Galway, Ireland
| | - M A Elnakeeb
- Al-Azhar University, Faculty of Agriculture, Fish Production Department, Nasr City, Cairo, Egypt
| | - M M El-Nawasany
- Al-Azhar University, Faculty of Agriculture, Fish Production Department, Nasr City, Cairo, Egypt
| | - A A El-Bahlol
- Al-Azhar University, Faculty of Agriculture, Fish Production Department, Nasr City, Cairo, Egypt
| | - M A Bauomi
- Al-Azhar University, Faculty of Agriculture, Fish Production Department, Nasr City, Cairo, Egypt
| | - A H Abu-Almaaty
- Port Said University, Faculty of Science, Zoology Department, Port Said, Egypt
| | - M Y Omer
- National Institute of Oceanography and Fisheries, Hurghada, Egypt
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Analysis of Genetic Diversity and Population Structure in Yam (Dioscorea Species) Germplasm Using Start Codon Targeted (SCoT) Molecular Markers. INTERNATIONAL JOURNAL OF PLANT BIOLOGY 2023. [DOI: 10.3390/ijpb14010025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023] Open
Abstract
Yam (Dioscorea spp.) is an important food security crop with economic, nutritional, and medicinal value. It is a source of carbohydrates for millions of people in tropical and sub-tropical regions of Africa, Asia, South America, the Caribbean, and the South Pacific Islands. Determining the appropriate parents for breeding programs is the most important decision that plant breeders must make to maximize genetic variability and produce excellent recombinant varieties. However, adequate genetic diversity and the population structure of yam accessions in Kenya are not available to guide accurate selection of parents for breeding. In the present study, 25 start-codon-targeted (SCoT) molecular markers were used to determine the genetic diversity and population structure among 20 yam accessions grown in Kenya. A total of 294 fragments were amplified, of which 95% were polymorphic with an average of 11.16 polymorphic fragments per primer. The polymorphic information content (PIC) value and primer resolving power (Rp) of 0.58 and 5.91, respectively, revealed high genetic diversity among the accessions. A dendrogram based on the unweighted pair group method of arithmetic means (UPGMA) grouped the 20 yam accessions into two clusters at 0.61 genetic similarity coefficients. Bayesian structure analysis revealed the existence of three subpopulations and some admixed accessions. Analysis of molecular variance (AMOVA) revealed a variance of 60% within the subpopulations and 40% among the subpopulations. The high degree of genetic diversity in the yam accessions successfully exhibited by SCoT molecular markers may serve as a valuable aid to widen the genetic base in yam breeding programs. The selection and hybridization of parental lines from the different clusters and sub-clusters identified could provide a foundation and could be exploited for yam breeding and variety development.
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Avramidou E, Sarri E, Ganopoulos I, Madesis P, Kougiteas L, Papadopoulou EA, Aliferis KA, Abraham EM, Tani E. Genetic and Metabolite Variability among Commercial Varieties and Advanced Lines of Vicia faba L. PLANTS (BASEL, SWITZERLAND) 2023; 12:908. [PMID: 36840256 PMCID: PMC9967272 DOI: 10.3390/plants12040908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 01/25/2023] [Accepted: 02/14/2023] [Indexed: 06/18/2023]
Abstract
Vicia faba L. (faba bean) is one of the most promising pulse crops due to its nutritional value and high nitrogen fixation capacity. The aim of the present study was to compare the genetic diversity and the seed metabolite profiles of five genetic materials of faba bean. Specifically, three newly developed advanced lines (KK18, KK14 and KK10) and two commercial cultivars (POLIKARPI and TANAGRA), were evaluated for this purpose. Genetic diversity among populations was assessed by SCoT molecular markers. Through UPGMA dendrogram, genetic distances between populations were estimated. Untargeted metabolomics analysis of the seeds was performed employing GC/EI/MS. The cultivar POLYKARPI exhibited the highest polymorphism. All varieties showed a higher within-cultivars and advanced lines variability than between. POLYKARPI and KK14 had the lowest genetic distances, while KK18 and TANAGRA presented the highest ones. The advanced line KK18 displayed the best nutritional profile, the highest concentration of desirable metabolites (lactic acid and trehalose), the lowest concentration of anti-nutritional factors (oxalic acid) and the lowest concentration of saturated fatty acids (palmitic and stearic acid). According to the results of the present study, KK18 line is a very promising material for further exploration and utilization in breeding programs.
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Affiliation(s)
- Eleni Avramidou
- Department of Forestry and Natural Environment, School of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
- Institute of Applied Bioscience, CERTH, Thermi, 57001 Thessaloniki, Greece
| | - Efi Sarri
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece
| | - Ioannis Ganopoulos
- Institute of Plant Breeding and Genetic Resources, HAO-Dimitra, Thermi, 57001 Thessaloniki, Greece
| | - Panagiotis Madesis
- Institute of Applied Bioscience, CERTH, Thermi, 57001 Thessaloniki, Greece
- School of Agricultural Sciences, Department of Agriculture Crop Production and Rural Environment, University of Thessaly, 38446 Volos, Greece
| | - Leonidas Kougiteas
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece
| | - Evgenia-Anna Papadopoulou
- Laboratory of Pesticide Science, Department of Crop Science, Agricultural University of Athens, 11855 Athens, Greece
| | - Konstantinos A. Aliferis
- Laboratory of Pesticide Science, Department of Crop Science, Agricultural University of Athens, 11855 Athens, Greece
- Department of Plant Science, McGill University, Macdonald Campus, Ste-Anne-de-Bellevue, QC H9X 3V9, Canada
| | - Eleni M. Abraham
- Department of Forestry and Natural Environment, School of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Eleni Tani
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece
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Rai MK. Start codon targeted (SCoT) polymorphism marker in plant genome analysis: current status and prospects. PLANTA 2023; 257:34. [PMID: 36622439 DOI: 10.1007/s00425-023-04067-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 01/04/2023] [Indexed: 06/17/2023]
Abstract
The present review illustrates a comprehensive overview of the start codon targeted (SCoT) polymorphism marker and their utilization in various applications related to genetic and genomic studies. Start codon targeted (SCoT) polymorphism marker, a targeted fingerprinting marker technique, has gained considerable importance in plant genetics, genomics, and molecular breeding due to its many desirable features. SCoT marker targets the region flanking the start codon, a highly conserved region in plant genes. Therefore, it can distinguish genetic variations in a specific gene that link to a specific trait. It is a simple, novel, cost-effective, highly polymorphic, and reproducible molecular marker for which there is no need for prior sequence information. In the recent past, SCoT markers have been employed in many commercially important and underutilized plant species for a variety of applications, including genetic diversity analysis, interspecific/generic genetic relationships, cultivar/hybrid/species identification, sex determination, construction of linkage map, association mapping/analysis, differential gene expression, and genetic fidelity analysis of tissue culture-raised plants. The main aim of this review is to provide up-to-date information on SCoT markers and their application in many commercially important and underutilized plant species, mainly progress made in the last 8-10 years.
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Affiliation(s)
- Manoj K Rai
- Department of Environmental Science, Indira Gandhi National Tribal University, Amarkantak, MP, 484887, India.
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Alavilli H, Poli Y, Verma KS, Kumar V, Gupta S, Chaudhary V, Jyoti A, Sahi SV, Kothari SL, Jain A. Miracle Tree Moringa oleifera: Status of the Genetic Diversity, Breeding, In Vitro Propagation, and a Cogent Source of Commercial Functional Food and Non-Food Products. PLANTS (BASEL, SWITZERLAND) 2022; 11:3132. [PMID: 36432862 PMCID: PMC9694164 DOI: 10.3390/plants11223132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 10/30/2022] [Accepted: 11/07/2022] [Indexed: 06/16/2023]
Abstract
Moringa oleifera Lam. (MO) is a fast-growing drought-resistant tree belonging to the family Moringaceae and native to the Indian subcontinent and cultivated and/or naturalized worldwide with a semi-arid climate. MO is also popularly known as a miracle tree for its repertoire of nutraceutical, pharmacological, and phytochemical properties. The MO germplasm is collected, conserved, and maintained by various institutions across the globe. Various morphological, biochemical, and molecular markers are used for determining the genetic diversity in MO accessions. A higher yield of leaves and pods is often desirable for making various products with commercial viability and amenable for trade in the international market. Therefore, breeding elite varieties adapted to local agroclimatic conditions and in vitro propagation are viable and sustainable approaches. Here, we provide a comprehensive overview of MO germplasm conservation and various markers that are employed for assessing the genetic diversity among them. Further, breeding and in vitro propagation of MO for various desirable agronomic traits are discussed. Finally, trade and commerce of various functional and biofortified foods and non-food products are enumerated albeit with a need for a rigorous and stringent toxicity evaluation.
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Affiliation(s)
- Hemasundar Alavilli
- Department of Bioresources Engineering, Sejong University, Seoul 05006, Republic of Korea
| | - Yugandhar Poli
- ICAR-Indian Institute of Rice Research, Hyderabad 500030, India
| | - Kumar Sambhav Verma
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur 303002, India
| | - Vikram Kumar
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur 303002, India
| | - Swati Gupta
- Department of Biosciences, Manipal University Jaipur, Jaipur 303007, India
| | - Vigi Chaudhary
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur 303002, India
| | - Anupam Jyoti
- Biotechnology Department, Chandigarh University, National Highway-95, Ludhiana-Chandigarh State Highway, Chandigarh 160055, India
| | - Shivendra V. Sahi
- Department of Biology, Saint Joseph’s University (University City Campus), 600 South 43rd Street, Philadelphia, PA 19104, USA
| | - Shanker Lal Kothari
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur 303002, India
| | - Ajay Jain
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur 303002, India
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March of molecular breeding techniques in the genetic enhancement of herbal medicinal plants: present and future prospects. THE NUCLEUS 2022. [DOI: 10.1007/s13237-022-00406-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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Lei X, Huo P, Xie Y, Wang Y, Liu G, Tu H, Shi Q, Mo Z, Zhang S. Dendrobium nobile Lindl polysaccharides improve testicular spermatogenic function in streptozotocin‐induced diabetic rats. Mol Reprod Dev 2022; 89:202-213. [DOI: 10.1002/mrd.23556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 11/27/2021] [Accepted: 12/01/2021] [Indexed: 11/06/2022]
Affiliation(s)
- Xiaocan Lei
- Department of Histology and Embryology, Clinical Anatomy & Reproductive Medicine Application Institute University of South China Hengyang China
| | - Peng Huo
- School of Public and Health Guilin Medical University Guilin China
| | - Yuan‐jie Xie
- Department of Histology and Embryology, Clinical Anatomy & Reproductive Medicine Application Institute University of South China Hengyang China
| | - Yaohui Wang
- School of Basic Medical Sciences Zunyi Medical University Zunyi China
| | - Guanghai Liu
- School of Basic Medical Sciences Zunyi Medical University Zunyi China
| | - Haoyan Tu
- Department of Reproductive Medical Center The Affiliated Hospital of Guilin Medical University Guilin China
| | - Qingxiang Shi
- School of Basic Medical Sciences Zunyi Medical University Zunyi China
| | - Zhong‐cheng Mo
- Department of Histology and Embryology, Clinical Anatomy & Reproductive Medicine Application Institute University of South China Hengyang China
| | - Shun Zhang
- Department of Reproductive Medical Center The Affiliated Hospital of Guilin Medical University Guilin China
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Dissection of genetic diversity and population structure in oregano (Origanum acutidens L.) genotypes based on agro-morphological properties and start codon targeted (SCoT) markers. Biologia (Bratisl) 2022. [DOI: 10.1007/s11756-021-00989-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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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] [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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Abd El Azim AM, Khashaba EHK. Genetic variability among three Egyptian isolates of Heterorhabditis indica using a new marker technique (SCoT). EGYPTIAN JOURNAL OF BIOLOGICAL PEST CONTROL 2021; 31:71. [DOI: 10.1186/s41938-021-00419-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Accepted: 04/13/2021] [Indexed: 09/02/2023]
Abstract
Abstract
Background
Entomopathogenic nematodes (EPNs) are a group of nematode families, have the ability to search for their hosts, and are considered as promising biological control candidates for insect pests, providing protection to non-target organisms and the environment.
Results
This study was conducted to isolate indigenous EPN isolates from Egyptian agricultural soils for further use in biological control programs and study their genetic polymorphism among the previously isolated isolates under accession no. MH553167 and MK300683 and the new isolate (MH496627), using the start codon targeted (SCoT) marker. One out of 15 soil samples obtained from a banana cultivated field was positive for the presence of EPNs, using the Galleria baiting method. Morphological analysis and sequencing of the internal transcribed spacer (ITS) region suggested that the isolate obtained belongs to Heterorhabditis indica. The sequence of the ITS was submitted to the National Center for Biotechnology Information (NCBI) and registered under accession no. MH496627. Ten SCoT primers were used in the study; the polymorphic bands were 68 out of 76 with 89% as polymorphism percentage. The highest numbers of bands were 10 bands generated by SCoT 1 and SCoT 18 while SCoT 48 and SCoT 60 recorded the lowest band number (5 bands).
Conclusions
The present study is considered as a preliminary study to demonstrate the effectiveness of the SCoT marker for the first time in assessing genetic relationships in EPNs.
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Borah R, Bhattacharjee A, Rao SR, Kumar V, Sharma P, Upadhaya K, Choudhury H. Genetic diversity and population structure assessment using molecular markers and SPAR approach in Illicium griffithii, a medicinally important endangered species of Northeast India. J Genet Eng Biotechnol 2021; 19:118. [PMID: 34374870 PMCID: PMC8355293 DOI: 10.1186/s43141-021-00211-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 07/18/2021] [Indexed: 11/10/2022]
Abstract
BACKGROUND Illicium griffithii is an aromatic medicinal tree species that has been listed in the IUCN Red List as an endangered species. Dried seed pods of I. griffithii have a good market potential in the spices and pharmaceutical industries. Fruits are the potential source of shikimic acid and used for the production of oseltamivir (a drug against bird flu). However, in recent years, unscientific harvesting and rampant exploitation of the species has caused a negative and adverse effect on its natural population. Proper knowledge of genetic diversity and population structure is crucial to understand the population dynamics, adaptation, and evolutionary pattern of a particular species for conservation. It was from this view point that the present study was undertaken so as to compare the various types of DNA-based molecular markers namely RAPD, ISSR, DAMD, and SCoT by their efficiency and SPAR approach to evaluate the genetic diversity of I. griffithii as well as to analyze population genetic structure for conservation purpose. RESULT A total of 250 discernible bands were generated with 246 bands (98.40 %) being polymorphic in nature. All the primers in combination gave a mean polymorphic information content (PIC) of 0.81 and Rp value (resolving power) of 4.32. Nei's, Gst, and AMOVA analysis showed similar values of genetic differentiation among populations (Gst = 0.396, FST = 0.30, respectively), revealing a low level of genetic differentiation among the eight sampled populations. I. griffithii with an estimated gene flow value of Nm = 0.761 was significantly low among populations. Clustering pattern obtained with Bayesian structure and PCoA diagram revealed that intermixing of genetic material across populations is only possible when the populations lie close to each other. This is further validated with UPGMA clustering method where a positive correlation of genetic variability with geographical distance among closely related populations could be clearly seen. CONCLUSION The result aids in the identification, collection, and preservation of diverse germplasm of I. griffithii from Arunachal Pradesh and Meghalaya of Northeast India. This would further help in understanding the population structure and genetic diversity among other Illicium species in order to formulate effective conservation strategies for the improvement of this endangered taxa.
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Affiliation(s)
- Rajib Borah
- Department of Basic Sciences and Social Sciences, School of Technology, North-Eastern Hill University, Shillong, Meghalaya, 793022, India.,Department of Biotechnology and Bioinformatics, School of Life Sciences, North-Eastern Hill University, Shillong, Meghalaya, 793022, India
| | - Atanu Bhattacharjee
- Department of Biotechnology and Bioinformatics, School of Life Sciences, North-Eastern Hill University, Shillong, Meghalaya, 793022, India
| | - Satyawada Rama Rao
- Department of Biotechnology and Bioinformatics, School of Life Sciences, North-Eastern Hill University, Shillong, Meghalaya, 793022, India
| | - Vineet Kumar
- Chemistry and Bioprospecting Division, Forest Research Institute, Indian Council of Forestry Research & Education, Dehradun, Uttarakhand, 248006, India
| | - Pradeep Sharma
- Chemistry and Bioprospecting Division, Forest Research Institute, Indian Council of Forestry Research & Education, Dehradun, Uttarakhand, 248006, India
| | - Krishna Upadhaya
- Department of Basic Sciences and Social Sciences, School of Technology, North-Eastern Hill University, Shillong, Meghalaya, 793022, India
| | - Hiranjit Choudhury
- Department of Basic Sciences and Social Sciences, School of Technology, North-Eastern Hill University, Shillong, Meghalaya, 793022, India.
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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. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 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] [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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15
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Phylogenetic relationships and DNA barcoding of nine endangered medicinal plant species endemic to Saint Katherine protectorate. Saudi J Biol Sci 2021; 28:1919-1930. [PMID: 33732078 PMCID: PMC7938155 DOI: 10.1016/j.sjbs.2020.12.043] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 12/20/2020] [Accepted: 12/23/2020] [Indexed: 11/21/2022] Open
Abstract
A high degree of endemism has been recorded for several plant groups collectively in Saint Katherine Protectorate (SKP) in the Sinai Peninsula. Nine endangered endemic plant species in SKP were selected to test the variable abilities of three different DNA barcodes; Riboluse-1,5- Biphosphate Carboxylase/Oxygenase Large subunit (rbcL), Internal Transcribed Spacer (ITS), and the two regions of the plastid gene (ycf1) as well as Start Codon Targeted (SCoT) Polymorphism to find the phylogenetic relationships among them. The three barcodes were generally more capable of finding the genetic relationships among the plant species under study, new barcodes were introduced to the National Centre for Biotechnology Information (NCBI) for the first time through our work. The barcode sequences were efficient in finding the genetic relationships between the nine species. However, SCoT polymorphism could only cluster plant species belonging to the same genus together in one group, but it could not cluster plant species belonging to the same families except for some primers solely. RbcL was the most easily amplified and identified barcode in eight out of the nine species at the species level and the ninth barcode to the genus level. ITS identified all the species to the genus level. Finally, ycf1 identified six out of the eight species, but it could not identify two of the eight species to the genus level.
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Zhao X, Zou G, Zhao J, Hu L, Lan Y, He J. Genetic relationships and diversity among populations of Paris polyphylla assessed using SCoT and SRAP markers. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2020; 26:1281-1293. [PMID: 32549689 PMCID: PMC7266889 DOI: 10.1007/s12298-020-00808-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 03/07/2020] [Accepted: 03/27/2020] [Indexed: 05/22/2023]
Abstract
The genetic diversity of 33 Paris polyphylla samples collected from the Dabie Mountains was analyzed using SCoT and SRAP molecular markers, revealing the genetic relationships among Paris polyphylla resources in the Dabie Mountains at the molecular level and providing a theoretical basis for genetic improvement and conservation. As a result, a total of 134 bands were amplified with 9 SCoT primers, the percentage of polymorphic bands was 100%, the average number of primers amplified was 14.89, the PIC value was 94.83% and the genetic similarity coefficient ranged from 0.463 to 0.896. Ten pairs of SRAP primer combinations amplified 135 bands, including 129 polymorphic bands, and the percentage of polymorphic bands was 95.56%. The average number of polymorphic bands obtained with each pair of SRAP primer combinations was 12.9, the PIC value was 93.91%, and the genetic similarity coefficient ranged from 0.533 to 0.904. This study showed that both SCoT and SRAP markers were suitable for the genetic diversity analysis of P. polyphylla, which belongs to a genus in which SRAP marker technology has not previously been applied, despite its application in a variety of other plants.
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Affiliation(s)
- Xiaopei Zhao
- School of Life Sciences, Anhui Agricultural University, Hefei, 230061 People’s Republic of China
| | - Gaofen Zou
- School of Life Sciences, Anhui Agricultural University, Hefei, 230061 People’s Republic of China
| | - Jie Zhao
- School of Life Sciences, Anhui Agricultural University, Hefei, 230061 People’s Republic of China
| | - Linyi Hu
- School of Life Sciences, Anhui Agricultural University, Hefei, 230061 People’s Republic of China
| | - Yuefeng Lan
- School of Life Sciences, Anhui Agricultural University, Hefei, 230061 People’s Republic of China
| | - Jinling He
- School of Life Sciences, Anhui Agricultural University, Hefei, 230061 People’s Republic of China
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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] [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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18
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Ma X, Meng Y, Wang P, Tang Z, Wang H, Xie T. Bioinformatics-assisted, integrated omics studies on medicinal plants. Brief Bioinform 2019; 21:1857-1874. [PMID: 32706024 DOI: 10.1093/bib/bbz132] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 09/03/2019] [Accepted: 09/19/2019] [Indexed: 12/14/2022] Open
Abstract
The immense therapeutic and economic values of medicinal plants have attracted increasing attention from the worldwide researchers. It has been recognized that production of the authentic and high-quality herbal drugs became the prerequisite for maintaining the healthy development of the traditional medicine industry. To this end, intensive research efforts have been devoted to the basic studies, in order to pave a way for standardized authentication of the plant materials, and bioengineering of the metabolic pathways in the medicinal plants. In this paper, the recent advances of omics studies on the medicinal plants were summarized from several aspects, including phenomics and taxonomics, genomics, transcriptomics, proteomics and metabolomics. We proposed a multi-omics data-based workflow for medicinal plant research. It was emphasized that integration of the omics data was important for plant authentication and mechanistic studies on plant metabolism. Additionally, the computational tools for proper storage, efficient processing and high-throughput analyses of the omics data have been introduced into the workflow. According to the workflow, authentication of the medicinal plant materials should not only be performed at the phenomics level but also be implemented by genomic and metabolomic marker-based examination. On the other hand, functional genomics studies, transcriptional regulatory networks and protein-protein interactions will contribute greatly for deciphering the secondary metabolic pathways. Finally, we hope that our work could inspire further efforts on the bioinformatics-assisted, integrated omics studies on the medicinal plants.
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Affiliation(s)
- Xiaoxia Ma
- Hangzhou Normal University, Hangzhou 311121, P.R. China.,Holistic Integrative Pharmacy Institutes, Hangzhou Normal University, Hangzhou 311121, P.R. China.,Key Laboratory of Elemene Class Anti-cancer Chinese Medicine of Zhejiang Province and Engineering Laboratory of Development and Application of Traditional Chinese Medicine from Zhejiang Province, Hangzhou Normal University, Hangzhou 311121, P.R. China.,College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou 310014, P.R. China
| | - Yijun Meng
- Hangzhou Normal University, Hangzhou 311121, P.R. China.,College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, P.R. China
| | - Pu Wang
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou 310014, P.R. China
| | - Zhonghai Tang
- College of Food Science and Technology, Hunan Agricultural University, Changsha 410128, P.R. China
| | - Huizhong Wang
- Hangzhou Normal University, Hangzhou 311121, P.R. China.,College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, P.R. China
| | - Tian Xie
- Hangzhou Normal University, Hangzhou 311121, P.R. China.,Holistic Integrative Pharmacy Institutes, Hangzhou Normal University, Hangzhou 311121, P.R. China.,Key Laboratory of Elemene Class Anti-cancer Chinese Medicine of Zhejiang Province and Engineering Laboratory of Development and Application of Traditional Chinese Medicine from Zhejiang Province, Hangzhou Normal University, Hangzhou 311121, P.R. China
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19
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Gupta V, Jatav PK, Haq SU, Verma KS, Kaul VK, Kothari SL, Kachhwaha S. Translation initiation codon (ATG) or SCoT markers-based polymorphism study within and across various Capsicum accessions: insight from their amplification, cross-transferability and genetic diversity. J Genet 2019. [DOI: 10.1007/s12041-019-1095-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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20
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Basak S, Chakrabartty I, Hedaoo V, Shelke RG, Rangan L. Assessment of genetic variation among wild Alpinia nigra (Zingiberaceae) population: an approach based on molecular phylogeny. Mol Biol Rep 2018; 46:177-189. [PMID: 30415443 DOI: 10.1007/s11033-018-4458-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 10/30/2018] [Indexed: 10/27/2022]
Abstract
Genetic structure was evaluated among wild Alpinia nigra (Gaertn.) B.L. Burtt, populations. The information of genetic relatedness was developed using random amplified polymorphic DNA (RAPD), inter-simple sequence repeat (ISSR) and barcoding loci (plastid and mitochondrial). The order (high to low) of Shannon's information index (I) and Nei's gene diversity (h) from the populations was: "IIT Guwahati" > "Amingaon" > "Saraighat". Genetic diversity decreased and genetic differentiation increased among the three populations. We observed no isolation by distance thus lower amount of gene flow was observed. Narrow range of genetic distance among the three populations and appearance of two distinct clusters strengthened the geographical isolation in dendrogram and principal component analysis. No mutation among the three populations was observed for seven plastid loci and two mitochondrial tested suggesting the taxonomic homogeneity. The phylogeny based on nine barcoding loci supported our observation that individuals of IIT Guwahati were partially isolated from the outside populations. Our study will provide a backbone for developing strategies to resist habitat fragmentation of Zingiberaceous plants.
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Affiliation(s)
- Supriyo Basak
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781 039, Assam, India.,Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 650201, Kunming, China
| | - Ishani Chakrabartty
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781 039, Assam, India
| | - Vivek Hedaoo
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781 039, Assam, India
| | - Rahul G Shelke
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781 039, Assam, India
| | - Latha Rangan
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781 039, Assam, India.
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Amer A, Taha H, Ammar N, Salama M, El-Alfy T. Applicability of Different Molecular Markers Techniques for Genetic Distinguish Between Two Genera <I>Cressa</I> Linn. and <I>Cuscuta</I> Yunck. Family Convolvulaceae. Pak J Biol Sci 2018; 21:179-186. [PMID: 30311474 DOI: 10.3923/pjbs.2018.179.186] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
BACKGROUND AND OBJECTIVE The DNA fingerprinting is used to determine the relationship between species in the same genus or between genera related to the same family. The aim of this study was to determine the relationships between two samples related to the same family Convolvulaceae, representing two genera, Cressa Linn. and Cuscuta Yunck. by RAPD, ISSR and SCoT molecular techniques (PCR based DNA fingerprint). MATERIALS AND METHODS The RAPD, ISSR and SCoT based DNA fingerprinting techniques were implemented to identify the fingerprint diversity between two genera, Cressa Linn. and Cuscuta Yunck-belonging to the family Convolvulaceae. RESULTS Applying of RAPD technique revealed that using OP-A02, OP-A09, OP-A10, OP-C04 and OP-M01 primers recorded 60, 83.33, 100, 50 and 70.66% polymorphism, respectively. On the other hand, ISSR technique recorded 40, 50, 100, 66.67, 33.33 and 37.5% polymorphism with 44B, HB-08, HB-09, HB-10, HB-11 and HB-12 primers, respectively. However, amplification of SCoT technique, SCoT 1, SCoT 2, SCoT 3, SCoT 4, SCoT 6, SCoT 8, SCoT 10 and SCoT 12 primers recorded 33.33, 28.57, 14.28, 66.66, 25, 40, 42.85 and 50%, respectively . The total polymorphism recorded 73.33, 54.58 and 37.7% for RAPD, ISSR and SCoT techniques, respectively. CONCLUSION The result of this study indicated that SCoT technique was more efficient and sustainable for distinguish between two genera under investigation.
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Shekhawat JK, Rai MK, Shekhawat NS, Kataria V. Exploring genetic variability in Prosopis cineraria using two gene targeted CAAT box-derived polymorphism (CBDP) and start codon targeted (SCoT) polymorphism markers. Mol Biol Rep 2018; 45:2359-2367. [PMID: 30255277 DOI: 10.1007/s11033-018-4400-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 09/21/2018] [Indexed: 10/28/2022]
Abstract
Two gene targeted molecular marker systems, CAAT box-derived polymorphism (CBDP) and start codon targeted (SCoT) polymorphism, were used to assess the genetic diversity and relatedness in Prosopis cineraria, a tree of abiotic stress tolerance, agroforestry and ethano-botanical importance. A total of ten wild populations consisting 49 individuals collected from different locations of Indian Thar Desert were examined for the genetic analysis of P. cineraria. Ten CBDP and seven SCoT primers, total 17 primers, generated 204 bands with an average of 12 bands per primer, of which 159 (76.8%) were polymorphic. The average PIC values for both CBDP and SCoT marker were 0.543 and 0.547, respectively. The cumulative data of these two markers were used to analyze different genetic diversity indices and compute pair-wise distances. The population genetic diversity analysis based on cumulative data of CBDP and SCoT markers revealed the high levels of genetic differentiation (GST = 0.341; GST > 0.15 as high), low value of gene flow (Nm = 0.966; Nm > 1 as high) and high fixation index (FST = 0. 415). The highest genetic diversity was observed among NGBAR populations followed by CHR populations, while SIK populations showed lowest genetic diversity. AMOVA revealed the percent molecular variation was higher within the populations (77%) compared to that of among populations (23%). The clustering pattern based on UPGMA and PCoA plot clearly demonstrated the genetic relationship among the genotypes collected from the different regions of Indian Thar Desert.
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Affiliation(s)
- Jatan K Shekhawat
- Biotechnology Unit, Department of Botany (UGC-Centre of Advanced Study), Jai Narain Vyas University, Jodhpur, Rajasthan, 342001, India
| | - Manoj K Rai
- Biotechnology Unit, Department of Botany (UGC-Centre of Advanced Study), Jai Narain Vyas University, Jodhpur, Rajasthan, 342001, India.,Department of Environmental Science, Indira Gandhi National Tribal University, Amarkantak, 484887, India
| | - N S Shekhawat
- Biotechnology Unit, Department of Botany (UGC-Centre of Advanced Study), Jai Narain Vyas University, Jodhpur, Rajasthan, 342001, India
| | - Vinod Kataria
- Biotechnology Unit, Department of Botany (UGC-Centre of Advanced Study), Jai Narain Vyas University, Jodhpur, Rajasthan, 342001, India.
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Rafizadeh A, Koohi-Dehkordi M, Sorkheh K. Molecular insights of genetic variation in milk thistle (Silybum marianum [L.] Gaertn.) populations collected from southwest Iran. Mol Biol Rep 2018; 45:601-609. [PMID: 29882084 DOI: 10.1007/s11033-018-4198-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 05/24/2018] [Indexed: 10/14/2022]
Abstract
Milk thistle (Silybum marianum) is among the world's popular medicinal plants. Start Codon Targeted (SCoT) marker system was utilized to investigate the genetic variability of 80 S. marianum genotypes from eight populations in Iran. SCoT marker produced 255 amplicons and 84.03% polymorphism was generated. The SCoT marker system's polymorphism information content value was 0.43. The primers' resolving power values were between 4.18 and 7.84. The percentage of polymorphic bands was between 33.3 and 100%. The Nei's gene diversity (h) was 0.19-1.30 with an average 0.72. The Shannon's index (I) ranged from 0.29 to 1.38 with an average value of 0.83. The average gene flow (0.37) demonstrated a high genetic variation among the studied populations. The variation of 42% was displayed by the molecular variance analysis among the populations while a recorded variation of 58% was made within the populations. Current investigation suggested that SCoT marker system could effectively evaluate milk thistle genotypes genetic diversity.
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Affiliation(s)
- Azam Rafizadeh
- Department of Agricultural Science, Payame-Noor University, P. O. Box 19395-3697, Tehran, Iran
| | - Mehrana Koohi-Dehkordi
- Department of Agricultural Science, Payame-Noor University, P. O. Box 19395-3697, Tehran, Iran.
| | - Karim Sorkheh
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, Shahid Chamran University of Ahvaz, P. O. Box 61355/144, Ahvaz, Iran
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Bhattacharyya P, van Staden J. Molecular insights into genetic diversity and population dynamics of five medicinal Eulophia species: a threatened orchid taxa of Africa. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2018; 24:631-641. [PMID: 30042618 PMCID: PMC6041235 DOI: 10.1007/s12298-018-0523-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 11/16/2017] [Accepted: 03/05/2018] [Indexed: 05/22/2023]
Abstract
Genetic diversity existing amongst five Eulophia orchid species were assessed using start codon targeted polymorphism (SCoT) and inter-retrotransposon amplified polymorphism (IRAP) markers. A total of 12 SCoT and 5 IRAP markers revealed an average of 63% genetic variability [SCoT = 63.87; IRAP = 64.95%] amongst the five Eulophia species investigated. The genetic similarities were assessed using both UPGMA and Bayesian approaches which indicated identical clustering patterns at a genetic similarity level of 50%. Analysis of molecular variance (AMOVA) revealed the presence of a significant degree of genetic variability, mostly compartmentalized within the species level. Amongst the five assessed Eulophia species, E. parviflora was the most genetically diverse representative whereas E. welwitschii was found to be least diverse based on a comparative assessment of various population genetic parameters like Nei's gene diversity (h) and Shannon's information index (I) with an overall gene flow value greater than 1. In order to evaluate the comparative marker efficiency, SCoT and IRAP marker data were subjected to various benchmark analyses like marker index, resolving power, polymorphic index content, multiplex ratio and effective multiplex ratio which revealed the robustness of both the marker techniques in assessment of genetic diversity. The present report provides the first molecular insights into the aspects of inter and intra specific genetic variability in medicinally as well as horticulturally important Eulophia species along with addressing their conservation concerns. In a nutshell, the present approach is simple, rapid and cost effective and can be extended for analysis of genetic diversity of other related plant species.
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Affiliation(s)
- Paromik Bhattacharyya
- Research Centre for Plant Growth and Development, School of Life Sciences, University of KwaZulu-Natal, Pietermaritzburg, Private Bag X01, Scottsville, 3209 South Africa
| | - Johannes van Staden
- Research Centre for Plant Growth and Development, School of Life Sciences, University of KwaZulu-Natal, Pietermaritzburg, Private Bag X01, Scottsville, 3209 South Africa
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Etminan A, Pour-Aboughadareh A, Noori A, Ahmadi-Rad A, Shooshtari L, Mahdavian Z, Yousefiazar-Khanian M. Genetic relationships and diversity among wild Salvia accessions revealed by ISSR and SCoT markers. BIOTECHNOL BIOTEC EQ 2018. [DOI: 10.1080/13102818.2018.1447397] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
Affiliation(s)
- Alireza Etminan
- Department of Plant Breeding, Kermanshah Branch, Islamic Azad University, Kermanshah, Iran
| | - Alireza Pour-Aboughadareh
- Department of Genetics and Plant Breeding, Faculty of Agricultural and Natural Resources, Imam Khomeini International University, Qazvin, Iran
| | - Afsaneh Noori
- Department of Plant Breeding, Kermanshah Branch, Islamic Azad University, Kermanshah, Iran
| | - Amin Ahmadi-Rad
- Young Researchers and Elite Club, Kermanshah Branch, Islamic Azad University, Kermanshah, Iran
| | - Lia Shooshtari
- Department of Plant Breeding, Kermanshah Branch, Islamic Azad University, Kermanshah, Iran
| | - Zahra Mahdavian
- Department of Plant Breeding, Kermanshah Branch, Islamic Azad University, Kermanshah, Iran
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Al-Qurainy F, Khan S, Nadeem M, Tarroum M, Gaafar ARZ. Antioxidant System Response and cDNA-SCoT Marker Profiling in Phoenix dactylifera L. Plant under Salinity Stress. Int J Genomics 2017; 2017:1537538. [PMID: 28702461 PMCID: PMC5494121 DOI: 10.1155/2017/1537538] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 04/23/2017] [Accepted: 05/02/2017] [Indexed: 01/24/2023] Open
Abstract
Many Phoenix dactylifera (date palm) cultivars are grown in the arid and semiarid regions of the world, including Saudi Arabia. P. dactylifera is highly tolerant to salinity stress. To investigate the response of Khalas cultivar of P. dactylifera, two-month-old plants were treated with sodium chloride (50, 100, and 150 mM NaCl) for three months. Our result showed that proline content was higher in all treated plants compared to control plants. Thiobarbituric acid reactive substances (TBARS) were increased at 100 and 150 mM NaCl treatments; however, the result was found nonsignificant between control and plants treated at 50 mM NaCl. Similarly, enzyme activities of catalase (CAT) and superoxide dismutase (SOD) were 0.805 and 0.722 U/mg protein/min, respectively, and were greater at 100 and 150 mM NaCl treatments compared to the control plants. Total chlorophyll content and fresh weight of shoots and roots decreased substantially with the increase of salinity. A cDNA start codon-targeted (cDNA-SCoT) marker showed a variation in different gene expressions profiling between treated and untreated plants under various NaCl concentrations.
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Affiliation(s)
- Fahad Al-Qurainy
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Salim Khan
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Mohammad Nadeem
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Mohamed Tarroum
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Abdel-Rhman Z. Gaafar
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
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Petrovičová L, Balážová Ž, Vivodík M, Gálová Z. Detection genetic variability of secale cereale L. by scot markers. POTRAVINARSTVO 2017. [DOI: 10.5219/726] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Rye (Secale cereale L.) is our traditional cereal used for baking. The genetic variability of grown rye has been reduced by modern agronomic practices, which subsequently prompted the importance of search for species that could be useful as a gene pool for the improving of flour quality for human consumption or for other industrial uses. Therefore, the aim of this study was to detect genetic variability among the set of 45 rye genotypes using 8 SCoT markers. Amplification of genomic DNA of 45 genotypes, using SCoT analysis, yielded 114 fragments, with an average of 14.25 polymorphic fragments per primer. The most polymorphic primer was SCoT 36, where 21 polymorphic amplification products were detected. In contract the lowest polymorphic primer was SCoT 45 with 5 polymorphic products. Genetic polymorphism was characterized based on diversity index (DI), probability of identity (PI) and polymorphic information content (PIC). The hierarchical cluster analysis showed that the rye genotypes were divided into 2 main clusters. One rye genotype Motto, origin from Poland formed a separate subcluster (1b). Subscluster 2a included only genotype Valtické (CSK). In this experiment, SCoT proved to be a rapid, reliable and practicable method for revealing of polymorphism in the rye cultivars.
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Chai X, Dong R, Liu W, Wang Y, Liu Z. Optimizing Sample Size to Assess the Genetic Diversity in Common Vetch (Vicia sativa L.) Populations Using Start Codon Targeted (SCoT) Markers. Molecules 2017; 22:molecules22040567. [PMID: 28362323 PMCID: PMC6154542 DOI: 10.3390/molecules22040567] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2017] [Revised: 03/28/2017] [Accepted: 03/29/2017] [Indexed: 11/16/2022] Open
Abstract
Common vetch (Vicia sativa subsp. sativa L.) is a self-pollinating annual forage legume with worldwide importance. Here, we investigate the optimal number of individuals that may represent the genetic diversity of a single population, using Start Codon Targeted (SCoT) markers. Two cultivated varieties and two wild accessions were evaluated using five SCoT primers, also testing different sampling sizes: 1, 2, 3, 5, 8, 10, 20, 30, 40, 50, and 60 individuals. The results showed that the number of alleles and the Polymorphism Information Content (PIC) were different among the four accessions. Cluster analysis by Unweighted Pair Group Method with Arithmetic Mean (UPGMA) and STRUCTURE placed the 240 individuals into four distinct clusters. The Expected Heterozygosity (HE) and PIC increased along with an increase in sampling size from 1 to 10 plants but did not change significantly when the sample sizes exceeded 10 individuals. At least 90% of the genetic variation in the four germplasms was represented when the sample size was 10. Finally, we concluded that 10 individuals could effectively represent the genetic diversity of one vetch population based on the SCoT markers. This study provides theoretical support for genetic diversity, cultivar identification, evolution, and marker-assisted selection breeding in common vetch.
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Affiliation(s)
- Xutian Chai
- The State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China.
| | - Rui Dong
- The State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China.
| | - Wenxian Liu
- The State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China.
| | - Yanrong Wang
- The State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China.
| | - Zhipeng Liu
- The State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China.
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Satya P, Banerjee R, Karan M, Mukhopadhyay E, Chaudhary B, Bera A, Maruthi R, Sarkar S. Insight into genetic relation and diversity of cultivated and semi-domesticated under-utilized Crotalaria species gained using start codon targeted (SCoT) markers. BIOCHEM SYST ECOL 2016. [DOI: 10.1016/j.bse.2016.02.032] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Zhang Y, Yan H, Jiang X, Wang X, Huang L, Xu B, Zhang X, Zhang L. Genetic variation, population structure and linkage disequilibrium in Switchgrass with ISSR, SCoT and EST-SSR markers. Hereditas 2016; 153:4. [PMID: 28096766 PMCID: PMC5226102 DOI: 10.1186/s41065-016-0007-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 03/29/2016] [Indexed: 11/29/2022] Open
Abstract
Background To evaluate genetic variation, population structure, and the extent of linkage disequilibrium (LD), 134 switchgrass (Panicum virgatum L.) samples were analyzed with 51 markers, including 16 ISSRs, 20 SCoTs, and 15 EST-SSRs. Results In this study, a high level of genetic variation was observed in the switchgrass samples and they had an average Nei’s gene diversity index (H) of 0.311. A total of 793 bands were obtained, of which 708 (89.28 %) were polymorphic. Using a parameter marker index (MI), the efficiency of the three types of markers (ISSR, SCoT, and EST-SSR) in the study were compared and we found that SCoT had a higher marker efficiency than the other two markers. The 134 switchgrass samples could be divided into two sub-populations based on STRUCTURE, UPGMA clustering, and principal coordinate analyses (PCA), and upland and lowland ecotypes could be separated by UPGMA clustering and PCA analyses. Linkage disequilibrium analysis revealed an average r2 of 0.035 across all 51 markers, indicating a trend of higher LD in sub-population 2 than that in sub-population 1 (P < 0.01). Conclusions The population structure revealed in this study will guide the design of future association studies using these switchgrass samples.
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Affiliation(s)
- Yu Zhang
- Grassland Science Department, Sichuan Agricultural University, Chengdu, 611130 China.,IRTA. Centre de Recerca en Agrigenòmica (CSIC-IRTA-UAB), Campus UAB - Edifici CRAG, Bellaterra - Cerdanyola del Vallès, Barcelona, 08193 Spain
| | - Haidong Yan
- Grassland Science Department, Sichuan Agricultural University, Chengdu, 611130 China
| | - Xiaomei Jiang
- Grassland Science Department, Sichuan Agricultural University, Chengdu, 611130 China
| | - Xiaoli Wang
- Guizhou Institute of Prataculture, Guiyang, 550006 PR China
| | - Linkai Huang
- Grassland Science Department, Sichuan Agricultural University, Chengdu, 611130 China
| | - Bin Xu
- College of Grassland Science, Nanjing Agricultural University, Nanjing, 210095 China
| | - Xinquan Zhang
- Grassland Science Department, Sichuan Agricultural University, Chengdu, 611130 China
| | - Lexin Zhang
- Grassland Science Department, Sichuan Agricultural University, Chengdu, 611130 China
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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] [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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Teixeira da Silva JA, Jin X, Dobránszki J, Lu J, Wang H, Zotz G, Cardoso JC, Zeng S. Advances in Dendrobium molecular research: Applications in genetic variation, identification and breeding. Mol Phylogenet Evol 2016; 95:196-216. [DOI: 10.1016/j.ympev.2015.10.012] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 10/09/2015] [Accepted: 10/13/2015] [Indexed: 10/22/2022]
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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] [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] [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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Bhattacharyya P, Kumaria S, Tandon P. Applicability of ISSR and DAMD markers for phyto-molecular characterization and association with some important biochemical traits of Dendrobium nobile, an endangered medicinal orchid. PHYTOCHEMISTRY 2015; 117:306-316. [PMID: 26125940 DOI: 10.1016/j.phytochem.2015.06.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Revised: 06/18/2015] [Accepted: 06/22/2015] [Indexed: 06/04/2023]
Abstract
Dendrobium nobile is an important medicinal orchid having profound importance in traditional herbal drug preparations and pharmacopeias worldwide. Due to various anthropogenic pressures the natural populations of this important orchid species are presently facing threats of extinction. In the present study, genetic and chemical diversity existing amongst 6 natural populations of D. nobile were assessed using molecular markers, and the influence of genetic factors on its phytochemical activity especially antioxidant potential was determined. Molecular fingerprinting of the orchid taxa was performed using ISSR and DAMD markers along with the estimation of total phenolics, flavonoids and alkaloid contents. Antioxidant activity was also measured using DPPH and FRAP assays which cumulatively revealed a significant level of variability across the sampled populations. The representatives from Sikkim in Northeast India revealed higher phytochemical activity whereas those from Mizoram showed lesser activity. Analysis of molecular variance (AMOVA) revealed that variation amongst the populations was significantly higher than within the populations. The data generated by UPGMA and Bayesian analytical models were compared in order to estimate the genetic relationships amongst the D. nobile germplasm sampled from different geographical areas of Northeast India. Interestingly, identical grouping patterns were exhibited by both the approaches. The results of the present study detected a high degree of existing genetic and phytochemical variation amongst the populations in relation to bioclimatic and geographic locations of populations. Our results strongly establish that the cumulative marker approach could be the best suited for assessing the genetic relationships with high accuracy amongst distinct D. nobile accessions.
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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
| | - Suman Kumaria
- Plant Biotechnology Laboratory, Department of Botany, Centre for Advanced Studies, North-Eastern Hill University, Shillong 793022, Meghalaya, India.
| | - Pramod Tandon
- Plant Biotechnology Laboratory, Department of Botany, Centre for Advanced Studies, North-Eastern Hill University, Shillong 793022, Meghalaya, India
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Feng S, He R, Yang S, Chen Z, Jiang M, Lu J, Wang H. Start codon targeted (SCoT) and target region amplification polymorphism (TRAP) for evaluating the genetic relationship of Dendrobium species. Gene 2015; 567:182-8. [DOI: 10.1016/j.gene.2015.04.076] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2014] [Revised: 04/15/2015] [Accepted: 04/28/2015] [Indexed: 11/29/2022]
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Heikrujam M, Kumar J, Agrawal V. Genetic diversity analysis among male and female Jojoba genotypes employing gene targeted molecular markers, start codon targeted (SCoT) polymorphism and CAAT box-derived polymorphism (CBDP) markers. Meta Gene 2015; 5:90-7. [PMID: 26110116 PMCID: PMC4477110 DOI: 10.1016/j.mgene.2015.06.001] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Revised: 06/03/2015] [Accepted: 06/03/2015] [Indexed: 11/25/2022] Open
Abstract
To detect genetic variations among different Simmondsia chinensis genotypes, two gene targeted markers, start codon targeted (SCoT) polymorphism and CAAT box-derived polymorphism (CBDP) were employed in terms of their informativeness and efficiency in analyzing genetic relationships among different genotypes. A total of 15 SCoT and 17 CBDP primers detected genetic polymorphism among 39 Jojoba genotypes (22 females and 17 males). Comparatively, CBDP markers proved to be more effective than SCoT markers in terms of percentage polymorphism as the former detecting an average of 53.4% and the latter as 49.4%. The Polymorphic information content (PIC) value and marker index (MI) of CBPD were 0.43 and 1.10, respectively which were higher than those of SCoT where the respective values of PIC and MI were 0.38 and 1.09. While comparing male and female genotype populations, the former showed higher variation in respect of polymorphic percentage and PIC, MI and Rp values over female populations. Nei's diversity (h) and Shannon index (I) were calculated for each genotype and found that the genotype “MS F” (in both markers) was highly diverse and genotypes “Q104 F” (SCoT) and “82–18 F” (CBDP) were least diverse among the female genotype populations. Among male genotypes, “32 M” (CBDP) and “MS M” (SCoT) revealed highest h and I values while “58-5 M” (both markers) was the least diverse. Jaccard's similarity co-efficient of SCoT markers ranged from 0.733 to 0.922 in female genotypes and 0.941 to 0.746 in male genotype population. Likewise, CBDP data analysis also revealed similarity ranging from 0.751 to 0.958 within female genotypes and 0.754 to 0.976 within male genotype populations thereby, indicating genetically diverse Jojoba population. Employing the NTSYS (Numerical taxonomy and multivariate analysis system) Version 2.1 software, both the markers generated dendrograms which revealed that all the Jojoba genotypes were clustered into two major groups, one group consisting of all female genotypes and another group comprising of all male genotypes. During the present investigation, CBDP markers proved more informative in studying genetic diversity among Jojoba. Such genetically diverse genotypes would thus be of great significance for breeding, management and conservation of elite (high yielding) Jojoba germplasm. SCoT and CBDP markers were used to detect genetic diversity in Jojoba genotypes. CAAT markers proved to be more effective over SCoT markers in evaluating genetic diversity. Males showed more variations over females in terms of polymorphic percentage, PIC, MI and Rp values. Besides, Nei's diversity (h) and Shannon index (I) values calculated for the genotypes displayed diverse male and female genotypes.
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Affiliation(s)
| | - Jatin Kumar
- Department of Botany, University of Delhi, Delhi 110007, India
| | - Veena Agrawal
- Department of Botany, University of Delhi, Delhi 110007, India
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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] [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] [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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Luo C, He XH, Hu Y, Yu HX, Ou SJ, Fang ZB. Oligo-dT anchored cDNA-SCoT: a novel differential display method for analyzing differential gene expression in response to several stress treatments in mango (Mangifera indica L.). Gene 2014; 548:182-9. [PMID: 25017057 DOI: 10.1016/j.gene.2014.07.024] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Revised: 07/03/2014] [Accepted: 07/09/2014] [Indexed: 10/25/2022]
Abstract
Differential display is a powerful technique for analyzing differences in gene expression. Oligo-dT cDNAstart codon targeted marker (cDNA-SCoT) technique is a novel, simple, cheap, rapid, and efficient method for differential gene expression research. In the present study, the oligo-dT anchored cDNA-SCoT technique was exploited to identify differentially expressed genes during several stress treatments in mango. A total of 37 primers combined with oligo-dT anchor primers 3side amplified approximately 150 fragments of 150 bp to 1500 bp in length. Up to 100 fragments were differentially expressed among the stress treatments and control samples, among which 92 were obtained and sequenced. Out of the 92 transcript derived fragments (TDFs), 70% were highly homologous to known genes, and 30% encoded unclassified proteins with unknown functions. The expression pattern of nine genes with known functions involved in several abiotic stresses in other species was confirmed by quantitative reverse transcription polymerase chain reaction (qRT-PCR) under cold (4 °C), salinity (NaCl), polyethylene glycol (PEG, MW 6000), and heavy metal treatments in leaves and stems at different time points (0, 24, 48, and 72 h). The expression patterns of the genes (TDF4, TDF7, TDF23, TDF45, TDF49, TDF50, TDF57, TDF91 and TDF92) that had direct or indirect relationships with cold, salinity, drought and heavy metal stress response were analyzed through qRT-PCR. The possible roles of these genes are discussed. This study suggests that the oligo-dT anchored cDNA-SCoT differential display method is a useful tool to serve as an initial step for characterizing transcriptional changes induced by abiotic stresses and provide gene information for further study and application in genetic improvement and breeding in mango.
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Affiliation(s)
- Cong Luo
- College of Agriculture, Guangxi University, Nanning, Guangxi 530004, China
| | - Xin-Hua He
- College of Agriculture, Guangxi University, Nanning, Guangxi 530004, China; Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Nanning, Guangxi 530007, China.
| | - Ying Hu
- College of Agriculture, Guangxi University, Nanning, Guangxi 530004, China
| | - Hai-xia Yu
- College of Agriculture, Guangxi University, Nanning, Guangxi 530004, China
| | - Shi-Jin Ou
- College of Agriculture, Guangxi University, Nanning, Guangxi 530004, China
| | - Zhong-Bin Fang
- College of Agriculture, Guangxi University, Nanning, Guangxi 530004, China
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Genetic diversity of orchardgrass (Dactylis glomerata L.) germplasms with resistance to rust diseases revealed by Start Codon Targeted (SCoT) markers. BIOCHEM SYST ECOL 2014. [DOI: 10.1016/j.bse.2013.12.028] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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