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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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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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Large-Scale In Vitro Multiplication and Phytochemical Analysis of Himantoglossum affine (Boiss.) Schltr.: An Endangered Euro-Mediterranean Terrestrial Orchid. DIVERSITY 2022. [DOI: 10.3390/d14121137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Himantoglossum affine is a threatened terrestrial orchid. We aimed to optimize asymbiotic seed germination and direct embryogenesis and to analyze the phytochemical profile and physico-biochemical analysis of leaf and tuber. The individual use of organic nitrogen compounds resulted in higher germination efficiencies, while the shortest times to germination were observed using coconut water plus casein hydrolysate. Plantlets grown on media supplemented with pineapple juice and peptone had the highest plantlet length and weight. For embryogenesis, the highest regeneration rate (44%) and embryo number/explant (10.12 ± 2.08) were observed in young protocorm-like body (PLB) explants with 0.5 mg/L naphthalene acetic acid (NAA) and 1 mg/L thidiazuron (TDZ). During the acclimatization process, the scattered vascular tubes converted to fully developed vascular tissues, ensuring maximum sap flux. Gas chromatography–mass spectrometry analysis identified 1,2,3-propanetriol, monoacetate, 4H-pyran-4-one, 2,3-dihydro-3,5-dihydroxy-6-methyl, and 2-butenedioic acid, 2-methyl-, (E)- as the most prevalent compounds. We reported higher contents of total phenolics and flavonoids and antioxidant activity compared to other terrestrial orchids. The glucomannan content (36.96%) was also higher than starch content (31.31%), comparable to those reported in other tuberous orchids. Based on the fragmentation of H. affine populations in the Middle East and Euro-Mediterranean countries due to over-harvesting, climate change, and/or human impact, our procedure offers a tool for the re-introduction of in vitro-raised plants to threatened areas.
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Mafakheri M, Bakhshipour M, Omrani M, Gholizadeh H, Rahimi N, Mobaraki A, Rahimi M. The impact of environmental and climatic variables on genetic diversity and plant functional traits of the endangered tuberous orchid (Orchis mascula L.). Sci Rep 2022; 12:19765. [PMID: 36396718 PMCID: PMC9672365 DOI: 10.1038/s41598-022-19864-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 09/06/2022] [Indexed: 11/18/2022] Open
Abstract
Understanding how environmental factors shape patterns of genetic and phenotypic variations in a species is necessary for conservation and plant breeding. However, these factors have not yet been completely understood in tuberous orchid species used to make 'Salep', an important ingredient in traditional medicine and beverages in middle eastern countries and India. In many areas, increasing demand has pushed species to the brink of extinction. In this study, 198 genotypes from 18 populations of the endangered species Orchis mascula L. spanning a large-scale climatic gradient in northern Iran were used to investigate patterns of genetic diversity and plant functional traits. Populations were sampled from three land cover types (woodland, shrubland, and pastureland/grassland). Plant height, stem length, number of flowers, bulb fresh and dry weight, glucomannan, and starch concentrations showed high variation among populations and were significantly related to land cover type. In general, genetic diversity was high, particularly in those from eastern Hyrcanian; additionally, populations showed a high level of genetic differentiation (G'st = 0.35) with low gene flow (Nm = 0.46). The majority of genetic differentiation occurred within populations (49%) and land cover types (20%). The population structural analysis using the AFLP marker data in K = 4 showed a high geographical affinity for 198 O. mascula genotypes, with some genotypes having mixed ancestry. Temperature and precipitation were found to shape genetic and phenotypic variation profoundly. Significant isolation by the environment was observed, confirming the strong effect of environmental variables on phenotypic and genetic variation. Marker-trait association studies based on MLM1 and MLM2 models revealed significant associations of P-TGG + M-CTT-33 and E-AGG + M-CGT-22 markers with plant height and glucomannan content. Overall, a combination of large-scale climatic variables and land cover types significantly shaped genetic diversity and functional trait variation in O. mascula populations.
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Affiliation(s)
- Mohammad Mafakheri
- grid.27860.3b0000 0004 1936 9684Department of Plant Sciences, University of California - Davis, Davis, CA 95616 USA
| | - Mehdi Bakhshipour
- grid.411872.90000 0001 2087 2250Department of Horticultural Sciences, Faculty of Agricultural Sciences, University of Guilan, P.O. Box, Rasht, 41635-1314 Iran
| | - Mina Omrani
- grid.1020.30000 0004 1936 7371School of Science and Technology, Faculty of Science, Agriculture, Business and Law, University of New England, Armidale, NSW 2351 Australia
| | - Hamid Gholizadeh
- grid.411622.20000 0000 9618 7703Department of Plant Biology, Faculty of Basic Sciences, University of Mazandaran, Babolsar, Mazandaran Iran
| | - Najmeh Rahimi
- grid.24805.3b0000 0001 0687 2182Department of Chemistry and Biochemistry, New Mexico State University, Las Cruces, NM USA
| | - Ali Mobaraki
- grid.411872.90000 0001 2087 2250Department of Horticultural Sciences, Faculty of Agricultural Sciences, University of Guilan, P.O. Box, Rasht, 41635-1314 Iran
| | - Mehdi Rahimi
- grid.448905.40000 0004 4910 146XDepartment of Biotechnology, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman, Iran
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Aydın F, Özer G, Alkan M, Çakır İ. Start Codon Targeted (SCoT) markers for the assessment of genetic diversity in yeast isolated from Turkish sourdough. Food Microbiol 2022; 107:104081. [DOI: 10.1016/j.fm.2022.104081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 06/13/2022] [Accepted: 06/13/2022] [Indexed: 11/28/2022]
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Chen M, He X, Huang X, Lu T, Zhang Y, Zhu J, Yu H, Luo C. Cis-element amplified polymorphism (CEAP), a novel promoter- and gene-targeted molecular marker of plants. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2022; 28:1407-1419. [PMID: 36051234 PMCID: PMC9424407 DOI: 10.1007/s12298-022-01212-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 02/08/2022] [Accepted: 07/14/2022] [Indexed: 06/15/2023]
Abstract
UNLABELLED In this study, we selected eight cis-elements: AAAG, ACGTG, CCGA, ACTCAT, GGTCA, TATCC, TGAC and GATAA, which are closely related to plant growth and development, signal transduction and stress response. The CEAP primers were 18 nucleotides long and consisted of a central cis-element nucleotide core flanked by a filler sequence at the 5' end and di- or tri-nucleotides at the 3' end. A total of two hundred and twenty-four primers were developed, and the PCR procedure consisted of 5 cycles of low-temperature annealing and 35 subsequent cycles of annealing at 50°C. The PCR products are electrophoretically separated by 1.8-2.3% agarose. The polymorphism of the CEAP marker was amplified in eight mango (Mangifera indica L.) species. The results showed that the CEAP primers could amplify clear, repeatable bands in mango and combine at least four cis-elements from which a large number of bands were amplified and six highly polymorphic primers for each cis-element can reach an accurate clustering result. The results of CEAP marker assays compared with ISSR, CBDP and iPBS marker assays showed that CEAP marker was better than the other three markers in the number of fragment bands, H and I indexes. In addition, we also tested the CEAP markers in rice, tomato, potato, wax gourd, citrus and longan and the results showed that the CEAP marker assay could amplify clear polymorphic bands in different species. Our results indicate that the CEAP markers could be universally used in different species for genetic diversity analysis, relationship analysis, and marker-assisted selection for breeding. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-022-01212-5.
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Affiliation(s)
- Meiyan Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, 530004 Guangxi People’s Republic of China
| | - Xinhua He
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, 530004 Guangxi People’s Republic of China
| | - Xing Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, 530004 Guangxi People’s Republic of China
| | - Tingting Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, 530004 Guangxi People’s Republic of China
| | - Yili Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, 530004 Guangxi People’s Republic of China
| | - Jiawei Zhu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, 530004 Guangxi People’s Republic of China
| | - Haixia Yu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, 530004 Guangxi People’s Republic of China
| | - Cong Luo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, 530004 Guangxi People’s Republic of China
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