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Nunziata A, De Benedetti L, Marchioni I, Cervelli C. High throughput measure of diversity in cytoplasmic and nuclear traits for unravelling geographic distribution of rosemary. Ecol Evol 2019; 9:3728-3739. [PMID: 31015962 PMCID: PMC6468057 DOI: 10.1002/ece3.4998] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 01/23/2019] [Accepted: 01/29/2019] [Indexed: 11/21/2022] Open
Abstract
In the present work, variability of both cytoplasmic and nuclear microsatellite traits was investigated with the aim of characterizing a set of rosemary germplasm resources (Salvia rosmarinus). Most of the materials were collected in Italy and France. High-resolution melting curves were compared each other computing their Euclidean distances and estimating the differences within their principal component as a measure of genetic diversity. Mantel correlation results combined to linear discriminant analysis allowed examined populations to be divided in four principal groups corresponding to four geographic areas, with few interesting and discussed exceptions. As rosemary propagates by seeds coming from insect mediated pollination, steady wild populations can be expected to be in panmictic equilibrium. Gained results confirmed and extended precedent characterization of rosemary genotypes and are compatible with the distribution of other Mediterranean species, as well as with the presence of a glacial refugium in the north-east area of Sardinia previously described. As the officinal use of this aromatic shrub is spreading, characterization and conservation of wild Mediterranean germplasm is gaining strategic importance. A core collection of 100 genotypes was pointed out as suitable for a cheaper biodiversity ex situ preservation as well as for subsequent metabolic and linkage disequilibrium analyses.
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Affiliation(s)
- Angelina Nunziata
- Research Centre for Olive, Citrus and Tree Fruit (OFA)C.R.E.A. Council for Agricultural Research and EconomicsCasertaItaly
| | - Laura De Benedetti
- Research Centre for Vegetable and Ornamental Crops (OF)C.R.E.A. Council for Agricultural Research and EconomicsSanremoItaly
| | - Ilaria Marchioni
- Research Centre for Vegetable and Ornamental Crops (OF)C.R.E.A. Council for Agricultural Research and EconomicsSanremoItaly
- Department of Agriculture, Food and Environment (DAFE)Università di PisaPisaItaly
| | - Claudio Cervelli
- Research Centre for Vegetable and Ornamental Crops (OF)C.R.E.A. Council for Agricultural Research and EconomicsSanremoItaly
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Speranskaya AS, Krinitsina AA, Shipulin GA, Khafizov KF, Logacheva MD. High-Throughput Sequencing for the Authentication of Food Products: Problems and Perspectives. RUSS J GENET+ 2018. [DOI: 10.1134/s1022795418090132] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Sarrou E, Ganopoulos I, Xanthopoulou A, Masuero D, Martens S, Madesis P, Mavromatis A, Chatzopoulou P. Genetic diversity and metabolic profile of Salvia officinalis populations: implications for advanced breeding strategies. PLANTA 2017; 246:201-215. [PMID: 28314999 DOI: 10.1007/s00425-017-2666-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 02/10/2017] [Indexed: 05/24/2023]
Abstract
As a result of this work, we were able to characterize seven indigenous to Greece Salvia officinalis populations using genetic and metabolomic tools. These tools can be used to select the most promising genotypes, capable to design future breeding programs for high valuable varieties. An initial investigation was carried out to compare the genetic and metabolic diversity in S. officinalis grown in Greece and to discern the relationship between the two sets of data. Analysis of inter-simple sequence repeats (ISSR) revealed significant genetic differences among seven sage populations, which were grouped into three main clusters according to an UPGMA ISSR data-based dendrogram and Principle Coordinate Analysis. 80 loci were scored of which up to 90% were polymorphic at species level. According to the composition of their essential oil, the populations were classified into two chemotypes: 1.8 cineole/α-thujone and α-thujone/1.8 cineole. Additionally, a targeted ultra performance liquid chromatography (UPLC-MS/MS) method was used to qualify and quantify phenolic compounds in methanolic extracts of the seven sage genotypes according to which they were districted in six clusters among the sage populations. The main compounds characterizing the seven genotypes were rosmarinic acid and carnosol, followed by apigenin-7-O-glucoside (Ap7glc), and luteolin-7-O-glucoside (Lu7glc). The correlation between matrices obtained from ISSR data and metabolic profiles was non-significant. However, based on the differences in metabolic fingerprint, we aimed to define populations using as main selection criteria the high polyphenol content and desired essential oil composition, using state to the art analytical tools for the identification of parent lines for breeding programs.
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Affiliation(s)
- Eirini Sarrou
- Department of Medicinal and Aromatic Plants, Hellenic Agricultural Organization DEMETER, Plant Breeding and Genetic Resources Institute, PB&GRI, Thermi, Thessaloniki, 57001, Greece.
- Laboratory of Genetics and Plant Breeding, Department of Agriculture, Faculty of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, Thessaloniki, Greece.
| | - Ioannis Ganopoulos
- Institute of Applied Biosciences, CERTH, 6th km Charilaou-Thermis Road, Thermi, 57001, Thessaloniki, Greece
| | - Aliki Xanthopoulou
- Institute of Applied Biosciences, CERTH, 6th km Charilaou-Thermis Road, Thermi, 57001, Thessaloniki, Greece
| | - Domenico Masuero
- Department of Food Quality and Nutrition Department, IASMA Research and Innovation Centre, Fondazione Edmund Mach (FEM), Via E. Mach 1, 38010, San Michele all'Adige (TN), Italy
| | - Stefan Martens
- Department of Food Quality and Nutrition Department, IASMA Research and Innovation Centre, Fondazione Edmund Mach (FEM), Via E. Mach 1, 38010, San Michele all'Adige (TN), Italy
| | - Panagiotis Madesis
- Institute of Applied Biosciences, CERTH, 6th km Charilaou-Thermis Road, Thermi, 57001, Thessaloniki, Greece
| | - Athanasios Mavromatis
- Laboratory of Genetics and Plant Breeding, Department of Agriculture, Faculty of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Paschalina Chatzopoulou
- Department of Medicinal and Aromatic Plants, Hellenic Agricultural Organization DEMETER, Plant Breeding and Genetic Resources Institute, PB&GRI, Thermi, Thessaloniki, 57001, Greece
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Simko I. High-Resolution DNA Melting Analysis in Plant Research. TRENDS IN PLANT SCIENCE 2016; 21:528-537. [PMID: 26827247 DOI: 10.1016/j.tplants.2016.01.004] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Revised: 12/05/2015] [Accepted: 01/05/2016] [Indexed: 05/22/2023]
Abstract
Genetic and genomic studies provide valuable insight into the inheritance, structure, organization, and function of genes. The knowledge gained from the analysis of plant genes is beneficial to all aspects of plant research, including crop improvement. New methods and tools are continually being developed to facilitate rapid and accurate mapping, sequencing, and analyzing of genes. Here, I review the recent progress in the application of high-resolution melting (HRM) analysis of DNA, a method that allows detecting polymorphism in double-stranded DNA by comparing profiles of melting curves. Use of HRM has expanded considerably in the past few years as the method was successfully applied for high-throughput genotyping, mapping genes, testing food products and seeds, and other areas of plant research.
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Affiliation(s)
- Ivan Simko
- United States Department of Agriculture, Agricultural Research Service, U.S. Agricultural Research Station, 1636 E. Alisal St, Salinas, CA 93905, USA.
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Yan GX, Wu XM, Li D, Zeng CL, Lv PJ, Gao GZ, Chen BY, Xu K, Lv XD. Assessing high-resolution melt curve analysis for accurate detection of DNA polymorphisms in the chloroplast gene accD of Crucifer species. BIOCHEM SYST ECOL 2012. [DOI: 10.1016/j.bse.2012.06.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Kuster CJ, Von Elert E. High-resolution melting analysis: a genotyping tool for population studies on Daphnia. Mol Ecol Resour 2012; 12:1048-57. [PMID: 22925691 DOI: 10.1111/j.1755-0998.2012.03177.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2012] [Revised: 07/05/2012] [Accepted: 07/17/2012] [Indexed: 11/27/2022]
Abstract
Determining genetic variation at the DNA level within and between natural populations is important for understanding the role of natural selection on phenotypic traits, but many techniques of screening for genetic variation are either cost intensive, not sensitive enough or too labour- and time-consuming. Here, we demonstrate high-resolution melting analysis (HRMA) as a cost-effective and powerful tool for screening variable target genes in natural populations. HRMA is based on monitoring the melting of PCR amplicons. Owing to saturating concentrations of a dye that binds at high concentrations to double-stranded DNA, it is possible to genotype high numbers of samples rapidly and accurately. We analysed digestive trypsins of two Daphnia magna populations as an application example for HRMA. One population originated from a pond containing toxic cyanobacteria that possibly produce protease inhibitors and the other from a pond without such cyanobacteria. The hypothesis was that D. magna clones from ponds with cyanobacteria have undergone selection by these inhibitors, which has led to different trypsin alleles. We first sequenced pooled genomic PCR products of trypsins from both populations to identify variable DNA sequences of active trypsins. Second, we screened variable DNA sequences of each D. magna clone from both populations for single nucleotide polymorphisms via HRMA. The HRMA results revealed that both populations exhibited phenotypic differences in the analysed trypsins. Our results indicate that HRMA is a powerful genotyping tool for studying the variation of target genes in response to selection within and between natural Daphnia populations.
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Affiliation(s)
- C J Kuster
- Zoological Institute, Aquatic Chemical Ecology, University of Cologne, Cologne, Germany.
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A simple and efficient DNA isolation method for Salvia officinalis. Biochem Genet 2012; 50:881-92. [PMID: 22847363 DOI: 10.1007/s10528-012-9528-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2012] [Accepted: 04/10/2012] [Indexed: 10/28/2022]
Abstract
We report an efficient, simple, and cost-effective protocol for the isolation of genomic DNA from an aromatic medicinal plant, common sage (Salvia officinalis L.). Our modification of the standard CTAB protocol includes two polyphenol adsorbents (PVP 10 and activated charcoal), high NaCl concentrations (4 M) for removing polysaccharides, and repeated Sevag treatment to remove proteins and other carbohydrate contaminants. The mean DNA yield obtained with our Protocol 2 was 330.6 μg DNA g(-1) of dry leaf tissue, and the absorbance ratios 260/280 and 260/230 nm averaged 1.909 and 1.894, respectively, revealing lack of contamination. PCR amplifications of one nuclear (26S rDNA) and one chloroplast (rps16-trnK) locus indicated that our DNA isolation protocol may be used in common sage and other aromatic and medicinal plants containing essential oil for molecular biologic and biotechnological studies and for population genetics, phylogeographic, and conservation surveys in which nuclear or chloroplast genomes would be studied in large numbers of individuals.
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Rapid and cost-effective screening of newly identified microsatellite loci by high-resolution melting analysis. Mol Genet Genomics 2011; 286:225-35. [PMID: 21847526 DOI: 10.1007/s00438-011-0641-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2011] [Accepted: 08/04/2011] [Indexed: 12/13/2022]
Abstract
This study describes a new method for identifying microsatellite loci that will reliably amplify and show high degree of polymorphism in a given species. Microsatellites are the most powerful codominant markers available today, but the development of novel loci remains a labour-intensive and expensive process. In de novo isolation, approaches using next generation sequencing (NGS) are gradually replacing ones using Escherichia coli libraries, resulting in unparalleled numbers of candidate loci available. We present a systematic review of published microsatellite primer notes and show that, on average, about half of all candidate loci are lost due to insufficient PCR amplification, monomorphism or multicopy status in the genome, no matter what isolation strategy is used. Thus, the screening of candidate loci remains a major step in marker development. Re-assessing capillary-electrophoresis genotyped loci via high-resolution melting analysis (HRM), we evaluate the usefulness of HRM for this step. We demonstrate its applicability in a genotyping case study and introduce a fast, HRM-based workflow for the screening of microsatellite loci. This workflow may readily be applied to NGS-based marker development and has the potential to cut the costs of traditional testing by half to three quarters.
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Lamien-Meda A, Nell M, Lohwasser U, Börner A, Franz C, Novak J. Investigation of antioxidant and rosmarinic acid variation in the sage collection of the genebank in Gatersleben. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2010; 58:3813-9. [PMID: 20187608 DOI: 10.1021/jf903993f] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The total phenolic and flavonoid contents and 2,2-diphenyl-1-picrylhydrazyl (DPPH) and ferric reduction antioxidant power (FRAP) antioxidant capacities of 19 accessions of Salvia officinalis from the sage collection of the genebank in Gatersleben (Germany) were evaluated. The major phenolic compounds of sage, that is, rosmarinic acid, caffeic acid, carnosol, and carnosic acid, were quantified by reverse-phase high-performance liquid chromatography. The aerial parts of different individual plants of each accession were collected in two consecutive years from the same experimental field at the beginning of their flowering period. The results demonstrated a high variability between accessions. A general decreasing tendency from 2007 to 2008 was observed in most of the estimated parameters, that is, total phenolic, total flavonoid, rosmarinic acid, and caffeic acid contents and DPPH antioxidant activity. A slight opposite trend was obtained with the FRAP antioxidant capacity. Low but variable quantities of carnosol and carnosic acid were evaluated in the sample extracts. Individual plants within accessions were identified with high phenolic content and strong antioxidant activity. The rosmarinic acid content showed up to 8-fold differences between the lowest and the highest values. Overall, the study demonstrated a high variability in secondary metabolites present in sage, which could be used for breeding of highly antioxidative genotypes of S. officinalis.
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Affiliation(s)
- Aline Lamien-Meda
- Department of Farm Animal and Public Health in Veterinary Medicine, Institute for Applied Botany and Pharmacognosy, University of Veterinary Medicine, Veterinarplatz 1, Vienna, Austria.
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