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Thomatou AA, Mazarakioti EC, Zotos A, Kokkotos E, Kontogeorgos A, Patakas A, Ladavos A. Stable Isotope Ratio Analysis for the Geographic Origin Discrimination of Greek Beans "Gigantes-Elefantes" ( Phaseolus coccineus L.). Foods 2024; 13:2107. [PMID: 38998613 PMCID: PMC11241270 DOI: 10.3390/foods13132107] [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: 05/30/2024] [Revised: 06/18/2024] [Accepted: 06/29/2024] [Indexed: 07/14/2024] Open
Abstract
Adulteration of high-value agricultural products is a critical issue worldwide for consumers and industries. Discrimination of the geographical origin can verify food authenticity by reducing risk and detecting adulteration. Between agricultural products, beans are a very important crop cultivated worldwide that provides food rich in iron and vitamins, especially for people in third-world countries. The aim of this study is the construction of a map of the locally characteristic isotopic fingerprint of giant beans, "Fasolia Gigantes-Elefantes PGI", a Protected Geographical Indication product cultivated in the region of Kastoria and Prespes, Western Macedonia, Greece, with the ultimate goal of the discrimination of beans from the two areas. In total, 160 samples were collected from different fields in the Prespes region and 120 samples from Kastoria during each cultivation period (2020-2021 and 2021-2022). The light element (C, N, and S) isotope ratios were measured using Isotope Ratio Mass Spectrometry (IRMS), and the results obtained were analyzed using chemometric techniques, including a one-way ANOVA and Binomial logistic regression. The mean values from the one-way ANOVA were δ15NAIR = 1.875‱, δ13CV-PDB = -25.483‱, and δ34SV-CDT = 4.779‱ for Kastoria and δ15NAIR = 1.654‱, δ13CV-PDB = -25.928‱, and δ34SV-CDT = -0.174‱ for Prespes, and showed that stable isotope ratios of C and S were statistically different for the areas studied while the Binomial logistic regression analysis that followed correctly classified more than 78% of the samples.
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Affiliation(s)
- Anna-Akrivi Thomatou
- Department of Food Science & Technology, University of Patras, 30100 Agrinio, Greece
| | - Eleni C Mazarakioti
- Department of Food Science & Technology, University of Patras, 30100 Agrinio, Greece
| | - Anastasios Zotos
- Department of Sustainable Agriculture, University of Patras, 30100 Agrinio, Greece
| | - Efthimios Kokkotos
- Department of Food Science & Technology, University of Patras, 30100 Agrinio, Greece
| | - Achilleas Kontogeorgos
- Department of Agriculture, International Hellenic University, 57001 Thessaloniki, Greece
| | - Angelos Patakas
- Department of Food Science & Technology, University of Patras, 30100 Agrinio, Greece
| | - Athanasios Ladavos
- Department of Food Science & Technology, University of Patras, 30100 Agrinio, Greece
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Authentication of carnaroli rice by HRM analysis targeting nucleotide polymorphisms in the Alk and Waxy genes. Food Control 2022. [DOI: 10.1016/j.foodcont.2022.108829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Stavridou E, Voulgari G, Michailidis M, Kostas S, Chronopoulou EG, Labrou NE, Madesis P, Nianiou-Obeidat I. Overexpression of A Biotic Stress-Inducible Pvgstu Gene Activates Early Protective Responses in Tobacco under Combined Heat and Drought. Int J Mol Sci 2021; 22:2352. [PMID: 33652971 PMCID: PMC7956764 DOI: 10.3390/ijms22052352] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 02/22/2021] [Accepted: 02/24/2021] [Indexed: 12/20/2022] Open
Abstract
Drought and heat stresses are major factors limiting crop growth and productivity, and their effect is more devastating when occurring concurrently. Plant glutathione transferases (GSTs) are differentially expressed in response to different stimuli, conferring tolerance to a wide range of abiotic stresses. GSTs from drought-tolerant Phaseolus vulgaris var. "Plake Megalosperma Prespon" is expected to play an important role in the response mechanisms to combined and single heat and drought stresses. Herein, we examined wild-type N. tabacum plants (cv. Basmas Xanthi) and T1 transgenic lines overexpressing the stress-induced Pvgstu3-3 and Pvgstu2-2 genes. The overexpression of Pvgstu3-3 contributed to potential thermotolerance and greater plant performance under combined stress. Significant alterations in the primary metabolism were observed in the transgenic plants between combined stress and stress-free conditions. Stress-responsive differentially expressed genes (DEGs) and transcription factors (TFs) related to photosynthesis, signal transduction, starch and sucrose metabolism, osmotic adjustment and thermotolerance, were identified under combined stress. In contrast, induction of certain DEGs and TF families under stress-free conditions indicated that transgenic plants were in a primed state. The overexpression of the Pvgstu3-3 is playing a leading role in the production of signaling molecules, induction of specific metabolites and activation of the protective mechanisms for enhanced protection against combined abiotic stresses in tobacco.
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Affiliation(s)
- Evangelia Stavridou
- Laboratory of Genetics and Plant Breeding, School of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, P.O. Box 261, GR-54124 Thessaloniki, Greece; (E.S.); (G.V.)
- Institute of Applied Biosciences, CERTH, 6th km Charilaou-Thermis Road, Thermi, P.O. Box 361, GR-57001 Thessaloniki, Greece;
| | - Georgia Voulgari
- Laboratory of Genetics and Plant Breeding, School of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, P.O. Box 261, GR-54124 Thessaloniki, Greece; (E.S.); (G.V.)
| | - Michail Michailidis
- Laboratory of Pomology, Department of Horticulture, School of Agriculture, Aristotle University of Thessaloniki, GR-54124 Thessaloniki, Greece;
| | - Stefanos Kostas
- Laboratory of Floriculture, School of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, GR-54124 Thessaloniki, Greece;
| | - Evangelia G. Chronopoulou
- Laboratory of Enzyme Technology, Department of Biotechnology, School of Food, Biotechnology and Development, Agricultural University of Athens, 75 Iera Odos Street, 11855 Athens, Greece; (E.G.C.); (N.E.L.)
| | - Nikolaos E. Labrou
- Laboratory of Enzyme Technology, Department of Biotechnology, School of Food, Biotechnology and Development, Agricultural University of Athens, 75 Iera Odos Street, 11855 Athens, Greece; (E.G.C.); (N.E.L.)
| | - Panagiotis Madesis
- Institute of Applied Biosciences, CERTH, 6th km Charilaou-Thermis Road, Thermi, P.O. Box 361, GR-57001 Thessaloniki, Greece;
- Laboratory of Molecular Biology of Plants, School of Agricultural Sciences, University of Thessaly, 38446 Thessaly, Greece
| | - Irini Nianiou-Obeidat
- Laboratory of Genetics and Plant Breeding, School of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, P.O. Box 261, GR-54124 Thessaloniki, Greece; (E.S.); (G.V.)
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Chedid E, Rizou M, Kalaitzis P. Application of high resolution melting combined with DNA-based markers for quantitative analysis of olive oil authenticity and adulteration. Food Chem X 2020; 6:100082. [PMID: 32154510 PMCID: PMC7058896 DOI: 10.1016/j.fochx.2020.100082] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 02/18/2020] [Accepted: 02/18/2020] [Indexed: 02/07/2023] Open
Abstract
A plethora of biotechnological methodologies is used to authenticate quality olive oils. Among the DNA-based approaches, SNPs and SSRs combined with high resolution melting (HRM) provide certain advantages such as speed, simplicity and reliability. SNP-HRM and SSR-HRM were used for the authentication of monovarietal olive oils as well as the quantification of varietal composition in olive oil DNA admixtures and olive oil blends of two different cultivars. The SSR-HRM was more efficient in distinguishing monovarietal olive oils while the SNP-HRM assay was more reliable in discriminating olive oil blends. HRM was also used for the detection of adulteration of olive oil with oils of different plant origin by using plastid trnL indels and SNPs. The trnL-indels-HRM showed higher discrimination power than the trnL-SNP-HRM in determining adulteration in olive oil. These results indicate that traceability of adulteration might be more reliable than authentication of the varietal origin in olive oil blends.
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Affiliation(s)
| | | | - Panagiotis Kalaitzis
- Department of Horticultural Genetics & Biotechnology, Mediterranean Agronomic Institute of Chania, Crete, Greece
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Expanding Phaseolus coccineus Genomic Resources: De Novo Transcriptome Assembly and Analysis of Landraces 'Gigantes' and 'Elephantes' Reveals Rich Functional Variation. Biochem Genet 2019; 57:747-766. [PMID: 30997627 DOI: 10.1007/s10528-019-09920-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 04/01/2019] [Indexed: 10/27/2022]
Abstract
Beans are one of the most important staple crops in the world. Runner bean (Phaseolus coccineus L.) is a small-scale agriculture crop compared to common bean (Phaseolusvulgaris). Beans have been introduced to Europe from the Central America to Europe and since then they have been scattered to different geographical regions. This has resulted in the generation of numerous local cultivars and landraces with distinguished characters and adaptive potential. To identify and characterize the underlying genomic variation of two very closely related runner bean cultivars, we performed RNA-Seq with de novo transcriptome assembly in two landraces of P. coccineus, 'Gigantes' and 'Elephantes' phenotypically distinct, differing in seed size and shape. The cleaned reads generated 37,379 and 37,774 transcripts for 'Gigantes' and 'Elephantes,' respectively. A total of 1896 DEGs were identified between the two cultivars, 1248 upregulated in 'Elephantes' and 648 upregulated in 'Gigantes.' A significant upregulation of defense-related genes was observed in 'Elephantes,' among those, numerous members of the AP2-EREBP, WRKY, NAC, and bHLH transcription factor families. In total, 3956 and 4322 SSRs were identified in 'Gigantes' and 'Elephantes,' respectively. Trinucleotide repeats were the most dominant repeat motif, accounting for 41.9% in 'Gigantes' and 40.1% in 'Elephantes' of the SSRs identified, followed by dinucleotide repeats (29.1% in both cultivars). Additionally, 19,281 putative SNPs were identified, among those 3161 were non-synonymous, thus having potential functional implications. High-confidence non-synonymous SNPs were successfully validated with an HRM assay, which can be directly adopted for P. coccineus molecular breeding. These results significantly expand the number of polymorphic markers within P. coccineus genus, enabling the robust identification of runner bean cultivars, the construction of high-resolution genetic maps, potentiating genome-wide association studies. They finally contribute to the genetic reservoir for the improvement of the closely related and intercrossable Phaseolus vulgaris.
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De Ron AM, Bebeli PJ, Negri V, Vaz Patto MC, Revilla P. Warm Season Grain Legume Landraces From the South of Europe for Germplasm Conservation and Genetic Improvement. FRONTIERS IN PLANT SCIENCE 2018; 9:1524. [PMID: 30405662 PMCID: PMC6204433 DOI: 10.3389/fpls.2018.01524] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 09/28/2018] [Indexed: 05/27/2023]
Abstract
Currently, there is a high concern from consumers regarding food quality, with emphasis on the origin of food sources. We here review the current situation of beans (Phaseolus spp.) and cowpea (Vigna unguiculata (L.) Walp.) landraces in the South of Europe focusing on morpho-agronomic and genetic diversity and physiological adaptation to the different agrosystems, including the symbiotic association with rhizobia. Despite the reduction in the production and consumption of grain legumes in Southern Europe, the variability of common bean, runner bean and cowpea landraces in this region is adequately preserved ex situ in germplasm banks and in breeder collections in Portugal, Spain, Italy and Greece; however, on-farm (in situ) conservation in isolated areas mainly in gardens and small fields for farmers own consumption and local markets is not guaranteed. This variability can be used for the genetic improvement of varieties, which will result in environmental-friendly improved legumes for a sustainable production in the South of Europe as well as in other regions of the World.
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Affiliation(s)
- Antonio M. De Ron
- Department of Genetics and Plant Breeding, Misión Biológica de Galicia, National Spanish Research Council (CSIC), Pontevedra, Spain
| | - Penelope J. Bebeli
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Athens, Greece
| | - Valeria Negri
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di Perugia, Perugia, Italy
| | - Maria Carlota Vaz Patto
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Pedro Revilla
- Department of Genetics and Plant Breeding, Misión Biológica de Galicia, National Spanish Research Council (CSIC), Pontevedra, Spain
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Druml B, Cichna-Markl M. High resolution melting (HRM) analysis of DNA--its role and potential in food analysis. Food Chem 2014; 158:245-54. [PMID: 24731338 DOI: 10.1016/j.foodchem.2014.02.111] [Citation(s) in RCA: 115] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Revised: 02/02/2014] [Accepted: 02/19/2014] [Indexed: 11/17/2022]
Abstract
DNA based methods play an increasing role in food safety control and food adulteration detection. Recent papers show that high resolution melting (HRM) analysis is an interesting approach. It involves amplification of the target of interest in the presence of a saturation dye by the polymerase chain reaction (PCR) and subsequent melting of the amplicons by gradually increasing the temperature. Since the melting profile depends on the GC content, length, sequence and strand complementarity of the product, HRM analysis is highly suitable for the detection of single-base variants and small insertions or deletions. The review gives an introduction into HRM analysis, covers important aspects in the development of an HRM analysis method and describes how HRM data are analysed and interpreted. Then we discuss the potential of HRM analysis based methods in food analysis, i.e. for the identification of closely related species and cultivars and the identification of pathogenic microorganisms.
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Affiliation(s)
- Barbara Druml
- Department of Analytical Chemistry, University of Vienna, Währinger Straße 38, A-1090 Vienna, Austria
| | - Margit Cichna-Markl
- Department of Analytical Chemistry, University of Vienna, Währinger Straße 38, A-1090 Vienna, Austria.
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Genetic Diversity and Seed Quality of the “Badda” Common Bean from Sicily (Italy). DIVERSITY 2013. [DOI: 10.3390/d5040843] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Abstract
Microsatellites are codominant molecular genetic markers, which are universally dispersed within genomes. These markers are highly popular because of their high level of polymorphism, relatively small size, and rapid detection protocols. They are widely used in a variety of fundamental and applied fields of biological sciences for plants and animal studies. Microsatellites are also extensively used in the field of agriculture, where they are used in characterizing genetic materials, plant selection, constructing dense linkage maps, mapping economically important quantitative traits, identifying genes responsible for these traits. In addition microsatellites are used for marker-assisted selection in breeding programs, thus speeding up the process. In this chapter, genomic distribution, evolution, and practical applications of microsatellites are considered, with special emphasis on plant breeding and agriculture. Moreover, novel advances in microsatellite technologies are also discussed.
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