Organic seeds production and differentiation from conventional systems: compositional signatures, analytical approaches and quality concerns

Abstract

Beyond the importance of organic seeds as key inputs in sustainable food production systems, when assessing the scientific evidence supporting their agronomic performance, commercialization, and quality/compositional characterization, several critical gaps remain. Aspects such as defining organic, agroecological and conventional seeds, regulatory frameworks, and compositional characteristics are frequently addressed in a fragmented manner in the literature. Discussing the implications of organic seed production, together with clarifying terms that are often used indiscriminately, is essential to ensure appropriate standards and product quality. At the same time, research-driven methodologies for control and data generation play a crucial role in overcoming challenges related to certification and traceability, particularly in the seed sector. Nevertheless, current evidence on organic seeds remains limited and largely exploratory, with variable results across studies and a strong influence of confounding factors (genetic, regional, climate). This situation complicates the identification of universal markers and the development of robust classification models. To address these limitations, this review integrates and reflects on the state-of-the-art knowledge on organic seed production, including agronomic, regulatory, and market traits. In addition, we synthesize major analytical approaches to assess organic seed authentication, highlighting the potential of intrinsic compositional features through fingerprinting strategies using elemental, isotopic, and metabolomic profiles as complementary tools from the traditionally used techniques based on physicochemical and physiological parameters (e.g., vigour, germination, purity). The remaining challenge lies in connecting academic research and practical application. While holistic approaches, such as omics, provide insights into seed composition and marker discovery, their use is restricted to laboratory settings due to the need for costly instrumentation and complex data processing. Advancing this field requires translating these findings into accessible tools by using the identified markers that support regulatory frameworks, which finally promote agronomic practices and market expansion, also ensuring transparency in the organic seed sector.

Keywords

organic / seeds / sustainability / analytical methods / quality assessment / omics / chemometrics

References

[1] Bourn D, Prescott J. A Comparison of the Nutritional Value, Sensory Qualities, and Food Safety of Organically and Conventionally Produced Foods. Crit Rev Food Sci Nutr. 2010;42:1-34.

[2] Bordeleau G, Myers—Smith I, Midak M, Szeremeta A. Food Quality: A comparison of organic and conventional fruits and vegetables. Ecol Agric. 2002.

[3] Shenoy KR, Ranjith VK, Nayak S, Anirvinna C. Conceptualizing organic food consumption: a consumer motive perspective. Cogent Soc Sci. 2024;10:e10.

[4] Lozano—Castellón J, Laveriano—Santos EP, Abuhabib MM, Pozzoli C, Pérez M, Vallverdú—Queralt A, et al. Proven traceability strategies using chemometrics for organic food authenticity. Trends Food Sci Technol. 2024;147:104430.

[5] Macdougall NA. The Certified Organic Seed Market: Implications of Delayed Development. ageconsearch; 2005.

[6] Orsini S, Costanzo A, Solfanelli F, Zanoli R, Padel S, Messmer MM, et al. Factors Affecting the Use of Organic Seed by Organic Farmers in Europe. Sustainability. 2020;12:8540.

[7] Granval N, González M, Maffei J. Los alimentos orgánicos y la calidad y seguridad alimentaria. Aliment Argent. 2014:50-3.

[8] IICA SENASA. La producción orgánica en la Argentina: compilación de experiencias institucionales y productivas. Buenos Aires (Argentina): IICA; 2009.

[9] Desclaux D. Organic seeds of the future: simple material? Org Agric. 2020;10:23-6.

[10] Fernandez PG. ORGANIC SEED AS BASIS FOR SUSTAINABLE AGRICULTURE. Philipp J Crop Sci. 2001;26:15-30.

[11] Sripathy KV, Hosamani J, Bellundagi A, Prabhakar I. Organic Seed Production. Environ Ecol. 2012;30:102—5.

[12] Nabooji Scholar A, Nabooji A, Nadukeri SV. Organic seed production: Concept and practices. Pharma Innov J. 2022:1070-4.

[13] FiBL & IFOAM—Organics International. The world of organic agriculture—Statistics & Emerging Trends 2024. FiBL; 2024.

[14] Malhotra B. Global Seed Market Update: Soaring Growth, GM Seeds, China and What’s Ahead. Seed World; 2024.

[15] Shoham J. Revisiting seed company sales and profit. FAO; 2024.

[16] Precedence Research. Organic Seed Market Size and Forecast 2025 to 2034. Precedence Research ; 2025.

[17] Maricic D, Spicnagel AM. LiveSeeding project—Insights into the opportunities and bottlenecks in the organic seed and plant breeding sector. Int Symp Agric. 2024.

[18] Winter E, Grovermann C, Messmer MM, Aurbacher J. Assessing seed and breeding interventions for organic farming using a multiagent value chain approach. Agric Food Econ. 2023;11:e22.

[19] Merfield CN. Problems and progress for organic seed production. Agron N Z. 2012;42.

[20] Orsini F, Maggio A, Rouphael Y, De Pascale S. “Physiological quality” of organically grown vegetables. Sci Hortic. 2016;208:131-9.

[21] Durham TC, Mizik T. Comparative Economics of Conventional, Organic, and Alternative Agricultural Production Systems. Economies. 2021;9:64.

[22] Souza JTA, Costa CAD, Brandão Junior DDS, Menezes JBDC, Nascimento WM, Cardoso WJ. Yield and quality of seeds of lettuce genotypes produced under organic management. J Seed Sci. 2019;41:352—8.

[23] Portal RKVP, Nascimento WM, Vidal VL, Coelho M, Peixoto N. Productivity in seeds of the green bean produced under conventional and organic systems. Semina: Ciênc Agrár. 2018;39:1389.

[24] Magkos F, Arvaniti F, Zampelas A. Organic food: nutritious food or food for thought? A review of the evidence. Int J Food Sci Nutr. 2009;54:357-71.

[25] Rosa EA, Bennett RN, Aires A. Levels and potential health impacts of nutritionally relevant phytochemicals in organic and conventional food production systems. In: Handbook of Organic Food Safety and Quality. Elsevier Ltd.; 2007. pp. 297-329.

[26] Mie A, Laursen KH, Aberg KM, Forshed J, Lindahl A, Thorup—Kristensen K, et al. Discrimination of conventional and organic white cabbage from a long—term field trial study using untargeted LC—MS—based metabolomics. Anal Bioanal Chem. 2014;406:2885-97.

[27] Brandt K, Leifert C, Sanderson R, Seal CJ. Agroecosystem Management and Nutritional Quality of Plant Foods: The Case of Organic Fruits and Vegetables. Crit Rev Plant Sci. 2011;30:177-97.

[28] Cruz—Carrión Á, Ruiz de Azua MJ, Muguerza B, Mulero M, Bravo FI, Arola—Arnal A, et al. Organic vs. Non—Organic Plant—Based Foods—A Comparative Study on Phenolic Content and Antioxidant Capacity. Plants. 2023;12:183.

[29] Doria E, Campion B, Sparvoli F, Tava A, Nielsen E. Anti—nutrient components and metabolites with health implications in seeds of 10 common bean (Phaseolus vulgaris L. andPhaseolus lunatus L.) landraces cultivated in southern Italy . J Food Compos Anal. 2012;26:72-80.

[30] Taie HAA, El—Mergawi R, Radwan S. Isoflavonoids, flavonoids, phenolic acids profiles and antioxidant activity of soybean seeds as affected by organic and bioorganic fertilization. American—Eurasian J Agric Environ Sci. 2008;4:207-13.

[31] Radulescu C, Buruleanu LC, Nicolescu CM, Olteanu RL, Bumbac M, Holban GC, et al. Phytochemical Profiles, Antioxidant and Antibacterial Activities of Grape (Vitis vinifera L.) Seeds and Skin from Organic and Conventional Vineyards . Plants. 2020;9:1470.

[32] Alvites—Misajel K, García—Gutiérrez M, Miranda—Rodríguez C, Ramos—Escudero F. Organically vs conventionally—grown dark and white chia seeds (Salvia hispanica L.): fatty acid composition, antioxidant activity and techno—functional properties . Grasas Aceites. 2019;70:e299.

[33] Lima GPP, Da Rocha SA, Takaki M, Ramos PRR, Ono EO. Comparison of polyamine, phenol and flavonoid contents in plants grown under conventional and organic methods. Int J Food Sci Technol. 2008;43:1838—43.

[34] Gupta—Elera G, Garrett A, Martinez A, Kraus RD, Robison R, O’Neill K. A Comparison of Antioxidant Properties in Organic and Conventional Blueberries. J Food Res. 2012;1:1.

[35] Amarowicz R, Cwalina—Ambroziak B, Janiak MA, Damszel M, Stępień A, Sulewska K, et al. Effect of Fertilization on Phenolics of Rapeseeds and Their Antioxidant Potential. Foods. 2024;13:561.

[36] Crinnion WJ. Organic Foods Contain Higher Levels of Certain Nutrients, Lower Levels of Pesticides, and May Provide Health Benefits for the Consumer. Altern Med Rev. 2010;15:4-11.

[37] Agati G, Tattini M. Multiple functional roles of flavonoids in photoprotection. New Phytol. 2010;186:786-93.

[38] Cubero—Leon E, Rudder O De, Maquet A. Metabolomics for organic food authentication: Results from a long—term field study in carrots. Food Chem. 2018;239:760-70.

[39] FAO. Quality declared seed system. FAO; 2006.

[40] OECD. Seed Schemes Rules and Regulations. OECD; 2026.

[41] Opara LU, Mazaud F. Food Traceability from Field to Plate. Outlook Agric. 2001;30:239—47.

[42] Bayen S, Elliott C, Arlorio M, Ballin NZ, Birse N, Brockmeyer J, et al. Towards a harmonized approach for food authenticity marker validation and accreditation. Trends Food Sci Technol. 2024;149:104550.

[43] Teles D, Silva P, Nascimento W. Vegetable seed production under conventional and organic farming systems. Acta Hortic. 2019;1249:193—4.

[44] Rahman A, Cho B. Assessment of seed quality using non—destructive measurement techniques: a review. Seed Sci Res. 2016;26:285-305.

[45] Rajendra Prasad S. Testing Seed for Quality. In: Seed Science and Technology. Singapore: Springer Nature; 2023. pp. 299-334.

[46] Alves EU, Oliveira APD, Bruno RDLA, Sader R, Alves AU. Rendimento e qualidade fisiológica de sementes de coentro cultivado com adubação orgânica e mineral. Rev Bras Sementes. 2005;27:132-7.

[47] Lappay—Aquino A, Fernandez PG. COMPARATIVE PRODUCTIVITY & SEED QUALITY OF MUNGBEAN GROWN UNDER ORGANIC & CONVENTIONAL PRODUCTION SYSTEMS. Philipp J Crop Sci. 2001;26:45-51.

[48] Dadlani M, Yadava DK. Seed Science and Technology: Biology, Production, Quality. Seed Science and Technology: Biology, Production, Quality. Springer Nature; 2023.

[49] Shatadal P, Jayas DS, Hehn JL, Bulley N. Seed classification using machine vision. Can Agric Eng. 1995;37.

[50] Caramês ETDS, Baqueta MR, Fernández Pierna JA, Pallone JAL, Baeten V. Advanced chemometric discrimination of intact organic and conventional brown rice kernels: Comparing NIR benchtop, hand—held NIR and NIR hyperspectral imaging. J Food Compos Anal. 2025;139:107120.

[51] Shrestha S, Knapič M, Žibrat U, Deleuran LC, Gislum R. Single seed near—infrared hyperspectral imaging in determining tomato (Solanum lycopersicum L.) seed quality in association with multivariate data analysis . Sens Actuators B: Chem. 2016;237:1027—34.

[52] Denis A, Desclee B, Migdall S, Hansen H, Bach H, Ott P, et al. Multispectral Remote Sensing as a Tool to Support Organic Crop Certification: Assessment of the Discrimination Level between Organic and Conventional Maize. Remote Sensing. 2021;13:117.

[53] Danezis GP, Tsagkaris AS, Camin F, Brusic V, Georgiou CA. Food authentication: Techniques, trends & emerging approaches. TrAC Trends Anal Chem. 2016;85:123—32.

[54] Capuano E, Boerrigter—Eenling R, van der Veer G, van Ruth SM. Analytical authentication of organic products: An overview of markers. J Sci Food Agric. 2013;93:12-28.

[55] Meyvisch T, Willems E, Everaert M. Micronutrient Seed Coatings of Layered Double Hydroxides Overcome Seedling Toxicity and Improve Micronutrient Uptake in Comparison with Soluble Micronutrient Coatings. J Agric Food Chem. 2025;73:1131—44.

[56] Bings NH, Bogaerts A, Broekaert JA. Atomic Spectroscopy: A Review. Anal Chem. 2010;82:4653-81.

[57] Laursen KH, Mihailova A, Kelly SD, Epov VN, Bérail S, Schjoerring JK, et al. Is it really organic?—Multi—isotopic analysis as a tool to discriminate between organic and conventional plants. Food Chem. 2013;141:2812—20.

[58] Laursen K, Schjoerring J, Kelly S, Husted S. Authentication of organically grown plants—advantages and limitations of atomic spectroscopy for multi—element and stable isotope analysis. TrAC Trends Anal Chem. 2014;59:73-82.

[59] Mihailova A, Pedentchouk N, Kelly SD. Stable isotope analysis of plant—derived nitrate—Novel method for discrimination between organically and conventionally grown vegetables. Food Chem. 2014;154:238-45.

[60] Rossi L, Costantini ML, Brilli M. Does stable isotope analysis separate transgenic and traditional corn (Zea mays L.) detritus and their consumers? Appl Soil Ecol. 2007;35:449-53.

[61] Ferrari AA, De Nadai Fernandes EA, Tagliaferro FS, Bacchi MA, Martins TCG. Chemical composition of tomato seeds affected by conventional and organic production systems. J Radioanal Nucl Chem. 2008;278:399-402.

[62] Fattobene M, Liu F, Conti P, Zamponi S, Governatori C, Nardi S, et al. Distribution of Elements in Durum Wheat Seed and Milling Products: Discrimination between Cultivation Methods through Multivariate Data Analysis. Foods. 2024;13:1924.

[63] Westermann D, Terán H, Muñoz—Perea C, Singh S. Plant and seed nutrient uptake in common bean in seven organic and conventional production systems. Can J Plant Sci. 2011;91:1089-99.

[64] Suzui N, Tanoi K, Furukawa J, Kawachi N. Recent Advances in Radioisotope Imaging Technology for Plant Science Research in Japan. Quantum Beam Sci. 2019;3:18.

[65] Pedrini S, Merritt DJ, Stevens J, Dixon K. Seed Coating: Science or Marketing Spin? Trends Plant Sci. 2017;22:106—16.

[66] Medina S, Perestrelo R, Silva P, Pereira JA, Câmara JS. Current trends and recent advances on food authenticity technologies and chemometric approaches. Trends Food Sci Technol. 2019;85:163-76.

[67] Valderrama P, S. Bruni AR. A Practical Guide to Verify which Analytical Techniques and Organic Foods have Already been Investigated. J Braz Chem Soc. 2025;36:e20240208.

[68] Lopes CRB, da Silva HDT, Courrol LC. Fluorescence spectroscopy study of conventional and organic soybean oil heated to 270°C. 2021 SBFot Int Opt Photonics Conf (SBFot IOPC). 2021:1-4.

[69] Terskikh V, Kermode AR. In Vivo Nuclear Magnetic Resonance Metabolite Profiling in Plant Seeds. Methods Mol Biol. 2011;773:307—18.

[70] Consonni R, Polla D, Cagliani LR. Organic and conventional coffee differentiation by NMR spectroscopy. Food Control. 2018;94:284—8.

[71] Esteki M, Shahsavari Z, Simal—Gandara J. Use of spectroscopic methods in combination with linear discriminant analysis for authentication of food products. Food Control. 2018;91:100-12.

[72] Griffiths PR, de Haseth JA. Fourier Transform Infrared Spectrometry. Wiley; 2006.

[73] Ambrose A, Lohumi S, Lee WH, Cho BK. Comparative nondestructive measurement of corn seed viability using Fourier transform near—infrared (FT—NIR) and Raman spectroscopy. Sens Actuators B Chem. 2016;224:500-6.

[74] Kusumaningrum D, Lee H, Lohumi S, Mo C, Kim MS, Cho BK. Non—destructive technique for determining the viability of soybean (Glycine max) seeds using FT—NIR spectroscopy . J Sci Food Agric. 2017;98:1734—42.

[75] Jia B, Wang W, Ni X, Chu X, Yoon S, Lawrence K. Detection of mycotoxins and toxigenic fungi in cereal grains using vibrational spectroscopic techniques: a review. World Mycotoxin J. 2020;13:163-78.

[76] Radulescu C, Olteanu RL, Nicolescu CM, Bumbac M, Buruleanu LC, Holban GC. Vibrational Spectroscopy Combined with Chemometrics as Tool for Discriminating Organic vs. Conventional Culture Systems for Red Grape Extracts. Foods. 2021;10:1856.

[77] Gordillo—Delgado F, Zárate—Rincón F, Mejía—Morales C. COMPARISON BETWEEN CONVENTIONAL AND ORGANIC RICE USING PHOTOACOUSTIC TECHNIQUE. Dyna (Medellin). 2012;79:7-13.

[78] Pérez—López R, Guardiola—Albert C, Felpeto A, Sanz—Mangas D, Méndez—Chazarra N, Abella R, et al. Investigating Coffee Samples by Raman Spectroscopy for Quality Control—Preliminary Study. Int J Exp Spectrosc Tech. 2016;16:1-5.

[79] Noriega P, Gortaire G, Osorio E. Mass Spectrometry and Its Importance for the Analysis and Discovery of Active Molecules in Natural Products. In: Natural Drugs from Plants. IntechOpen; 2022.

[80] Nawrocki A, Thorup—Kristensen K, Jensen ON. Quantitative proteomics by 2DE and MALDI MS/MS uncover the effects of organic and conventional cropping methods on vegetable products. J Proteomics. 2011;74:2810-25.

[81] Xie P, Chen J, Xia Y, Cai Z. MALDI and MALDI—2 mass spectrometry imaging contribute to revealing the alternations in lipid metabolism in germinating soybean seeds. Chin Chem Lett. 2025;36:110595.

[82] Pesavento IC, Bertazzo A, Flamini R, Vedova AD, De Rosso M, Seraglia R, et al. Differentiation ofVitis vinifera varieties by MALDI—MS analysis of the grape seed proteins . J Mass Spectrom. 2007;43:234-41.

[83] Cattaneo C, Givonetti A, Cavaletto M. Protein Mass Fingerprinting and Antioxidant Power of Hemp Seeds in Relation to Plant Cultivar and Environment. Plants. 2023;12:782.

[84] Wadood SA, Boli G, Xiaowen Z, Hussain I, Yimin W. Recent development in the application of analytical techniques for the traceability and authenticity of food of plant origin. Microchem J. 2020;152:104295.

[85] Esteki M, Simal—Gandara J, Shahsavari Z, Zandbaaf S, Dashtaki E, Vander Heyden Y. A review on the application of chromatographic methods, coupled to chemometrics, for food authentication. Food Control. 2018;93:165-82.

[86] Dadwal V, Jha DK, Joshi R, Balyan S, Patil BS. LC—MS—based metabolomics: targeted and untargeted analysis of phytochemicals. In: Phytochemical Analysis by Modern Techniques. Elsevier; 2026. pp. 351-78.

[87] Oliveira LFC, Pereira TFD, Matos TS, Sawaya ACHF, Sussulini A. Sustainable food metabolome: Discrimination of agroecological, organic, and conventional pinto beans (Phaseolus vulgaris L.) through the volatile organic compounds profile . Microchem J. 2024;200:110374.

[88] Liang S, Jiang Y, Zhang M. Integrative analysis of the effects of organic and conventional farming methods on peanut based on transcriptome and metabolomics. Food Res Int. 2023;171:113065.

[89] Bonte A, Neuweger H, Goesmann A, Thonar C, Mäder P, Langenkämper G, et al. Metabolite profiling on wheat grain to enable a distinction of samples from organic and conventional farming systems. J Sci Food Agric. 2014;94:2605—12.

[90] Varunjikar M, Bøhn T, Sanden M, Belghit I, Pineda—Pampliega J, Palmblad M, et al. Proteomics analyses of herbicide—tolerant genetically modified, conventionally, and organically farmed soybean seeds. Food Control. 2023;151:109795.

[91] Röhlig RM, Engel KH. Influence of the Input System (Conventional versus Organic Farming) on Metabolite Profiles of Maize (Zea mays) Kernels . J Agric Food Chem. 2010;58:3022—30.

[92] Mihailova A, Kelly SD, Chevallier OP, Elliott CT, Maestroni BM, Cannavan A. High—resolution mass spectrometry—based metabolomics for the discrimination between organic and conventional crops: A review. Trends Food Sci Technol. 2021;110:142-54.

[93] Rocchetti G, Senizza B, Zengin G, Bonini P, Bontempo L, Camin F, et al. The hierarchical contribution of organic vs. conventional farming, cultivar, and terroir on untargeted metabolomics phytochemical profile and functional traits of tomato fruits. Front Plant Sci. 2022;13:856513.

[94] Li W, Wu Z, Xu Y, Long H, Deng Y, Li S, et al. Emerging LC—MS/MS—based molecular networking strategy facilitates foodomics to assess the function, safety, and quality of foods: recent trends and future perspectives. Trends Food Sci Technol. 2023;139:104114.

[95] Videometer[Internet]. Videometer; [cited 2026 Mar 18]. Available from: https://videometer.com/

[96] Terskikh VV, Feurtado JA, Borchardt S, Giblin M, Abrams SR, Kermode AR. In vivo 13C NMR metabolite profiling: potential for understanding and assessing conifer seed quality. J Exp Bot. 2005;56:2253—65.