Integrative Biochemical and Genetic Analysis of Basil (Ocimum basilicum L.) Genotypes: Uncovering SNP Variations and Metabolic Pathway Links

Integrative Biochemical and Genetic Analysis of Basil (Ocimum basilicum L.) Genotypes: Uncovering SNP Variations and Metabolic Pathway Links | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Research Article Integrative Biochemical and Genetic Analysis of Basil (Ocimum basilicum L.) Genotypes: Uncovering SNP Variations and Metabolic Pathway Links Essam Y. Abdul-Hafeez, Khalaf R. Al-Rashidi, Mohamed I. Motawei This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-9322850/v1 This work is licensed under a CC BY 4.0 License Status: Posted Version 1 posted You are reading this latest preprint version Abstract Basil (Ocimum basilicum) exhibits remarkable biochemical and genetic diversity, yet the integration of genotype-specific metabolic profiles with molecular markers remains underexplored. This study characterizes three representative genotypes—Genovese, French, and Purple—using comprehensive biochemical assays, SSR and SNP markers, and multivariate analyses. Genovese basil showed the highest essential oil content (2.30%) and elevated flavonoids (rutin 40.0 μg mL⁻¹, luteolin 30.0 μg mL⁻¹), French basil accumulated caffeic (76.3 μg mL⁻¹) and benzoic acids (46.2 μg mL⁻¹), and Purple basil contained maximal apigenin (49.0 μg mL⁻¹) and hydroxycinnamic acids (coumaric 44.0 μg/mL, ferulic 23.5 μg mL⁻¹), revealing metabolic trade-offs between terpenoid and phenylpropanoid pathways. Pearson correlation and PCA confirmed coordinated regulation of metabolites and clearly separated genotypes based on biochemical specialization. SSR markers revealed 70% polymorphism, clustering French and Genovese together, while Purple formed a distinct lineage. Targeted SNP analysis identified genotype-specific nucleotide variations within amplified genomic regions, providing additional molecular signatures for genotype discrimination. The integration of biochemical traits with SNP-based clustering provides strong evidence that metabolic variation in basil is genetically structured. The identification of metabolite clusters linked to specific SNP groups offers crucial insights into the genetic basis of secondary metabolism, paving the way for enhanced breeding strategies aimed at optimizing aromatic plant traits. Ocimum basilicum SSR markers SNP markers essential oil phenolic acids flavonoids genetic diversity Full Text Additional Declarations No competing interests reported. Cite Share Download PDF Status: Posted Version 1 posted You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. We do this by developing innovative software and high quality services for the global research community. Our growing team is made up of researchers and industry professionals working together to solve the most critical problems facing scientific publishing. Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-9322850","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":622752205,"identity":"8e1ed38c-6cd6-479b-8b59-0bac71010bee","order_by":0,"name":"Essam Y. 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This study characterizes three representative genotypes—Genovese, French, and Purple—using comprehensive biochemical assays, SSR and SNP markers, and multivariate analyses. Genovese basil showed the highest essential oil content (2.30%) and elevated flavonoids (rutin 40.0 μg mL⁻¹, luteolin 30.0 μg mL⁻¹), French basil accumulated caffeic (76.3 μg mL⁻¹) and benzoic acids (46.2 μg mL⁻¹), and Purple basil contained maximal apigenin (49.0 μg mL⁻¹) and hydroxycinnamic acids (coumaric 44.0 μg/mL, ferulic 23.5 μg mL⁻¹), revealing metabolic trade-offs between terpenoid and phenylpropanoid pathways. Pearson correlation and PCA confirmed coordinated regulation of metabolites and clearly separated genotypes based on biochemical specialization. SSR markers revealed 70% polymorphism, clustering French and Genovese together, while Purple formed a distinct lineage. Targeted SNP analysis identified genotype-specific nucleotide variations within amplified genomic regions, providing additional molecular signatures for genotype discrimination. The integration of biochemical traits with SNP-based clustering provides strong evidence that metabolic variation in basil is genetically structured. The identification of metabolite clusters linked to specific SNP groups offers crucial insights into the genetic basis of secondary metabolism, paving the way for enhanced breeding strategies aimed at optimizing aromatic plant traits.","manuscriptTitle":"Integrative Biochemical and Genetic Analysis of Basil (Ocimum basilicum L.) 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