Molecular Characterization of Iranian pomegranate germplasm by using GBS analysis

Molecular Characterization of Iranian pomegranate germplasm by using GBS analysis | 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 Molecular Characterization of Iranian pomegranate germplasm by using GBS analysis Sara Razi, Ali Soleimani, Mehrshad Zeinalabedini, Mohammad Reza Vazifeshenas, and 1 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-8783530/v1 This work is licensed under a CC BY 4.0 License Status: Under Revision Version 1 posted 4 You are reading this latest preprint version Abstract Pomegranate ( Punica granatum L.) is a perennial fruit tree native to Iran and the Himalayan Mountains in northern India. In this study, genotyping-by-sequencing (GBS) approach was used for calling single nucleotide polymorphisms (SNPs) as well as genetic variation analysis in a collection of 214 Iranian accessions from different regions. All these individuals were grouped as commercial, wild, base and Ornamental-Pharmaceutical ones. A total of 281514 variants (259,268 SNPs, 11,311 insertions and 10,935 deletions) were identified. The average values of expected heterozygosity (He) and observed heterozygosity (Ho) were 0.22 and 0.26, respectively. The commercial and base groups showed the highest allelic richness. Harmonized results of genetic diversity, allelic richness and genetic differentiation strengthens the hypothesis that most current commercial trees have originated directly from wild genotypes through selection and introduction process rather than classic parental breeding or inbreeding programs. The structure and principal component analyses (PCA) clustered all accessions into three main groups with no special relationship with their geographical origin. For the first time, the LD pattern was investigated in the assayed population, and a partly rapid LD decay with a short range (∼250bp) for all pseudo chromosomes was revealed. This study provides new evidence for research areas in future marker-assisted selective approaches and genome-wide association analyses in pomegranate trees. Pomegranate Molecular marker linkage disequilibrium mapping Genotyping-by-sequencing Single nucleotide polymorphisms Full Text Additional Declarations No competing interests reported. Supplementary Files Razietal.SupplementaryMaterial.docx Cite Share Download PDF Status: Under Revision Version 1 posted Editorial decision: Revision requested 05 Apr, 2026 Editor assigned by journal 05 Feb, 2026 Submission checks completed at journal 05 Feb, 2026 First submitted to journal 04 Feb, 2026 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-8783530","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":617980507,"identity":"d954bc7c-b31e-430e-b041-b160e1c035aa","order_by":0,"name":"Sara Razi","email":"","orcid":"","institution":"Zanjan University","correspondingAuthor":false,"prefix":"","firstName":"Sara","middleName":"","lastName":"Razi","suffix":""},{"id":617980508,"identity":"d7588b3a-7ac4-4d74-acb7-a02724a213d4","order_by":1,"name":"Ali Soleimani","email":"","orcid":"","institution":"Zanjan 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In this study, genotyping-by-sequencing (GBS) approach was used for calling single nucleotide polymorphisms (SNPs) as well as genetic variation analysis in a collection of 214 Iranian accessions from different regions. All these individuals were grouped as commercial, wild, base and Ornamental-Pharmaceutical ones. A total of 281514 variants (259,268 SNPs, 11,311 insertions and 10,935 deletions) were identified. The average values of expected heterozygosity (He) and observed heterozygosity (Ho) were 0.22 and 0.26, respectively. The commercial and base groups showed the highest allelic richness. Harmonized results of genetic diversity, allelic richness and genetic differentiation strengthens the hypothesis that most current commercial trees have originated directly from wild genotypes through selection and introduction process rather than classic parental breeding or inbreeding programs. The structure and principal component analyses (PCA) clustered all accessions into three main groups with no special relationship with their geographical origin. For the first time, the LD pattern was investigated in the assayed population, and a partly rapid LD decay with a short range (\u0026sim;250bp) for all pseudo chromosomes was revealed. 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