Haplotype-phased genomes elucidate genetic architecture of environmental adaptation and domestication traits in Silphium

Haplotype-phased genomes elucidate genetic architecture of environmental adaptation and domestication traits in Silphium | 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 Article Haplotype-phased genomes elucidate genetic architecture of environmental adaptation and domestication traits in Silphium David Van Tassel, Renan Souza, Josh Clevenger, Jerry Jenkins, and 19 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-8753360/v1 This work is licensed under a CC BY 4.0 License Status: Under Review Version 1 posted You are reading this latest preprint version Abstract Developing native perennial crops is vital for climate-resilient agriculture, yet their domestication is often hindered by a lack of cost-effective genomic resources. To build a framework for genomics-accelerated domestication of perennials with large, complex genomes, we generated chromosome-scale, haplotype-phased assemblies for Silphium integrifolium Michx. and Silphium perfoliatum L., two deep-rooted native North American prairie species valued for drought tolerance and oil production. The genomes are characterized by the presence of a putative helical structure preserved during interphase with a loop circumference of 43 Mb. Using targeted sequencing of 14 Silphium species, we first refined the phylogeny of the genus, recovering the Composita and Silphium subgenera while identifying taxonomic discrepancies. We used a combination of low-coverage short-read sequencing and target-sequencing to characterize a 258-accession diversity panel to define ancestral populations and perform genome-wide association studies (GWAS) on several traits. We identified 81 loci associated with environmental adaptation and domestication traits; notably, variants in a MATE transporter, Alpha-Beta hydrolase and a ACR4 -related protein explained significant variance in seed number and floral architecture. These findings establish the genomic framework necessary to accelerate the domestication of Silphium and provide a model for unlocking the potential of other complex wild genomes. Biological sciences/Plant sciences/Plant breeding Biological sciences/Genetics/Genomics/Comparative genomics Biological sciences/Plant sciences/Plant genetics Biological sciences/Plant sciences/Plant domestication Biological sciences/Cell biology/Chromosomes Full Text Additional Declarations There is NO Competing Interest. Supplementary Files silphiumsupplementaryfilefinal.xlsx Supplementary data silphiumsupplementaryfiguresandtablesfinal.docx Supplementary figures and tables sintegrifolium.ann.5.7617700679632.zip Data Cite Share Download PDF Status: Under Review 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-8753360","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Article","associatedPublications":[],"authors":[{"id":586498911,"identity":"2ac27033-be9d-4b02-a8a0-692964480a78","order_by":0,"name":"David Van 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