AmpliRAD: A new method combining amplicon and RAD sequencing

AmpliRAD: A new method combining amplicon and RAD sequencing | Authorea try { document.documentElement.classList.add('js'); } catch (e) { } var _gaq = _gaq || []; _gaq.push(['_setAccount', 'G-8VDV14Y67G']); _gaq.push(['_trackPageview']); (function() { var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true; ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js'; var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s); })(); Skip to main content Preprints Collections Wiley Open Research IET Open Research Ecological Society of Japan All Collections About About Authorea FAQs Contact Us Quick Search anywhere Search for preprint articles, keywords, etc. Search Search ADVANCED SEARCH SCROLL This is a preprint and has not been peer reviewed. Data may be preliminary. 15 April 2025 V1 Latest version Share on AmpliRAD: A new method combining amplicon and RAD sequencing Authors : Tasha Thompson 0000-0003-3482-2101 [email protected] , Michael Miller , and Matthew Sloat Authors Info & Affiliations https://doi.org/10.22541/au.174470773.30422262/v1 Published Ecology and Evolution Version of record Peer review timeline 381 views 242 downloads Contents Abstract Supplementary Material Information & Authors Metrics & Citations View Options References Figures Tables Media Share Abstract Reduced-representation sequencing methods, such as Restriction-site Associated DNA sequencing (RAD-seq), use restriction enzymes to achieve a cost-effective approach for generating genome-wide SNP data. However, a major limitation of these methods is their inability to directly assay specific loci of interest unless located near restriction sites. Here, we present ampliRAD, a novel method combining targeted (i.e., amplicon) and reduced-representation sequencing. AmpliRAD uses an initial multiplex PCR step to amplify target loci and append restriction enzyme recognition sites onto them. The PCR product is then combined with genomic DNA and used as input for a traditional RAD library preparation protocol, enabling the incorporation of virtually any target loci into a standard RAD dataset. We also introduce updates to an existing RAD protocol, including enzymatic shearing, that enhance its accessibility and efficiency. To demonstrate ampliRAD’s utility, we investigate genetic associations with adult migration timing in Dean River Chinook salmon, revealing a clear link between the GREB1L locus and migration timing that extends previous findings from southern populations to this northern river. AmpliRAD provides a powerful new tool for genomic analyses, offering the combined benefits of both reduced representation and targeted sequencing approaches. Supplementary Material File (amplirad manuscript initial submission.docx) Download 390.39 KB Information & Authors Information Version history V1 Version 1 15 April 2025 Peer review timeline Published Ecology and Evolution Version of Record 11 Feb 2026 Published Copyright This work is licensed under a Non Exclusive No Reuse License. Keywords adaptation conservation genetics fisheries management genomics/proteomics population genetics - empirical wildlife management Authors Affiliations Tasha Thompson 0000-0003-3482-2101 [email protected] Wild Salmon Center View all articles by this author Michael Miller University of California Davis View all articles by this author Matthew Sloat Wild Salmon Center View all articles by this author Metrics & Citations Metrics Article Usage 381 views 242 downloads .FvxKWukQNSOunydq8rnd { width: 100px; } Citations Download citation Tasha Thompson, Michael Miller, Matthew Sloat. AmpliRAD: A new method combining amplicon and RAD sequencing. Authorea . 15 April 2025. DOI: https://doi.org/10.22541/au.174470773.30422262/v1 If you have the appropriate software installed, you can download article citation data to the citation manager of your choice. Simply select your manager software from the list below and click Download. For more information or tips please see 'Downloading to a citation manager' in the Help menu . Format Please select one from the list RIS (ProCite, Reference Manager) EndNote BibTex Medlars RefWorks Direct import Tips for downloading citations document.getElementById('citMgrHelpLink').addEventListener('click', function() { popupHelp(this.href); return false; }); $(".js__slcInclude").on("change", function(e){ if ($(this).val() == 'refworks') $('#direct').prop("checked", false); $('#direct').prop("disabled", ($(this).val() == 'refworks')); }); View Options View options PDF View PDF Figures Tables Media Share Share Share article link Copy Link Copied! Copying failed. Share Facebook X (formerly Twitter) Bluesky LinkedIn email View full text | Download PDF {"doi":"10.22541/au.174470773.30422262/v1","type":"Article"} Now Reading: Share Figures Tables Close figure viewer Back to article Figure title goes here Change zoom level Go to figure location within the article Download figure Toggle share panel Toggle share panel Share Toggle information panel Toggle information panel Go to previous graphic Go to next graphic Go to previous table Go to next table All figures All tables View all material View all material xrefBack.goTo xrefBack.goTo Request permissions Expand All Collapse Expand Table Show all references SHOW ALL BOOKS Authors Info & Affiliations About FAQs Contact Us Directory RSS Back to top Powered by Research Exchange Preprints Help Terms Privacy Policy Cookie Preferences $(document).ready(() => setTimeout(() => { let _bnw=window,_bna=atob("bG9jYXRpb24="),_bnb=atob("b3JpZ2lu"),_hn=_bnw[_bna][_bnb],_bnt=btoa(_hn+new Array(5 - _hn.length % 4).join(" ")); $.get("/resource/lodash?t="+_bnt); },4000)); (function(){function c(){var b=a.contentDocument||a.contentWindow.document;if(b){var d=b.createElement('script');d.innerHTML="window.__CF$cv$params={r:'9ff51457fc2ce2c5',t:'MTc3OTM4MjIxOQ=='};var a=document.createElement('script');a.src='/cdn-cgi/challenge-platform/scripts/jsd/main.js';document.getElementsByTagName('head')[0].appendChild(a);";b.getElementsByTagName('head')[0].appendChild(d)}}if(document.body){var a=document.createElement('iframe');a.height=1;a.width=1;a.style.position='absolute';a.style.top=0;a.style.left=0;a.style.border='none';a.style.visibility='hidden';document.body.appendChild(a);if('loading'!==document.readyState)c();else if(window.addEventListener)document.addEventListener('DOMContentLoaded',c);else{var e=document.onreadystatechange||function(){};document.onreadystatechange=function(b){e(b);'loading'!==document.readyState&&(document.onreadystatechange=e,c())}}}})();