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This highlights the need for developing a reproducible panel of markers," /> <meta property="article:author" content="https://uniovi.academia.edu/YaiselJuanBorrellPichs" /> <meta name="description" content="The high number of multiplex PCRs developed for gilthead seabream (Sparus aurata L.) from many different microsatellite markers does not allow comparison among populations. This highlights the need for developing a reproducible panel of markers," /> <title>(PDF) Development of the first standardised panel of two new microsatellite multiplex PCRs for gilthead seabream (Sparus aurata L.) | Yaisel Juan Borrell Pichs - Academia.edu</title> <link rel="canonical" href="https://www.academia.edu/13299765/Development_of_the_first_standardised_panel_of_two_new_microsatellite_multiplex_PCRs_for_gilthead_seabream_Sparus_aurata_L_" /> <script async src="https://www.googletagmanager.com/gtag/js?id=G-5VKX33P2DS"></script> <script> window.dataLayer = window.dataLayer || []; function gtag(){dataLayer.push(arguments);} gtag('js', new Date()); gtag('config', 'G-5VKX33P2DS', { cookie_domain: 'academia.edu', send_page_view: false, }); gtag('event', 'page_view', { 'controller': "single_work", 'action': "show", 'controller_action': 'single_work#show', 'logged_in': 'false', 'edge': 'unknown', // Send nil if there is no A/B test bucket, in case some records get logged // with missing data - that way we can distinguish between the two cases. // ab_test_bucket should be of the form <ab_test_name>:<bucket> 'ab_test_bucket': null, }) </script> <script> var $controller_name = 'single_work'; var $action_name = "show"; var $rails_env = 'production'; var $app_rev = '92477ec68c09d28ae4730a4143c926f074776319'; var $domain = 'academia.edu'; var $app_host = "academia.edu"; var $asset_host = "academia-assets.com"; var $start_time = new Date().getTime(); var $recaptcha_key = "6LdxlRMTAAAAADnu_zyLhLg0YF9uACwz78shpjJB"; var $recaptcha_invisible_key = "6Lf3KHUUAAAAACggoMpmGJdQDtiyrjVlvGJ6BbAj"; var $disableClientRecordHit = false; </script> <script> window.require = { config: function() { return function() {} } } </script> <script> window.Aedu = window.Aedu || {}; window.Aedu.hit_data = null; window.Aedu.serverRenderTime = new Date(1732790881000); window.Aedu.timeDifference = new Date().getTime() - 1732790881000; </script> <script type="application/ld+json">{"@context":"https://schema.org","@type":"ScholarlyArticle","abstract":"The high number of multiplex PCRs developed for gilthead seabream (Sparus aurata L.) from many different microsatellite markers does not allow comparison among populations. This highlights the need for developing a reproducible panel of markers, which can be used with safety and reliability by all users. In this study, the first standardised panel of two new microsatellite multiplex PCRs was developed for this species. Primers of 138 specific microsatellites from the genetic linkage map were redesigned and evaluated according to their genetic variability, allele size range and genotyping reliability. A protocol to identify and classify genotyping errors or potential errors was proposed to assess the reliability of each marker. Two new multiplex PCRs from the best assessed markers were designed with 11 markers in each, named SMsa1 and SMsa2 (SuperMultiplex Sparus aurata). Three broodstocks (59, 47 and 98 breeders) from different Spanish companies, and a sample of 80 offspring from each one, were analysed to validate the usefulness of these multiplexes in the parental assignation. It was possible to assign each offspring to a single parent pair (100% success) using the exclusion method with SMsa1 and/or SMsa2. In each genotyped a reference sample (Ref-sa) was used, and its DNA is available on request similar to the kits of bin set to genotype by GENEMAPPER (v.3.7) software (kit-SMsa1 and kit-SMsa2). This will be a robust and effective tool for pedigree analysis or characterisation of populations and will be proposed as an international panel for this species.","author":[{"@context":"https://schema.org","@type":"Person","name":"Yaisel Juan Borrell Pichs"}],"contributor":[],"dateCreated":"2015-10-28","dateModified":"2015-10-28","datePublished":null,"headline":"Development of the first standardised panel of two new microsatellite multiplex PCRs for gilthead seabream (Sparus aurata L.)","inLanguage":"en","keywords":["Aquaculture","Microsatellite Markers","multiplex PCR","Sparus Aurata"],"locationCreated":null,"publication":null,"publisher":{"@context":"https://schema.org","@type":"Organization","name":null},"image":null,"thumbnailUrl":null,"url":"https://www.academia.edu/17413469/Development_of_the_first_standardised_panel_of_two_new_microsatellite_multiplex_PCRs_for_gilthead_seabream_Sparus_aurata_L_","sourceOrganization":[{"@context":"https://schema.org","@type":"EducationalOrganization","name":"uniovi"}]}</script><link rel="stylesheet" media="all" href="//a.academia-assets.com/assets/single_work_page/loswp-102fa537001ba4d8dcd921ad9bd56c474abc201906ea4843e7e7efe9dfbf561d.css" /><link rel="stylesheet" media="all" href="//a.academia-assets.com/assets/design_system/body-8d679e925718b5e8e4b18e9a4fab37f7eaa99e43386459376559080ac8f2856a.css" /><link rel="stylesheet" media="all" href="//a.academia-assets.com/assets/design_system/button-3cea6e0ad4715ed965c49bfb15dedfc632787b32ff6d8c3a474182b231146ab7.css" /><link rel="stylesheet" media="all" 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[{"id":39493704,"identifier":"Attachment_39493704","shouldShowBulkDownload":false}]; window.loswp.shouldDetectTimezone = true; window.loswp.shouldShowBulkDownload = true; window.loswp.showSignupCaptcha = false window.loswp.willEdgeCache = false; window.loswp.work = {"work":{"id":17413469,"created_at":"2015-10-28T06:19:09.155-07:00","from_world_paper_id":null,"updated_at":"2021-01-14T02:01:02.896-08:00","_data":{"abstract":"The high number of multiplex PCRs developed for gilthead seabream (Sparus aurata L.) from\nmany different microsatellite markers does not allow comparison among populations. This\nhighlights the need for developing a reproducible panel of markers, which can be used with\nsafety and reliability by all users. In this study, the first standardised panel of two new\nmicrosatellite multiplex PCRs was developed for this species. Primers of 138 specific\nmicrosatellites from the genetic linkage map were redesigned and evaluated according to\ntheir genetic variability, allele size range and genotyping reliability. A protocol to identify\nand classify genotyping errors or potential errors was proposed to assess the reliability of\neach marker. Two new multiplex PCRs from the best assessed markers were designed with\n11 markers in each, named SMsa1 and SMsa2 (SuperMultiplex Sparus aurata). Three\nbroodstocks (59, 47 and 98 breeders) from different Spanish companies, and a sample of 80\noffspring from each one, were analysed to validate the usefulness of these multiplexes in the\nparental assignation. It was possible to assign each offspring to a single parent pair (100%\nsuccess) using the exclusion method with SMsa1 and/or SMsa2. In each genotyped a\nreference sample (Ref-sa) was used, and its DNA is available on request similar to the kits of\nbin set to genotype by GENEMAPPER (v.3.7) software (kit-SMsa1 and kit-SMsa2). This will be a\nrobust and effective tool for pedigree analysis or characterisation of populations and will be\nproposed as an international panel for this species."},"document_type":"paper","pre_hit_view_count_baseline":null,"quality":"high","language":"en","title":"Development of the first standardised panel of two new microsatellite multiplex PCRs for gilthead seabream (Sparus aurata L.)","broadcastable":false,"draft":null,"has_indexable_attachment":true,"indexable":true}}["work"]; window.loswp.workCoauthors = [4373077]; window.loswp.locale = "en"; window.loswp.countryCode = "SG"; window.loswp.cwvAbTestBucket = ""; window.loswp.designVariant = "ds_vanilla"; window.loswp.fullPageMobileSutdModalVariant = "full_page_mobile_sutd_modal"; window.loswp.useOptimizedScribd4genScript = false; window.loswp.appleClientId = 'edu.academia.applesignon';</script><script defer="" src="https://accounts.google.com/gsi/client"></script><div class="ds-loswp-container"><div class="ds-work-card--grid-container"><div class="ds-work-card--container js-loswp-work-card"><div class="ds-work-card--cover"><div class="ds-work-cover--wrapper"><div class="ds-work-cover--container"><button class="ds-work-cover--clickable js-swp-download-button" data-signup-modal="{"location":"swp-splash-paper-cover","attachmentId":39493704,"attachmentType":"pdf"}"><img alt="First page of “Development of the first standardised panel of two new microsatellite multiplex PCRs for gilthead seabream (Sparus aurata L.)”" class="ds-work-cover--cover-thumbnail" src="https://0.academia-photos.com/attachment_thumbnails/39493704/mini_magick20190222-9684-1c3r5z7.png?1550892081" /><img alt="PDF Icon" class="ds-work-cover--file-icon" src="//a.academia-assets.com/assets/single_work_splash/adobe.icon-574afd46eb6b03a77a153a647fb47e30546f9215c0ee6a25df597a779717f9ef.svg" /><div class="ds-work-cover--hover-container"><span class="material-symbols-outlined" style="font-size: 20px" translate="no">download</span><p>Download Free PDF</p></div><div class="ds-work-cover--ribbon-container">Download Free PDF</div><div class="ds-work-cover--ribbon-triangle"></div></button></div></div></div><div class="ds-work-card--work-information"><h1 class="ds-work-card--work-title">Development of the first standardised panel of two new microsatellite multiplex PCRs for gilthead seabream (Sparus aurata L.)</h1><div class="ds-work-card--work-authors ds-work-card--detail"><a class="ds-work-card--author js-wsj-grid-card-author ds2-5-body-md ds2-5-body-link" data-author-id="4373077" href="https://uniovi.academia.edu/YaiselJuanBorrellPichs"><img alt="Profile image of Yaisel Juan Borrell Pichs" class="ds-work-card--author-avatar" src="https://0.academia-photos.com/4373077/1766728/32208411/s65_yaisel_juan.borrell_pichs.jpg" />Yaisel Juan Borrell Pichs</a></div><div class="ds-work-card--detail"></div><p class="ds-work-card--work-abstract ds-work-card--detail ds2-5-body-md">The high number of multiplex PCRs developed for gilthead seabream (Sparus aurata L.) from many different microsatellite markers does not allow comparison among populations. This highlights the need for developing a reproducible panel of markers, which can be used with safety and reliability by all users. In this study, the first standardised panel of two new microsatellite multiplex PCRs was developed for this species. Primers of 138 specific microsatellites from the genetic linkage map were redesigned and evaluated according to their genetic variability, allele size range and genotyping reliability. A protocol to identify and classify genotyping errors or potential errors was proposed to assess the reliability of each marker. Two new multiplex PCRs from the best assessed markers were designed with 11 markers in each, named SMsa1 and SMsa2 (SuperMultiplex Sparus aurata). Three broodstocks (59, 47 and 98 breeders) from different Spanish companies, and a sample of 80 offspring from each one, were analysed to validate the usefulness of these multiplexes in the parental assignation. It was possible to assign each offspring to a single parent pair (100% success) using the exclusion method with SMsa1 and/or SMsa2. In each genotyped a reference sample (Ref-sa) was used, and its DNA is available on request similar to the kits of bin set to genotype by GENEMAPPER (v.3.7) software (kit-SMsa1 and kit-SMsa2). This will be a robust and effective tool for pedigree analysis or characterisation of populations and will be proposed as an international panel for this species.</p><div class="ds-work-card--button-container"><button class="ds2-5-button js-swp-download-button" data-signup-modal="{"location":"continue-reading-button--work-card","attachmentId":39493704,"attachmentType":"pdf","workUrl":"https://www.academia.edu/17413469/Development_of_the_first_standardised_panel_of_two_new_microsatellite_multiplex_PCRs_for_gilthead_seabream_Sparus_aurata_L_"}">See full PDF</button><button class="ds2-5-button ds2-5-button--secondary js-swp-download-button" data-signup-modal="{"location":"download-pdf-button--work-card","attachmentId":39493704,"attachmentType":"pdf","workUrl":"https://www.academia.edu/17413469/Development_of_the_first_standardised_panel_of_two_new_microsatellite_multiplex_PCRs_for_gilthead_seabream_Sparus_aurata_L_"}"><span class="material-symbols-outlined" style="font-size: 20px" translate="no">download</span>Download PDF</button></div></div></div></div><div data-auto_select="false" data-client_id="331998490334-rsn3chp12mbkiqhl6e7lu2q0mlbu0f1b" data-doc_id="39493704" data-landing_url="https://www.academia.edu/17413469/Development_of_the_first_standardised_panel_of_two_new_microsatellite_multiplex_PCRs_for_gilthead_seabream_Sparus_aurata_L_" data-login_uri="https://www.academia.edu/registrations/google_one_tap" data-moment_callback="onGoogleOneTapEvent" id="g_id_onload"></div><div class="ds-top-related-works--grid-container"><div class="ds-related-content--container ds-top-related-works--container"><h2 class="ds-related-content--heading">Related papers</h2><div class="ds-related-work--container js-wsj-grid-card" data-collection-position="0" data-entity-id="5609035" data-sort-order="default"><a class="ds-related-work--title js-wsj-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/5609035/A_microsatellite_marker_tool_for_parentage_assessment_in_gilthead_seabream_Sparus_aurata">A microsatellite marker tool for parentage assessment in gilthead seabream ( Sparus aurata</a><div class="ds-related-work--metadata"><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="8024194" href="https://usc-es.academia.edu/JaimeCastro">Jaime Castro</a></div><p class="ds-related-work--metadata ds2-5-body-xs">Aquaculture, 2007</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"A microsatellite marker tool for parentage assessment in gilthead seabream ( Sparus aurata","attachmentId":49219692,"attachmentType":"pdf","work_url":"https://www.academia.edu/5609035/A_microsatellite_marker_tool_for_parentage_assessment_in_gilthead_seabream_Sparus_aurata","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-wsj-grid-card-view-pdf" href="https://www.academia.edu/5609035/A_microsatellite_marker_tool_for_parentage_assessment_in_gilthead_seabream_Sparus_aurata"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-wsj-grid-card" data-collection-position="1" data-entity-id="120308334" data-sort-order="default"><a class="ds-related-work--title js-wsj-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/120308334/Development_and_characterization_of_twelve_new_microsatellite_markers_for_gilthead_seabream_Sparus_aurata_">Development and characterization of twelve new microsatellite markers for gilthead seabream (Sparus aurata)</a><div class="ds-related-work--metadata"><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="306076452" href="https://independent.academia.edu/AnnaPozzi9">Anna Pozzi</a></div><p class="ds-related-work--abstract ds2-5-body-sm">Gilthead seabream (Sparus aurata) represents one of the most important species for aquaculture in the Mediterranean region and its interest in selective breeding programs is increasing, given the evidence of large potential gains for selective improvement of economical traits. 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In addition, we tested 11 already published microsatellite markers which were originally developed for the congeneric species, the Pectoral Sandpiper (C. melanotos). All loci were polymorphic, but five of the cross-species loci were not scorable due to suboptimal amplification patterns. The 12 successful loci were tested on 87 individuals, yielding an average of 9.0 (range 4–19) alleles per locus and mean expected heterozygosity of 0.70. Because this dataset contained families, tests for Hardy–Weinberg equilibrium, linkage disequilibrium and probability of identity were done on a subset of the data containing 25 adults caught in the same year. The overall probability of identity was 1.0 9 10-13. Only one locus displayed significant homozygote excess and all loci were unlinked. On the basis of female heterozygotes, all loci are assumed to be autosomal.</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"Novel and cross-species microsatellite markers for parentage analysis in Sanderling Calidris alba","attachmentId":5016262,"attachmentType":"pdf","work_url":"https://www.academia.edu/834947/Novel_and_cross_species_microsatellite_markers_for_parentage_analysis_in_Sanderling_Calidris_alba","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-wsj-grid-card-view-pdf" href="https://www.academia.edu/834947/Novel_and_cross_species_microsatellite_markers_for_parentage_analysis_in_Sanderling_Calidris_alba"><span 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Calcaterra</a></div><p class="ds-related-work--metadata ds2-5-body-xs">Journal of Fish Biology, 2015</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"Isolation and characterization of 20 polymorphic microsatellite loci in the migratory freshwater fish \u003ci\u003eLeporinus obtusidens\u003c/i\u003e (Characiformes: Anostomidae) using 454 shotgun pyrosequencing","attachmentId":109079086,"attachmentType":"pdf","work_url":"https://www.academia.edu/111582130/Isolation_and_characterization_of_20_polymorphic_microsatellite_loci_in_the_migratory_freshwater_fish_i_Leporinus_obtusidens_i_Characiformes_Anostomidae_using_454_shotgun_pyrosequencing","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a 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microsatellite multiplex PCRs for three sparid species: Gilthead seabream (Sparus auratus L.), red porgy (Pagrus pagrus L.) and redbanded seabream (P. auriga, Valenciennes, 1843) and their application to paternity studies</a><div class="ds-related-work--metadata"><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="41398918" href="https://independent.academia.edu/Mar%C3%ADaZamorano">María Zamorano</a></div><p class="ds-related-work--metadata ds2-5-body-xs">Aquaculture, 2008</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"Development of two new microsatellite multiplex PCRs for three sparid species: Gilthead seabream (Sparus auratus L.), red porgy (Pagrus pagrus L.) and redbanded seabream (P. auriga, Valenciennes, 1843) and their application to paternity 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