{"id":6228,"date":"2026-05-06T10:03:36","date_gmt":"2026-05-06T10:03:36","guid":{"rendered":"https:\/\/agrosynapsis.com\/?p=6228"},"modified":"2026-05-06T10:04:43","modified_gmt":"2026-05-06T10:04:43","slug":"how-do-i-decide-whether-to-use-biparental-qtl-mapping-or-gwas-for-marker-discovery","status":"publish","type":"post","link":"https:\/\/agrosynapsis.com\/es\/how-do-i-decide-whether-to-use-biparental-qtl-mapping-or-gwas-for-marker-discovery\/","title":{"rendered":"How do I decide whether to use biparental QTL mapping or GWAS for marker discovery?"},"content":{"rendered":"

\u00a0I received this question from someone in the audience during my lecture at the Department of Crop Science of the Agricultural University of Athens<\/a> on February 17.
Since I like to address real questions coming from real breeding and research projects, here\u2019s a step-by-step way to choose the right approach \ud83d\udc47

\ud835\udc12\ud835\udc2d\ud835\udc1e\ud835\udc29 \ud835\udfcf: Define your breeding goal
Ask yourself:
\ud83d\udd39 Do I want to rapidly develop a robust, diagnostic marker for selection within a specific breeding program?
\u2192 Biparental QTL mapping
\ud83d\udd39 Or do I want to understand the genetic architecture of a trait at the species level?
\u2192 GWAS

\ud835\udc12\ud835\udc2d\ud835\udc1e\ud835\udc29 \ud835\udfd0: Look at the genetic structure of the trait
\u2705 Choose biparental QTL mapping if:
– The trait is controlled by a rare gene
(e.g. a disease resistance coming from a unique wild accession)
– The trait segregates clearly between two parents
– You aim to build a Marker-Assisted Selection (MAS) tool for a specific breeding program
\ud83d\udc49 QTL mapping offers high detection power, low noise, and fast, clear interpretation.

\ud835\udc12\ud835\udc2d\ud835\udc1e\ud835\udc29 \ud835\udfd1: Assess your genomic and genotypic resources
\u2705 Choose biparental QTL mapping if:
– You are working with a new or orphan species
– A high-quality reference genome is missing
– There is limited access to high-throughput genotyping
\ud83d\udc49 Controlled crosses can work very well with a moderate number of markers, provided they homogeneously cover the genome.

\ud835\udc12\ud835\udc2d\ud835\udc1e\ud835\udc29 \ud835\udfd2: Consider population size & diversity
\u2705 Choose GWAS if:
– You have access to diverse germplasm (e.g. from a gene bank) or a pool of elite breeding liness
– You are studying a complex trait
(e.g. yield, stress tolerance, fruit quality such as Brix in tomato)
– You want to capture multiple alleles across the species
\ud83d\udc49 GWAS leverages historical recombination and broader genetic diversity.

\ud835\udc12\ud835\udc2d\ud835\udc1e\ud835\udc29 \ud835\udfd3: Think ahead to Genomic Selection
\u2705 Choose GWAS if:
– You are developing or training Genomic Selection (GS) models
– You need genotype\u2013phenotype relationships across many genetic backgrounds
\ud83d\udc49 GWAS is often part of the GS data ecosystem, rather than a standalone goal.

Final takeaway
When genotyping resources are limited and the favorable genotype is confined to one or very few lines, biparental QTL mapping provides a straightforward and powerful approach for rapid marker discovery.

\ud83d\udc49 If you\u2019d like to be informed about the upcoming workshops organized by AgroSynapsis, and receive early access and discounts, \ud835\uddf3\ud835\uddf6\ud835\uddf9\ud835\uddf9 \ud835\uddfc\ud835\ude02\ud835\ude01 \ud835\uddfc\ud835\ude02\ud835\uddff \ud835\ude00\ud835\uddf5\ud835\uddfc\ud835\uddff\ud835\ude01 \ud835\ude01\ud835\uddff\ud835\uddee\ud835\uddf6\ud835\uddfb\ud835\uddf6\ud835\uddfb\ud835\uddf4 \ud835\uddf6\ud835\uddfb\ud835\ude01\ud835\uddf2\ud835\uddff\ud835\uddf2\ud835\ude00\ud835\ude01 \ud835\uddf3\ud835\uddfc\ud835\uddff\ud835\uddfa here:

https:\/\/lnkd.in\/g3tApqPz<\/a><\/p>\n

<\/div>","protected":false},"excerpt":{"rendered":"

Discover how to choose between QTL mapping and GWAS based on your breeding goals, trait genetics, and available resources.<\/p>","protected":false},"author":2,"featured_media":6211,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_jetpack_memberships_contains_paid_content":false,"footnotes":""},"categories":[68],"tags":[],"class_list":["post-6228","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-tips"],"yoast_head":"\nHow do I decide whether to use biparental QTL mapping or GWAS for marker discovery? - AgroSynapsis<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/agrosynapsis.com\/es\/how-do-i-decide-whether-to-use-biparental-qtl-mapping-or-gwas-for-marker-discovery\/\" \/>\n<meta property=\"og:locale\" content=\"es_ES\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"How do I decide whether to use biparental QTL mapping or GWAS for marker discovery? - AgroSynapsis\" \/>\n<meta property=\"og:description\" content=\"Discover how to choose between QTL mapping and GWAS based on your breeding goals, trait genetics, and available resources.\" \/>\n<meta property=\"og:url\" content=\"https:\/\/agrosynapsis.com\/es\/how-do-i-decide-whether-to-use-biparental-qtl-mapping-or-gwas-for-marker-discovery\/\" \/>\n<meta property=\"og:site_name\" content=\"AgroSynapsis\" \/>\n<meta property=\"article:published_time\" content=\"2026-05-06T10:03:36+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2026-05-06T10:04:43+00:00\" \/>\n<meta property=\"og:image\" content=\"https:\/\/agrosynapsis.com\/wp-content\/uploads\/2026\/05\/5.jpg\" \/>\n\t<meta property=\"og:image:width\" content=\"1200\" \/>\n\t<meta property=\"og:image:height\" content=\"1200\" \/>\n\t<meta property=\"og:image:type\" content=\"image\/jpeg\" \/>\n<meta name=\"author\" content=\"Rachil Koumproglou\" \/>\n<meta name=\"twitter:card\" content=\"summary_large_image\" \/>\n<meta name=\"twitter:label1\" content=\"Escrito por\" \/>\n\t<meta name=\"twitter:data1\" content=\"Rachil Koumproglou\" \/>\n\t<meta name=\"twitter:label2\" content=\"Tiempo de lectura\" \/>\n\t<meta name=\"twitter:data2\" content=\"2 minutos\" \/>\n<script type=\"application\/ld+json\" class=\"yoast-schema-graph\">{\"@context\":\"https:\/\/schema.org\",\"@graph\":[{\"@type\":\"Article\",\"@id\":\"https:\/\/agrosynapsis.com\/how-do-i-decide-whether-to-use-biparental-qtl-mapping-or-gwas-for-marker-discovery\/#article\",\"isPartOf\":{\"@id\":\"https:\/\/agrosynapsis.com\/how-do-i-decide-whether-to-use-biparental-qtl-mapping-or-gwas-for-marker-discovery\/\"},\"author\":{\"name\":\"Rachil Koumproglou\",\"@id\":\"https:\/\/agrosynapsis.com\/#\/schema\/person\/ae7208ed31d8f16389985557afe894e8\"},\"headline\":\"How do I decide whether to use biparental QTL mapping or GWAS for marker discovery?\",\"datePublished\":\"2026-05-06T10:03:36+00:00\",\"dateModified\":\"2026-05-06T10:04:43+00:00\",\"mainEntityOfPage\":{\"@id\":\"https:\/\/agrosynapsis.com\/how-do-i-decide-whether-to-use-biparental-qtl-mapping-or-gwas-for-marker-discovery\/\"},\"wordCount\":388,\"commentCount\":0,\"publisher\":{\"@id\":\"https:\/\/agrosynapsis.com\/#organization\"},\"image\":{\"@id\":\"https:\/\/agrosynapsis.com\/how-do-i-decide-whether-to-use-biparental-qtl-mapping-or-gwas-for-marker-discovery\/#primaryimage\"},\"thumbnailUrl\":\"https:\/\/agrosynapsis.com\/wp-content\/uploads\/2026\/05\/5.jpg\",\"articleSection\":[\"tips\"],\"inLanguage\":\"es\",\"potentialAction\":[{\"@type\":\"CommentAction\",\"name\":\"Comment\",\"target\":[\"https:\/\/agrosynapsis.com\/how-do-i-decide-whether-to-use-biparental-qtl-mapping-or-gwas-for-marker-discovery\/#respond\"]}]},{\"@type\":\"WebPage\",\"@id\":\"https:\/\/agrosynapsis.com\/how-do-i-decide-whether-to-use-biparental-qtl-mapping-or-gwas-for-marker-discovery\/\",\"url\":\"https:\/\/agrosynapsis.com\/how-do-i-decide-whether-to-use-biparental-qtl-mapping-or-gwas-for-marker-discovery\/\",\"name\":\"How do I decide whether to use biparental QTL mapping or GWAS for marker discovery? - AgroSynapsis\",\"isPartOf\":{\"@id\":\"https:\/\/agrosynapsis.com\/#website\"},\"primaryImageOfPage\":{\"@id\":\"https:\/\/agrosynapsis.com\/how-do-i-decide-whether-to-use-biparental-qtl-mapping-or-gwas-for-marker-discovery\/#primaryimage\"},\"image\":{\"@id\":\"https:\/\/agrosynapsis.com\/how-do-i-decide-whether-to-use-biparental-qtl-mapping-or-gwas-for-marker-discovery\/#primaryimage\"},\"thumbnailUrl\":\"https:\/\/agrosynapsis.com\/wp-content\/uploads\/2026\/05\/5.jpg\",\"datePublished\":\"2026-05-06T10:03:36+00:00\",\"dateModified\":\"2026-05-06T10:04:43+00:00\",\"breadcrumb\":{\"@id\":\"https:\/\/agrosynapsis.com\/how-do-i-decide-whether-to-use-biparental-qtl-mapping-or-gwas-for-marker-discovery\/#breadcrumb\"},\"inLanguage\":\"es\",\"potentialAction\":[{\"@type\":\"ReadAction\",\"target\":[\"https:\/\/agrosynapsis.com\/how-do-i-decide-whether-to-use-biparental-qtl-mapping-or-gwas-for-marker-discovery\/\"]}]},{\"@type\":\"ImageObject\",\"inLanguage\":\"es\",\"@id\":\"https:\/\/agrosynapsis.com\/how-do-i-decide-whether-to-use-biparental-qtl-mapping-or-gwas-for-marker-discovery\/#primaryimage\",\"url\":\"https:\/\/agrosynapsis.com\/wp-content\/uploads\/2026\/05\/5.jpg\",\"contentUrl\":\"https:\/\/agrosynapsis.com\/wp-content\/uploads\/2026\/05\/5.jpg\",\"width\":1200,\"height\":1200},{\"@type\":\"BreadcrumbList\",\"@id\":\"https:\/\/agrosynapsis.com\/how-do-i-decide-whether-to-use-biparental-qtl-mapping-or-gwas-for-marker-discovery\/#breadcrumb\",\"itemListElement\":[{\"@type\":\"ListItem\",\"position\":1,\"name\":\"Home\",\"item\":\"https:\/\/agrosynapsis.com\/\"},{\"@type\":\"ListItem\",\"position\":2,\"name\":\"How do I decide whether to use biparental QTL mapping or GWAS for marker discovery?\"}]},{\"@type\":\"WebSite\",\"@id\":\"https:\/\/agrosynapsis.com\/#website\",\"url\":\"https:\/\/agrosynapsis.com\/\",\"name\":\"AgroSynapsis\",\"description\":\"\",\"publisher\":{\"@id\":\"https:\/\/agrosynapsis.com\/#organization\"},\"potentialAction\":[{\"@type\":\"SearchAction\",\"target\":{\"@type\":\"EntryPoint\",\"urlTemplate\":\"https:\/\/agrosynapsis.com\/?s={search_term_string}\"},\"query-input\":\"required name=search_term_string\"}],\"inLanguage\":\"es\"},{\"@type\":\"Organization\",\"@id\":\"https:\/\/agrosynapsis.com\/#organization\",\"name\":\"AgroSynapsis\",\"url\":\"https:\/\/agrosynapsis.com\/\",\"logo\":{\"@type\":\"ImageObject\",\"inLanguage\":\"es\",\"@id\":\"https:\/\/agrosynapsis.com\/#\/schema\/logo\/image\/\",\"url\":\"https:\/\/agrosynapsis.com\/wp-content\/uploads\/2024\/10\/logo-sin-fondo.png\",\"contentUrl\":\"https:\/\/agrosynapsis.com\/wp-content\/uploads\/2024\/10\/logo-sin-fondo.png\",\"width\":506,\"height\":134,\"caption\":\"AgroSynapsis\"},\"image\":{\"@id\":\"https:\/\/agrosynapsis.com\/#\/schema\/logo\/image\/\"}},{\"@type\":\"Person\",\"@id\":\"https:\/\/agrosynapsis.com\/#\/schema\/person\/ae7208ed31d8f16389985557afe894e8\",\"name\":\"Rachil Koumproglou\",\"image\":{\"@type\":\"ImageObject\",\"inLanguage\":\"es\",\"@id\":\"https:\/\/agrosynapsis.com\/#\/schema\/person\/image\/\",\"url\":\"https:\/\/secure.gravatar.com\/avatar\/59151e2a1e54e4386f583749402ab932771ebea8516b0ea81c6646b49cf3d960?s=96&d=mm&r=g\",\"contentUrl\":\"https:\/\/secure.gravatar.com\/avatar\/59151e2a1e54e4386f583749402ab932771ebea8516b0ea81c6646b49cf3d960?s=96&d=mm&r=g\",\"caption\":\"Rachil Koumproglou\"},\"sameAs\":[\"http:\/\/agrosynapsis.com\/\"],\"url\":\"https:\/\/agrosynapsis.com\/es\/author\/rachil-koumproglou\/\"}]}<\/script>\n<!-- \/ Yoast SEO plugin. -->","yoast_head_json":{"title":"How do I decide whether to use biparental QTL mapping or GWAS for marker discovery? - AgroSynapsis","robots":{"index":"index","follow":"follow","max-snippet":"max-snippet:-1","max-image-preview":"max-image-preview:large","max-video-preview":"max-video-preview:-1"},"canonical":"https:\/\/agrosynapsis.com\/es\/how-do-i-decide-whether-to-use-biparental-qtl-mapping-or-gwas-for-marker-discovery\/","og_locale":"es_ES","og_type":"article","og_title":"How do I decide whether to use biparental QTL mapping or GWAS for marker discovery? - AgroSynapsis","og_description":"Discover how to choose between QTL mapping and GWAS based on your breeding goals, trait genetics, and available resources.","og_url":"https:\/\/agrosynapsis.com\/es\/how-do-i-decide-whether-to-use-biparental-qtl-mapping-or-gwas-for-marker-discovery\/","og_site_name":"AgroSynapsis","article_published_time":"2026-05-06T10:03:36+00:00","article_modified_time":"2026-05-06T10:04:43+00:00","og_image":[{"width":1200,"height":1200,"url":"https:\/\/agrosynapsis.com\/wp-content\/uploads\/2026\/05\/5.jpg","type":"image\/jpeg"}],"author":"Rachil Koumproglou","twitter_card":"summary_large_image","twitter_misc":{"Escrito por":"Rachil Koumproglou","Tiempo de lectura":"2 minutos"},"schema":{"@context":"https:\/\/schema.org","@graph":[{"@type":"Article","@id":"https:\/\/agrosynapsis.com\/how-do-i-decide-whether-to-use-biparental-qtl-mapping-or-gwas-for-marker-discovery\/#article","isPartOf":{"@id":"https:\/\/agrosynapsis.com\/how-do-i-decide-whether-to-use-biparental-qtl-mapping-or-gwas-for-marker-discovery\/"},"author":{"name":"Rachil Koumproglou","@id":"https:\/\/agrosynapsis.com\/#\/schema\/person\/ae7208ed31d8f16389985557afe894e8"},"headline":"How do I decide whether to use biparental QTL mapping or GWAS for marker discovery?","datePublished":"2026-05-06T10:03:36+00:00","dateModified":"2026-05-06T10:04:43+00:00","mainEntityOfPage":{"@id":"https:\/\/agrosynapsis.com\/how-do-i-decide-whether-to-use-biparental-qtl-mapping-or-gwas-for-marker-discovery\/"},"wordCount":388,"commentCount":0,"publisher":{"@id":"https:\/\/agrosynapsis.com\/#organization"},"image":{"@id":"https:\/\/agrosynapsis.com\/how-do-i-decide-whether-to-use-biparental-qtl-mapping-or-gwas-for-marker-discovery\/#primaryimage"},"thumbnailUrl":"https:\/\/agrosynapsis.com\/wp-content\/uploads\/2026\/05\/5.jpg","articleSection":["tips"],"inLanguage":"es","potentialAction":[{"@type":"CommentAction","name":"Comment","target":["https:\/\/agrosynapsis.com\/how-do-i-decide-whether-to-use-biparental-qtl-mapping-or-gwas-for-marker-discovery\/#respond"]}]},{"@type":"WebPage","@id":"https:\/\/agrosynapsis.com\/how-do-i-decide-whether-to-use-biparental-qtl-mapping-or-gwas-for-marker-discovery\/","url":"https:\/\/agrosynapsis.com\/how-do-i-decide-whether-to-use-biparental-qtl-mapping-or-gwas-for-marker-discovery\/","name":"How do I decide whether to use biparental QTL mapping or GWAS for marker discovery? - AgroSynapsis","isPartOf":{"@id":"https:\/\/agrosynapsis.com\/#website"},"primaryImageOfPage":{"@id":"https:\/\/agrosynapsis.com\/how-do-i-decide-whether-to-use-biparental-qtl-mapping-or-gwas-for-marker-discovery\/#primaryimage"},"image":{"@id":"https:\/\/agrosynapsis.com\/how-do-i-decide-whether-to-use-biparental-qtl-mapping-or-gwas-for-marker-discovery\/#primaryimage"},"thumbnailUrl":"https:\/\/agrosynapsis.com\/wp-content\/uploads\/2026\/05\/5.jpg","datePublished":"2026-05-06T10:03:36+00:00","dateModified":"2026-05-06T10:04:43+00:00","breadcrumb":{"@id":"https:\/\/agrosynapsis.com\/how-do-i-decide-whether-to-use-biparental-qtl-mapping-or-gwas-for-marker-discovery\/#breadcrumb"},"inLanguage":"es","potentialAction":[{"@type":"ReadAction","target":["https:\/\/agrosynapsis.com\/how-do-i-decide-whether-to-use-biparental-qtl-mapping-or-gwas-for-marker-discovery\/"]}]},{"@type":"ImageObject","inLanguage":"es","@id":"https:\/\/agrosynapsis.com\/how-do-i-decide-whether-to-use-biparental-qtl-mapping-or-gwas-for-marker-discovery\/#primaryimage","url":"https:\/\/agrosynapsis.com\/wp-content\/uploads\/2026\/05\/5.jpg","contentUrl":"https:\/\/agrosynapsis.com\/wp-content\/uploads\/2026\/05\/5.jpg","width":1200,"height":1200},{"@type":"BreadcrumbList","@id":"https:\/\/agrosynapsis.com\/how-do-i-decide-whether-to-use-biparental-qtl-mapping-or-gwas-for-marker-discovery\/#breadcrumb","itemListElement":[{"@type":"ListItem","position":1,"name":"Home","item":"https:\/\/agrosynapsis.com\/"},{"@type":"ListItem","position":2,"name":"How do I decide whether to use biparental QTL mapping or GWAS for marker discovery?"}]},{"@type":"WebSite","@id":"https:\/\/agrosynapsis.com\/#website","url":"https:\/\/agrosynapsis.com\/","name":"AgroSynapsis","description":"","publisher":{"@id":"https:\/\/agrosynapsis.com\/#organization"},"potentialAction":[{"@type":"SearchAction","target":{"@type":"EntryPoint","urlTemplate":"https:\/\/agrosynapsis.com\/?s={search_term_string}"},"query-input":"required name=search_term_string"}],"inLanguage":"es"},{"@type":"Organization","@id":"https:\/\/agrosynapsis.com\/#organization","name":"AgroSynapsis","url":"https:\/\/agrosynapsis.com\/","logo":{"@type":"ImageObject","inLanguage":"es","@id":"https:\/\/agrosynapsis.com\/#\/schema\/logo\/image\/","url":"https:\/\/agrosynapsis.com\/wp-content\/uploads\/2024\/10\/logo-sin-fondo.png","contentUrl":"https:\/\/agrosynapsis.com\/wp-content\/uploads\/2024\/10\/logo-sin-fondo.png","width":506,"height":134,"caption":"AgroSynapsis"},"image":{"@id":"https:\/\/agrosynapsis.com\/#\/schema\/logo\/image\/"}},{"@type":"Person","@id":"https:\/\/agrosynapsis.com\/#\/schema\/person\/ae7208ed31d8f16389985557afe894e8","name":"Rachil Koumproglou","image":{"@type":"ImageObject","inLanguage":"es","@id":"https:\/\/agrosynapsis.com\/#\/schema\/person\/image\/","url":"https:\/\/secure.gravatar.com\/avatar\/59151e2a1e54e4386f583749402ab932771ebea8516b0ea81c6646b49cf3d960?s=96&d=mm&r=g","contentUrl":"https:\/\/secure.gravatar.com\/avatar\/59151e2a1e54e4386f583749402ab932771ebea8516b0ea81c6646b49cf3d960?s=96&d=mm&r=g","caption":"Rachil Koumproglou"},"sameAs":["http:\/\/agrosynapsis.com\/"],"url":"https:\/\/agrosynapsis.com\/es\/author\/rachil-koumproglou\/"}]}},"jetpack_featured_media_url":"https:\/\/agrosynapsis.com\/wp-content\/uploads\/2026\/05\/5.jpg","jetpack_sharing_enabled":true,"_links":{"self":[{"href":"https:\/\/agrosynapsis.com\/es\/wp-json\/wp\/v2\/posts\/6228","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/agrosynapsis.com\/es\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/agrosynapsis.com\/es\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/agrosynapsis.com\/es\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/agrosynapsis.com\/es\/wp-json\/wp\/v2\/comments?post=6228"}],"version-history":[{"count":2,"href":"https:\/\/agrosynapsis.com\/es\/wp-json\/wp\/v2\/posts\/6228\/revisions"}],"predecessor-version":[{"id":6230,"href":"https:\/\/agrosynapsis.com\/es\/wp-json\/wp\/v2\/posts\/6228\/revisions\/6230"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/agrosynapsis.com\/es\/wp-json\/wp\/v2\/media\/6211"}],"wp:attachment":[{"href":"https:\/\/agrosynapsis.com\/es\/wp-json\/wp\/v2\/media?parent=6228"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/agrosynapsis.com\/es\/wp-json\/wp\/v2\/categories?post=6228"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/agrosynapsis.com\/es\/wp-json\/wp\/v2\/tags?post=6228"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}