{"id":6243,"date":"2026-05-06T10:18:11","date_gmt":"2026-05-06T10:18:11","guid":{"rendered":"https:\/\/agrosynapsis.com\/?p=6243"},"modified":"2026-05-06T10:18:14","modified_gmt":"2026-05-06T10:18:14","slug":"linkage-disequilibrium-in-breeding-from-alleles-to-gwas-signals","status":"publish","type":"post","link":"https:\/\/agrosynapsis.com\/es\/linkage-disequilibrium-in-breeding-from-alleles-to-gwas-signals\/","title":{"rendered":"Linkage Disequilibrium in Breeding: From Alleles to GWAS Signals"},"content":{"rendered":"

If you want to truly understand how GWAS works, there is one concept you cannot skip:

\ud83d\udc49 Linkage Disequilibrium (LD)
What does it mean?
In simple terms, LD occurs when certain allele combinations appear together in a population more often than expected by chance. If alleles were inherited independently, their combinations would be random\u2014but LD tells us they are not.

\ud83d\udc49A simple example
Imagine two SNPs:
SNP1: A \/ a
SNP2: B \/ b
If the combination A\u2013B appears much more frequently than expected in our population, these loci are said to be in LD. Measuring LD allows us to quantify how strongly alleles co-occur on the same chromosome, which is the foundation for detecting marker\u2013trait associations in GWAS.

\ud83d\udc49Why does LD happen?
The most intuitive reason is physical proximity. Loci that are close together on a chromosome are less likely to be separated by recombination, so they tend to be inherited together.
However, LD is influenced by more than just distance. It is also shaped by:
1. Recombination rate
2. Population bottlenecks and founder effects
3. Genetic drift
4. Population admixture

In the context of a breeding program, \ud835\udc29\ud835\udc28\ud835\udc29\ud835\udc2e\ud835\udc25\ud835\udc1a\ud835\udc2d\ud835\udc22\ud835\udc28\ud835\udc27 \ud835\udc1a\ud835\udc1d\ud835\udc26\ud835\udc22\ud835\udc31\ud835\udc2d\ud835\udc2e\ud835\udc2b\ud835\udc1e is often the most important factor to consider before running GWAS.

Here\u2019s a practical example:
You mix two genetically distinct populations:
Population A: high fruit firmness
Population B: low firmness but high sugar content

Each population carries its own allele combinations. After mixing them, you create an admixed population where alleles from both sources coexist.

Now, some allele combinations (e.g., the firmness allele from A + nearby SNPs) appear together not because of physical linkage, but because they came from the same ancestral population. This can create long-range LD, even between loci on different chromosomes.

\u274cThis type of LD matters for GWAS because it may generate false positives, where a marker appears associated with a trait simply because it tracks population origin rather than causality.

\ud83d\udc49 How to avoid false positives due to population admixture
1\ufe0f\u20e3Run GWAS within a single, relatively uniform population.
2\ufe0f\u20e3Or, if using an admixed population, focus on traits not related to the phenotypic differences between the parental populations (e.g., disease resistance rather than fruit quality).
3\ufe0f\u20e3Use statistical models that account for population structure and relatedness.

\ud83d\udc49 If you\u2019d like to be informed about the upcoming workshops organized by AgroSynapsis<\/a>, 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 linkage disequilibrium drives GWAS and why population structure can create misleading associations if not properly controlled.<\/p>","protected":false},"author":2,"featured_media":6217,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_jetpack_memberships_contains_paid_content":false,"footnotes":""},"categories":[46],"tags":[],"class_list":["post-6243","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-knowledge-bites"],"yoast_head":"\nLinkage Disequilibrium in Breeding: From Alleles to GWAS Signals - 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\/linkage-disequilibrium-in-breeding-from-alleles-to-gwas-signals\/\" \/>\n<meta property=\"og:locale\" content=\"es_ES\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Linkage Disequilibrium in Breeding: From Alleles to GWAS Signals - AgroSynapsis\" \/>\n<meta property=\"og:description\" content=\"Discover how linkage disequilibrium drives GWAS and why population structure can create misleading associations if not properly controlled.\" \/>\n<meta property=\"og:url\" content=\"https:\/\/agrosynapsis.com\/es\/linkage-disequilibrium-in-breeding-from-alleles-to-gwas-signals\/\" \/>\n<meta property=\"og:site_name\" content=\"AgroSynapsis\" \/>\n<meta property=\"article:published_time\" content=\"2026-05-06T10:18:11+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2026-05-06T10:18:14+00:00\" \/>\n<meta property=\"og:image\" content=\"https:\/\/agrosynapsis.com\/wp-content\/uploads\/2026\/05\/Post-de-Instagram-Checklist-Residuos-Sostenible-Medioambiente-Ecologico-Sencillo-Corporativo-Verde-1.jpg\" \/>\n\t<meta property=\"og:image:width\" content=\"1080\" \/>\n\t<meta property=\"og:image:height\" content=\"1350\" \/>\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\/linkage-disequilibrium-in-breeding-from-alleles-to-gwas-signals\/#article\",\"isPartOf\":{\"@id\":\"https:\/\/agrosynapsis.com\/linkage-disequilibrium-in-breeding-from-alleles-to-gwas-signals\/\"},\"author\":{\"name\":\"Rachil Koumproglou\",\"@id\":\"https:\/\/agrosynapsis.com\/#\/schema\/person\/ae7208ed31d8f16389985557afe894e8\"},\"headline\":\"Linkage Disequilibrium in Breeding: From Alleles to GWAS Signals\",\"datePublished\":\"2026-05-06T10:18:11+00:00\",\"dateModified\":\"2026-05-06T10:18:14+00:00\",\"mainEntityOfPage\":{\"@id\":\"https:\/\/agrosynapsis.com\/linkage-disequilibrium-in-breeding-from-alleles-to-gwas-signals\/\"},\"wordCount\":396,\"commentCount\":0,\"publisher\":{\"@id\":\"https:\/\/agrosynapsis.com\/#organization\"},\"image\":{\"@id\":\"https:\/\/agrosynapsis.com\/linkage-disequilibrium-in-breeding-from-alleles-to-gwas-signals\/#primaryimage\"},\"thumbnailUrl\":\"https:\/\/agrosynapsis.com\/wp-content\/uploads\/2026\/05\/Post-de-Instagram-Checklist-Residuos-Sostenible-Medioambiente-Ecologico-Sencillo-Corporativo-Verde-1.jpg\",\"articleSection\":[\"Knowledge Bites\"],\"inLanguage\":\"es\",\"potentialAction\":[{\"@type\":\"CommentAction\",\"name\":\"Comment\",\"target\":[\"https:\/\/agrosynapsis.com\/linkage-disequilibrium-in-breeding-from-alleles-to-gwas-signals\/#respond\"]}]},{\"@type\":\"WebPage\",\"@id\":\"https:\/\/agrosynapsis.com\/linkage-disequilibrium-in-breeding-from-alleles-to-gwas-signals\/\",\"url\":\"https:\/\/agrosynapsis.com\/linkage-disequilibrium-in-breeding-from-alleles-to-gwas-signals\/\",\"name\":\"Linkage Disequilibrium in Breeding: From Alleles to GWAS Signals - AgroSynapsis\",\"isPartOf\":{\"@id\":\"https:\/\/agrosynapsis.com\/#website\"},\"primaryImageOfPage\":{\"@id\":\"https:\/\/agrosynapsis.com\/linkage-disequilibrium-in-breeding-from-alleles-to-gwas-signals\/#primaryimage\"},\"image\":{\"@id\":\"https:\/\/agrosynapsis.com\/linkage-disequilibrium-in-breeding-from-alleles-to-gwas-signals\/#primaryimage\"},\"thumbnailUrl\":\"https:\/\/agrosynapsis.com\/wp-content\/uploads\/2026\/05\/Post-de-Instagram-Checklist-Residuos-Sostenible-Medioambiente-Ecologico-Sencillo-Corporativo-Verde-1.jpg\",\"datePublished\":\"2026-05-06T10:18:11+00:00\",\"dateModified\":\"2026-05-06T10:18:14+00:00\",\"breadcrumb\":{\"@id\":\"https:\/\/agrosynapsis.com\/linkage-disequilibrium-in-breeding-from-alleles-to-gwas-signals\/#breadcrumb\"},\"inLanguage\":\"es\",\"potentialAction\":[{\"@type\":\"ReadAction\",\"target\":[\"https:\/\/agrosynapsis.com\/linkage-disequilibrium-in-breeding-from-alleles-to-gwas-signals\/\"]}]},{\"@type\":\"ImageObject\",\"inLanguage\":\"es\",\"@id\":\"https:\/\/agrosynapsis.com\/linkage-disequilibrium-in-breeding-from-alleles-to-gwas-signals\/#primaryimage\",\"url\":\"https:\/\/agrosynapsis.com\/wp-content\/uploads\/2026\/05\/Post-de-Instagram-Checklist-Residuos-Sostenible-Medioambiente-Ecologico-Sencillo-Corporativo-Verde-1.jpg\",\"contentUrl\":\"https:\/\/agrosynapsis.com\/wp-content\/uploads\/2026\/05\/Post-de-Instagram-Checklist-Residuos-Sostenible-Medioambiente-Ecologico-Sencillo-Corporativo-Verde-1.jpg\",\"width\":1080,\"height\":1350},{\"@type\":\"BreadcrumbList\",\"@id\":\"https:\/\/agrosynapsis.com\/linkage-disequilibrium-in-breeding-from-alleles-to-gwas-signals\/#breadcrumb\",\"itemListElement\":[{\"@type\":\"ListItem\",\"position\":1,\"name\":\"Home\",\"item\":\"https:\/\/agrosynapsis.com\/\"},{\"@type\":\"ListItem\",\"position\":2,\"name\":\"Linkage Disequilibrium in Breeding: From Alleles to GWAS Signals\"}]},{\"@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":"Linkage Disequilibrium in Breeding: From Alleles to GWAS Signals - 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\/linkage-disequilibrium-in-breeding-from-alleles-to-gwas-signals\/","og_locale":"es_ES","og_type":"article","og_title":"Linkage Disequilibrium in Breeding: From Alleles to GWAS Signals - AgroSynapsis","og_description":"Discover how linkage disequilibrium drives GWAS and why population structure can create misleading associations if not properly controlled.","og_url":"https:\/\/agrosynapsis.com\/es\/linkage-disequilibrium-in-breeding-from-alleles-to-gwas-signals\/","og_site_name":"AgroSynapsis","article_published_time":"2026-05-06T10:18:11+00:00","article_modified_time":"2026-05-06T10:18:14+00:00","og_image":[{"width":1080,"height":1350,"url":"https:\/\/agrosynapsis.com\/wp-content\/uploads\/2026\/05\/Post-de-Instagram-Checklist-Residuos-Sostenible-Medioambiente-Ecologico-Sencillo-Corporativo-Verde-1.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\/linkage-disequilibrium-in-breeding-from-alleles-to-gwas-signals\/#article","isPartOf":{"@id":"https:\/\/agrosynapsis.com\/linkage-disequilibrium-in-breeding-from-alleles-to-gwas-signals\/"},"author":{"name":"Rachil Koumproglou","@id":"https:\/\/agrosynapsis.com\/#\/schema\/person\/ae7208ed31d8f16389985557afe894e8"},"headline":"Linkage Disequilibrium in Breeding: From Alleles to GWAS Signals","datePublished":"2026-05-06T10:18:11+00:00","dateModified":"2026-05-06T10:18:14+00:00","mainEntityOfPage":{"@id":"https:\/\/agrosynapsis.com\/linkage-disequilibrium-in-breeding-from-alleles-to-gwas-signals\/"},"wordCount":396,"commentCount":0,"publisher":{"@id":"https:\/\/agrosynapsis.com\/#organization"},"image":{"@id":"https:\/\/agrosynapsis.com\/linkage-disequilibrium-in-breeding-from-alleles-to-gwas-signals\/#primaryimage"},"thumbnailUrl":"https:\/\/agrosynapsis.com\/wp-content\/uploads\/2026\/05\/Post-de-Instagram-Checklist-Residuos-Sostenible-Medioambiente-Ecologico-Sencillo-Corporativo-Verde-1.jpg","articleSection":["Knowledge Bites"],"inLanguage":"es","potentialAction":[{"@type":"CommentAction","name":"Comment","target":["https:\/\/agrosynapsis.com\/linkage-disequilibrium-in-breeding-from-alleles-to-gwas-signals\/#respond"]}]},{"@type":"WebPage","@id":"https:\/\/agrosynapsis.com\/linkage-disequilibrium-in-breeding-from-alleles-to-gwas-signals\/","url":"https:\/\/agrosynapsis.com\/linkage-disequilibrium-in-breeding-from-alleles-to-gwas-signals\/","name":"Linkage Disequilibrium in Breeding: From Alleles to GWAS Signals - AgroSynapsis","isPartOf":{"@id":"https:\/\/agrosynapsis.com\/#website"},"primaryImageOfPage":{"@id":"https:\/\/agrosynapsis.com\/linkage-disequilibrium-in-breeding-from-alleles-to-gwas-signals\/#primaryimage"},"image":{"@id":"https:\/\/agrosynapsis.com\/linkage-disequilibrium-in-breeding-from-alleles-to-gwas-signals\/#primaryimage"},"thumbnailUrl":"https:\/\/agrosynapsis.com\/wp-content\/uploads\/2026\/05\/Post-de-Instagram-Checklist-Residuos-Sostenible-Medioambiente-Ecologico-Sencillo-Corporativo-Verde-1.jpg","datePublished":"2026-05-06T10:18:11+00:00","dateModified":"2026-05-06T10:18:14+00:00","breadcrumb":{"@id":"https:\/\/agrosynapsis.com\/linkage-disequilibrium-in-breeding-from-alleles-to-gwas-signals\/#breadcrumb"},"inLanguage":"es","potentialAction":[{"@type":"ReadAction","target":["https:\/\/agrosynapsis.com\/linkage-disequilibrium-in-breeding-from-alleles-to-gwas-signals\/"]}]},{"@type":"ImageObject","inLanguage":"es","@id":"https:\/\/agrosynapsis.com\/linkage-disequilibrium-in-breeding-from-alleles-to-gwas-signals\/#primaryimage","url":"https:\/\/agrosynapsis.com\/wp-content\/uploads\/2026\/05\/Post-de-Instagram-Checklist-Residuos-Sostenible-Medioambiente-Ecologico-Sencillo-Corporativo-Verde-1.jpg","contentUrl":"https:\/\/agrosynapsis.com\/wp-content\/uploads\/2026\/05\/Post-de-Instagram-Checklist-Residuos-Sostenible-Medioambiente-Ecologico-Sencillo-Corporativo-Verde-1.jpg","width":1080,"height":1350},{"@type":"BreadcrumbList","@id":"https:\/\/agrosynapsis.com\/linkage-disequilibrium-in-breeding-from-alleles-to-gwas-signals\/#breadcrumb","itemListElement":[{"@type":"ListItem","position":1,"name":"Home","item":"https:\/\/agrosynapsis.com\/"},{"@type":"ListItem","position":2,"name":"Linkage Disequilibrium in Breeding: From Alleles to GWAS Signals"}]},{"@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\/Post-de-Instagram-Checklist-Residuos-Sostenible-Medioambiente-Ecologico-Sencillo-Corporativo-Verde-1.jpg","jetpack_sharing_enabled":true,"_links":{"self":[{"href":"https:\/\/agrosynapsis.com\/es\/wp-json\/wp\/v2\/posts\/6243","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=6243"}],"version-history":[{"count":1,"href":"https:\/\/agrosynapsis.com\/es\/wp-json\/wp\/v2\/posts\/6243\/revisions"}],"predecessor-version":[{"id":6244,"href":"https:\/\/agrosynapsis.com\/es\/wp-json\/wp\/v2\/posts\/6243\/revisions\/6244"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/agrosynapsis.com\/es\/wp-json\/wp\/v2\/media\/6217"}],"wp:attachment":[{"href":"https:\/\/agrosynapsis.com\/es\/wp-json\/wp\/v2\/media?parent=6243"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/agrosynapsis.com\/es\/wp-json\/wp\/v2\/categories?post=6243"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/agrosynapsis.com\/es\/wp-json\/wp\/v2\/tags?post=6243"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}