{"id":6226,"date":"2026-05-06T10:01:42","date_gmt":"2026-05-06T10:01:42","guid":{"rendered":"https:\/\/agrosynapsis.com\/?p=6226"},"modified":"2026-05-06T10:01:48","modified_gmt":"2026-05-06T10:01:48","slug":"how-to-identify-an-ssr-linked-to-a-gene-if-there-is-no-reference-genome","status":"publish","type":"post","link":"https:\/\/agrosynapsis.com\/es\/how-to-identify-an-ssr-linked-to-a-gene-if-there-is-no-reference-genome\/","title":{"rendered":"How to Identify an SSR Linked to a Gene if there is no Reference Genome?"},"content":{"rendered":"<p>In the last post of the <a href=\"https:\/\/www.linkedin.com\/company\/agrosynapsis\/\">AgroSynapsis<\/a> Tip series, I explained how to develop a PCR-detectable SSR marker for a known gene or trait using a public reference genome.<br><br>After that, I received a very relevant question:<br>\u2753 What if there is no reference genome available?<br><br>Here\u2019s the answer \ud83d\udc47<br>\ud835\udfed. \ud835\udde0\ud835\uddee\ud835\uddff\ud835\uddf8\ud835\uddf2\ud835\uddff \ud835\uddf1\ud835\uddf2\ud835\ude03\ud835\uddf2\ud835\uddf9\ud835\uddfc\ud835\uddfd\ud835\uddfa\ud835\uddf2\ud835\uddfb\ud835\ude01\u00a0(sequence-driven approaches)\ud83e\uddec<br>These steps generate candidate SSR markers, but do not yet prove genetic linkage.<br>1\ufe0f\u20e3 Comparative genomics with a related species<br>If a closely related species has a reference genome:<br>\u2022 Identify the orthologous gene or genomic region in a public genome browser.<br>\u2022 Extract flanking sequences (e.g. \u00b150\u2013100 kb).<br>\u2022 Search for SSRs and design primers.<br>\u2022 Test whether the markers transfer to your species.<br><br>2\ufe0f\u20e3 Develop gene-based SSRs from transcriptomic data<br>If the gene sequence is known:<br>\u2022 Identify the EST or transcript corresponding to the candidate gene (via annotation or homology).<br>\u2022 Use CDS, ESTs, or transcriptome assemblies.<br>\u2022 Scan the target transcript for SSR motifs.<br>\u2022 Design primers directly from genic regions.<br><br>3\ufe0f\u20e3 Genome skimming \/ low-coverage sequencing to mine SSRs<br>Even without a full genome:<br>\u2022 Perform genome skimming (low-depth whole-genome sequencing).<br>\u2022 If the gene is known: map reads to the candidate gene or an ortholog.<br>\u2022 Select SSRs in contigs anchored to the gene or its genomic neighborhood.<br><br>\ud835\udfee. \ud835\uddda\ud835\uddf2\ud835\uddfb\ud835\uddf2\ud835\ude01\ud835\uddf6\ud835\uddf0 \ud835\ude03\ud835\uddee\ud835\uddf9\ud835\uddf6\ud835\uddf1\ud835\uddee\ud835\ude01\ud835\uddf6\ud835\uddfc\ud835\uddfb &amp; \ud835\uddef\ud835\uddff\ud835\uddf2\ud835\uddf2\ud835\uddf1\ud835\uddf6\ud835\uddfb\ud835\uddf4 \ud835\uddf1\ud835\uddf2\ud835\uddfd\ud835\uddf9\ud835\uddfc\ud835\ude06\ud835\uddfa\ud835\uddf2\ud835\uddfb\ud835\ude01 \u2705<br>This step confirms linkage and determines whether an SSR is reliable for marker-assisted selection.<br>4\ufe0f\u20e3 Validate SSRs through linkage analysis<br>For traits with clear phenotypes:<br>\u2022 Develop a segregating population (F2, RILs, backcross).<br>\u2022 Genotype parents and progeny with candidate SSRs.<br>\u2022 Identify markers that co-segregate with the trait.<br>\u2022 Estimate recombination frequency between marker and phenotype.<br>\u2022 Validate linkage across multiple populations and environments.<br>\u27a1\ufe0f Only markers with stable, tight linkage should be used in selection.<br><br>\ud83d\udc49 If you\u2019d like to be informed about the upcoming workshops organized by <a href=\"https:\/\/www.linkedin.com\/company\/agrosynapsis\/\">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:<br><br><a href=\"https:\/\/lnkd.in\/g3tApqPz\">https:\/\/lnkd.in\/g3tApqPz<\/a><\/p>\n<div style=\"margin-top: 0px; margin-bottom: 0px;\" class=\"sharethis-inline-share-buttons\" ><\/div>","protected":false},"excerpt":{"rendered":"<p>Discover how to develop SSR markers even without a reference genome, using comparative genomics, transcript data, and low-coverage sequencing.<\/p>","protected":false},"author":2,"featured_media":6210,"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-6226","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-tips"],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v22.9 - 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