{"id":12408,"date":"2019-05-20T16:55:07","date_gmt":"2019-05-20T16:55:07","guid":{"rendered":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/?p=12408"},"modified":"2019-05-23T16:51:50","modified_gmt":"2019-05-23T16:51:50","slug":"how-agriseq-genotyping-technology-supports-agrigenomics-research","status":"publish","type":"post","link":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/how-agriseq-genotyping-technology-supports-agrigenomics-research\/","title":{"rendered":"How AgriSeq Genotyping Technology Supports Agrigenomics Research"},"content":{"rendered":"<p>Agrigenomics is an emerging and ever-more-important field of biology, linking the examination of entire genomes to agricultural outcomes that can affect the lives of vast populations of people. Thermo Fisher Scientific is at the forefront of animal and plant genomics tools, design and data collection, in particular via its Axiom Genotyping Solution, <a href=\"http:\/\/bit.ly\/2YvFDNG\">AgriSeq targeted genotyping by sequencing (GBS)<\/a> and associated services.<\/p>\n<p><iframe loading=\"lazy\" width=\"760\" height=\"428\" src=\"https:\/\/www.youtube.com\/embed\/bbqjWF86kHE?feature=oembed\" frameborder=\"0\" allow=\"accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture\" allowfullscreen><\/iframe><\/p>\n<p>Agricultural genomics can be challenging for a variety of reasons, including sequence complexity, high genetic diversity and limited sequence availability. Although reference genomes are increasingly widely available for numerous species of agricultural interest, many questions in agricultural science are best approached with custom tools, in particular custom genotyping panels tailored to the species of interest and intended inquiry. Thermo Fisher Scientific offers end-to-end project management services through panel design, wet-lab validation and data analysis to help ensure delivery of high-performance custom genomics panels for any project. Thermo Fisher Scientific works closely with customers to identify the appropriate reference genomes and other pre-existing information. We make sure that both researcher and service provider have the same understanding of the custom panel\u2019s ultimate use. The earlier in the process Thermo Fisher Scientific can be involved, the more effective the resulting panel will be.<\/p>\n<p>The <a href=\"http:\/\/bit.ly\/2WPMTDT\">AgriSeq<\/a> panel design team has worked on over 100 custom panels designed to provide genomics data for crops, vegetables, trees, livestock and companion animals, fish, shrimp and flies, <a href=\"http:\/\/bit.ly\/2JwhhjN\" target=\"_blank\" rel=\"noopener noreferrer\">among other organisms<\/a>. AgriSeq panels are flexible, allowing the addition of markers even after the panel is otherwise complete. This flexibility even extends to surveying multiple types of variants, such as SNPs and indels, in a single panel and to indel mutations of highly divergent size.<\/p>\n<p>The <a href=\"http:\/\/bit.ly\/2WPMTDT\">AgriSeq<\/a> team is constantly developing new tools and data pipelines. Research is ongoing to improve the inclusion of <a href=\"http:\/\/bit.ly\/2HnqV5D\" target=\"_blank\" rel=\"noopener noreferrer\">long indel mutations<\/a> and other difficult-to-sequence genetic variants into AgriSeq panels. Software development to improve the availability of results to researchers is also an active and ongoing endeavor, including <a href=\"http:\/\/assets.thermofisher.com\/TFS-Assets\/GSD\/posters\/data-visualization-gbs-poster.pdf\" target=\"_blank\" rel=\"noopener noreferrer\">the creation of new plugins<\/a> to collate and summarize complex genotype data. Development is also ongoing on a web tool to allow customers to pre-check their markers before submitting them to the designers, allowing markers to reach the designers pre-validated and save valuable time for all parties.<\/p>\n<p>AgriSeq genotyping technology offers many advantages to researchers. AgriSeq technology can not only improve reads of hotspot positions, but works to generate more novel calls, often two to three times the number the customer requested, allowing for more in-depth research than anticipated. AgriSeq\u2019s versatility allows an AgriSeq panel to be designed for 50 markers or 5,000, allowing this tool to serve goals as diverse as checking for predisposition to specific diseases and genomic selection, or exploratory studies.<\/p>\n<p>Whether your intended application is parentage, breeding, SNP detection or something else entirely, AgriSeq <a href=\"http:\/\/assets.thermofisher.com\/TFS-Assets\/GSD\/Flyers\/agriseq-pilot-flyer.pdf\" target=\"_blank\" rel=\"noopener noreferrer\">next-generation sequencing tools<\/a> can help you collect the information you need. <a href=\"http:\/\/bit.ly\/2JqvM8u\">Contact AgriSeq\u2019s team<\/a> for more information.<\/p>\n<p><!-- BEGIN KAPOST ANALYTICS CODE --><\/p>\n<p><!-- var _kaq = _kaq || []; _kaq.push([2, \"5cdf19dee11fee003c00000b\", \"5674227b963491538f00011d\"]); (function(){ var ka = document.createElement(\"script\"); ka.async=true; ka.id=\"ka_tracker\"; ka.src = (document.location.protocol == \"https:\" ? \"https\" : \"http\") + \":\/\/analytics.kapost.com\/ka.js\"; var s = document.getElementsByTagName(\"script\")[0]; s.parentNode.insertBefore(ka, s); })(); \/\/--><\/p>\n<p><!-- END KAPOST ANALYTICS CODE --><\/p>\n","protected":false},"excerpt":{"rendered":"<p>Agrigenomics is an emerging and ever-more-important field of biology, linking the examination of entire genomes to agricultural outcomes that can affect the lives of vast populations of people. Thermo Fisher Scientific is at the forefront of animal and plant genomics tools, design and data collection, in particular via its Axiom Genotyping Solution, AgriSeq targeted genotyping<\/p>\n","protected":false},"author":120,"featured_media":12411,"comment_status":"open","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"_kad_blocks_custom_css":"","_kad_blocks_head_custom_js":"","_kad_blocks_body_custom_js":"","_kad_blocks_footer_custom_js":"","_monsterinsights_skip_tracking":false,"_genesis_hide_title":false,"_genesis_hide_breadcrumbs":false,"_genesis_hide_singular_image":false,"_genesis_hide_footer_widgets":false,"_genesis_custom_body_class":"","_genesis_custom_post_class":"","_genesis_layout":"","_jetpack_newsletter_access":"","_jetpack_dont_email_post_to_subs":false,"_jetpack_newsletter_tier_id":0,"_jetpack_memberships_contains_paywalled_content":false,"_jetpack_memberships_contains_paid_content":false,"footnotes":""},"categories":[83],"tags":[262,261],"division":[],"class_list":{"0":"post-12408","1":"post","2":"type-post","3":"status-publish","4":"format-standard","5":"has-post-thumbnail","7":"category-animal-health-and-agrigenomics","8":"tag-agrigenomics","9":"tag-agriseq","10":"entry"},"_selected_authors":"","_selected_reviewers":"","acf":[],"yoast_head":"<!-- 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Can You Perform SNP Genotyping Without DNA Purification? The short answer: In many research workflows, direct-from-lysate SNP genotyping can be performed without traditional DNA purification\u2014when appropriate chemistries and verification procedures are used. Direct-from-lysate\u2026","rel":"","context":"In &quot;General&quot;","block_context":{"text":"General","link":"https:\/\/admin.acceleratingscience.com\/behindthebench\/general\/"},"img":{"alt_text":"Comparison of traditional DNA purification workflow and direct-from-lysate workflow using DNA Extract All Reagents for SNP genotyping prior to qPCR.","src":"https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/04\/blog-image-1.png?resize=350%2C200&ssl=1","width":350,"height":200,"srcset":"https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/04\/blog-image-1.png?resize=350%2C200&ssl=1 1x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/04\/blog-image-1.png?resize=525%2C300&ssl=1 1.5x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/04\/blog-image-1.png?resize=700%2C400&ssl=1 2x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/04\/blog-image-1.png?resize=1050%2C600&ssl=1 3x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/04\/blog-image-1.png?resize=1400%2C800&ssl=1 4x"},"classes":[]},{"id":19168,"url":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/understanding-dna-melting-analysis-using-uv-visible-spectroscopy\/","url_meta":{"origin":12408,"position":1},"title":"Understanding DNA Melting Analysis Using UV-Visible Spectroscopy","author":"Marlene Gasdia-Cochrane","date":"October 14, 2025","format":false,"excerpt":"DNA melting analysis is a vital molecular biology technique used to study the stability and properties of DNA by monitoring its transition from double-stranded to single-stranded form with increasing temperature. UV-visible spectroscopy measures changes in DNA absorbance during this process, providing insights into DNA stability, sequence composition, and molecular interactions.\u2026","rel":"","context":"In &quot;Pharma &amp; Biotech Manufacturing&quot;","block_context":{"text":"Pharma &amp; Biotech Manufacturing","link":"https:\/\/admin.acceleratingscience.com\/behindthebench\/pharmamfg\/"},"img":{"alt_text":"Close-up Of Dna Molecule On Blue Background","src":"https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2025\/10\/iStock-2200215349.jpg?resize=350%2C200&ssl=1","width":350,"height":200,"srcset":"https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2025\/10\/iStock-2200215349.jpg?resize=350%2C200&ssl=1 1x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2025\/10\/iStock-2200215349.jpg?resize=525%2C300&ssl=1 1.5x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2025\/10\/iStock-2200215349.jpg?resize=700%2C400&ssl=1 2x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2025\/10\/iStock-2200215349.jpg?resize=1050%2C600&ssl=1 3x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2025\/10\/iStock-2200215349.jpg?resize=1400%2C800&ssl=1 4x"},"classes":[]},{"id":19676,"url":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/avian-influenza-qpcr-assay-failure\/","url_meta":{"origin":12408,"position":2},"title":"Avian Influenza qPCR Testing: How Viral Evolution Contributes to Assay Failure\u2014and How Labs Can Stay Ahead","author":"Behind The Bench Staff","date":"May 1, 2026","format":false,"excerpt":"Molecular veterinary diagnostic laboratories rely on reverse transcriptase real-time PCR (RT qPCR) assays to detect avian influenza virus (AIV) quickly and accurately. These assays are central to surveillance programs, outbreak response, and disease control\u2014particularly for highly pathogenic avian influenza (HPAI) strains such as H5Nx. As Influenza A viruses continue to\u2026","rel":"","context":"In &quot;Animal Health and AgriGenomics&quot;","block_context":{"text":"Animal Health and AgriGenomics","link":"https:\/\/admin.acceleratingscience.com\/behindthebench\/animal-health-and-agrigenomics\/"},"img":{"alt_text":"Chickens in a flock on a farm representing poultry populations monitored for avian influenza surveillance.","src":"https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/05\/Untitled-3.png?resize=350%2C200&ssl=1","width":350,"height":200,"srcset":"https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/05\/Untitled-3.png?resize=350%2C200&ssl=1 1x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/05\/Untitled-3.png?resize=525%2C300&ssl=1 1.5x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/05\/Untitled-3.png?resize=700%2C400&ssl=1 2x"},"classes":[]},{"id":19461,"url":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/grapevine-downy-mildew-fungicide-resistance-detection\/","url_meta":{"origin":12408,"position":3},"title":"Tracking grape pathogens from air to vine \u2013 a conversation with Lexi Heger","author":"Behind The Bench Staff","date":"February 28, 2026","format":false,"excerpt":"On the Absolute Gene-ius podcast, Lexi Heger, PhD candidate in Plant Pathology and Molecular Plant Sciences at Michigan State University, explores the molecular detection of grapevine pathogens and how qPCR and digital PCR (dPCR) are transforming plant disease research. Her research centers on downy mildew of grape (Plasmopara viticola) and\u2026","rel":"","context":"In &quot;Animal Health and AgriGenomics&quot;","block_context":{"text":"Animal Health and AgriGenomics","link":"https:\/\/admin.acceleratingscience.com\/behindthebench\/animal-health-and-agrigenomics\/"},"img":{"alt_text":"Portrait of a smiling plant pathology researcher standing outdoors beside grapevine leaves.","src":"https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/02\/Heger-headshot-1_Jordan-Ruggieri-scaled.jpeg?resize=350%2C200&ssl=1","width":350,"height":200,"srcset":"https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/02\/Heger-headshot-1_Jordan-Ruggieri-scaled.jpeg?resize=350%2C200&ssl=1 1x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/02\/Heger-headshot-1_Jordan-Ruggieri-scaled.jpeg?resize=525%2C300&ssl=1 1.5x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/02\/Heger-headshot-1_Jordan-Ruggieri-scaled.jpeg?resize=700%2C400&ssl=1 2x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/02\/Heger-headshot-1_Jordan-Ruggieri-scaled.jpeg?resize=1050%2C600&ssl=1 3x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/02\/Heger-headshot-1_Jordan-Ruggieri-scaled.jpeg?resize=1400%2C800&ssl=1 4x"},"classes":[]},{"id":19883,"url":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/building-a-better-sample-qc-workflow-from-extraction-to-sequencing\/","url_meta":{"origin":12408,"position":4},"title":"Building a Better Sample QC Workflow: From Extraction to Sequencing","author":"Marlene Gasdia-Cochrane","date":"August 25, 2026","format":false,"excerpt":"Article Summary Successful genomics experiments don't begin with sequencing\u2014they begin with sample quality. Every downstream application, from PCR to next-generation sequencing (NGS), depends on starting with nucleic acids that are accurately quantified and free from contaminants that could compromise results. Establishing a consistent quality control workflow helps laboratories improve reproducibility\u2026","rel":"","context":"In &quot;General&quot;","block_context":{"text":"General","link":"https:\/\/admin.acceleratingscience.com\/behindthebench\/general\/"},"img":{"alt_text":"A pipette drops a liquid into a petri dish with a dna sequence background, science concept. It suggests medical or genetic research.","src":"https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/08\/iStock-2216731026_petridish-scaled.jpg?resize=350%2C200&ssl=1","width":350,"height":200,"srcset":"https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/08\/iStock-2216731026_petridish-scaled.jpg?resize=350%2C200&ssl=1 1x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/08\/iStock-2216731026_petridish-scaled.jpg?resize=525%2C300&ssl=1 1.5x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/08\/iStock-2216731026_petridish-scaled.jpg?resize=700%2C400&ssl=1 2x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/08\/iStock-2216731026_petridish-scaled.jpg?resize=1050%2C600&ssl=1 3x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/08\/iStock-2216731026_petridish-scaled.jpg?resize=1400%2C800&ssl=1 4x"},"classes":[]},{"id":19888,"url":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/streptococcus-pneumoniae-serotype-identification-qpcr-nested-pcr\/","url_meta":{"origin":12408,"position":5},"title":"qPCR, Nested PCR, and the Search for Bacterial Serotypes","author":"Ashleigh Barlow","date":"August 5, 2026","format":false,"excerpt":"Article Summary In this episode of Absolute Gene-ius, Donna Paznar, former Head of Molecular Infection Diagnostics at the Medical University of Vienna, discusses her research on Streptococcus pneumoniae and its impact across the Austrian population. She explains why children can act as asymptomatic reservoirs, why tracking bacterial serotypes matters, and\u2026","rel":"","context":"In &quot;Infectious Diseases&quot;","block_context":{"text":"Infectious Diseases","link":"https:\/\/admin.acceleratingscience.com\/behindthebench\/infectious-diseases\/"},"img":{"alt_text":"Donna Paznar discussing molecular methods for identifying Streptococcus pneumoniae serotypes.","src":"https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/08\/Paznar_Headshot_Jordan-Ruggieri-scaled.jpg?resize=350%2C200&ssl=1","width":350,"height":200,"srcset":"https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/08\/Paznar_Headshot_Jordan-Ruggieri-scaled.jpg?resize=350%2C200&ssl=1 1x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/08\/Paznar_Headshot_Jordan-Ruggieri-scaled.jpg?resize=525%2C300&ssl=1 1.5x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/08\/Paznar_Headshot_Jordan-Ruggieri-scaled.jpg?resize=700%2C400&ssl=1 2x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/08\/Paznar_Headshot_Jordan-Ruggieri-scaled.jpg?resize=1050%2C600&ssl=1 3x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/08\/Paznar_Headshot_Jordan-Ruggieri-scaled.jpg?resize=1400%2C800&ssl=1 4x"},"classes":[]}],"jetpack_sharing_enabled":true,"jetpack_featured_media_url":"https:\/\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2019\/05\/bbqjwf86khe.jpg","_links":{"self":[{"href":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/wp-json\/wp\/v2\/posts\/12408","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/wp-json\/wp\/v2\/users\/120"}],"replies":[{"embeddable":true,"href":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/wp-json\/wp\/v2\/comments?post=12408"}],"version-history":[{"count":0,"href":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/wp-json\/wp\/v2\/posts\/12408\/revisions"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/wp-json\/wp\/v2\/media\/12411"}],"wp:attachment":[{"href":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/wp-json\/wp\/v2\/media?parent=12408"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/wp-json\/wp\/v2\/categories?post=12408"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/wp-json\/wp\/v2\/tags?post=12408"},{"taxonomy":"division","embeddable":true,"href":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/wp-json\/wp\/v2\/division?post=12408"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}